U.S. patent application number 10/334793 was filed with the patent office on 2004-01-29 for methods for placing, accepting, and filling orders for products and services.
Invention is credited to Avi-Itzhak, Hadar I., Bellon, Laurent R., De La Vega, Francisco M., Eddins, Susan, Gilbert, Dennis A., Gire, Harold Carey, Glanowski, Stephen, Heil, Jeremy, Hunkapiller, Michael W., Koehler, Ryan T., Livak, Kenneth J., Madden, Dawn, McMullen, Ivy, Rhodes, Michael, Scafe, Charles R., Scott, John, Smith, Leila G., Spier, Eugene G., Stevens, Junko, Wang, Yu N., Williams, Julie, Winn-Deen, Emily, Wu, Lini, Xu, Lily, You, Xiaoqing, Ziegle, Janet S..
Application Number | 20040018506 10/334793 |
Document ID | / |
Family ID | 27671405 |
Filed Date | 2004-01-29 |
United States Patent
Application |
20040018506 |
Kind Code |
A1 |
Koehler, Ryan T. ; et
al. |
January 29, 2004 |
Methods for placing, accepting, and filling orders for products and
services
Abstract
Methods and systems for ordering assays which detect SNPs or
gene expression are provided. The methods use PCR and RT-PCR
procedures. Collections of stock assays are assembled using pre-
and post-manufacturing quality control procedures and made
available to consumers via the Internet. In addition, custom assays
are prepared upon order from the consumer and these assays are also
prepared using pre- and post-manufacturing quality control
procedures. The assays are then delivered to the consumer.
Inventors: |
Koehler, Ryan T.; (Hayward,
CA) ; Livak, Kenneth J.; (San Jose, CA) ;
Stevens, Junko; (Menlo Park, CA) ; De La Vega,
Francisco M.; (San Mateo, CA) ; Rhodes, Michael;
(San Mateo, CA) ; Bellon, Laurent R.; (San Mateo,
CA) ; Ziegle, Janet S.; (Berkeley, CA) ;
Williams, Julie; (Montara, CA) ; Madden, Dawn;
(Half Moon Bay, CA) ; Gilbert, Dennis A.; (San
Franciso, CA) ; Scafe, Charles R.; (San Francisco,
CA) ; Avi-Itzhak, Hadar I.; (Los Altos, CA) ;
Wang, Yu N.; (Pittsburgh, PA) ; Spier, Eugene G.;
(Palo Alto, CA) ; You, Xiaoqing; (San Mateo,
CA) ; Xu, Lily; (South San Francisco, CA) ;
Heil, Jeremy; (Derwood, MD) ; Glanowski, Stephen;
(Great Falls, VA) ; Scott, John; (Damascus,
MD) ; Winn-Deen, Emily; (Livermore, CA) ;
McMullen, Ivy; (Towson, MD) ; Wu, Lini;
(Boyds, MD) ; Gire, Harold Carey; (Columbia,
MD) ; Eddins, Susan; (San Diego, CA) ;
Hunkapiller, Michael W.; (San Carlos, CA) ; Smith,
Leila G.; (San Francisco, CA) |
Correspondence
Address: |
HARNESS, DICKEY & PIERCE, P.L.C.
P.O. BOX 828
BLOOMFIELD HILLS
MI
48303
US
|
Family ID: |
27671405 |
Appl. No.: |
10/334793 |
Filed: |
January 2, 2003 |
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Current U.S.
Class: |
435/6.12 ;
705/2 |
Current CPC
Class: |
G16B 30/00 20190201;
G16B 35/20 20190201; G16H 10/40 20180101; G06Q 30/0621 20130101;
G16B 45/00 20190201; G06Q 30/0633 20130101; G16B 50/00 20190201;
G16B 35/00 20190201; B01L 2300/021 20130101; G16B 50/10 20190201;
G16B 25/10 20190201; G16B 25/00 20190201; G16C 20/60 20190201; C12Q
2600/156 20130101; G16B 30/10 20190201; G01N 35/00663 20130101;
G16B 30/20 20190201; B01L 3/5453 20130101; G06Q 50/22 20130101;
B01L 3/545 20130101; C12Q 1/6858 20130101; G06Q 30/0641 20130101;
C12Q 1/6858 20130101; C12Q 2547/101 20130101 |
Class at
Publication: |
435/6 ;
705/2 |
International
Class: |
G06F 017/60; C12Q
001/68 |
Claims
What is claimed is:
1. A method for providing to a consumer, assays configured to
detect presence or expression of genetic material, said method
comprising: providing a web-based user interface configured to
receive an order for one or more stock assays; providing a
web-based user interface configured to receive a request for design
of one or more custom assays and an order for said custom assays;
and delivering to the consumer at least one custom or stock assay
in response to an order for said one on more custom or stock assay
placed by the consumer.
2. A method in accordance with claim 1, further comprising
providing a web-based gene exploration platform configured to
provide information to assist a consumer in selecting one or both
of a stock assay and a custom assay.
3. A method in accordance with claim 2 wherein said information is
genomic and biomedical information from at least one public or
private source.
4. A method in accordance with claim 1, wherein providing a user
interface configured to receive an order for stock assays comprises
providing a graphical user interface.
5. A method in accordance with claim 4, further comprising
providing a graphical user interface configured for the consumer to
perform at least one search for at least one information item used
to identify genetic material for a stock assay.
6. A method in accordance with claim 5, wherein the at least one
information item used to identify the genetic material is a gene
identification item selected from the group consisting of gene
symbol, gene name, RefSeq accession number, Panther function,
Panther process, GO function, GO process, GO identifier, Applied
Biosystems identifier, Celera gene identifier (hCG), Celera
transcript identifier (hCT), Celera protein identifier (hCP),
LocusLink identifier, GenBank nucleotide identifier, GenBank
protein identifier, species identifier, chromosome identifier,
haplotype identifier, cytoband identifier, RefSeq GI identifier,
and combinations thereof.
7. A method in accordance with claim 5, wherein said at least one
search comprises a batch search.
8. A method in accordance with claim 5, wherein the search for at
least one information item comprises a gene classification
search.
9. A method in accordance with claim 8, wherein the gene
classification search comprises a molecular function search.
10. A method in accordance with claim 8, wherein the gene
classification search comprises a biological process search.
11. A method in accordance with claim 4, further comprising
providing reference information to the consumer concerning genetic
material that is detectable by an assay that is ordered by the
consumer.
12. A method in accordance with claim 11, wherein the reference
information is selected from the group consisting of RefSeq
identifier, LocusLink gene name, molecular function, biological
process, Celera identification number, gene location, and
combinations thereof.
13. A method in accordance with claim 4 wherein the graphical user
interface is configured to receive an order for at least one SNP
assay.
14. A method in accordance with claim 13 wherein the graphical user
interface is configured to receive an order for at least one SNP
assay from a group of at least 40,000 SNP assays.
15. A method in accordance with claim 14 wherein each SNP assay is
configured to detect presence of one of at least 40,000 pairs of
SNP alleles located in gene regions.
16. A method in accordance with claim 15 wherein each of the 40,000
pairs of SNP alleles are spaced apart by about 10 kilobases within
gene regions.
17. A method in accordance with claim 13 wherein the graphical user
interface is configured to receive an order for at least one SNP
assay from a group of at least 100,000 SNP assays.
18. A method in accordance with claim 17 wherein each SNP assay is
configured to detect presence of one of at least 100,000 pairs of
SNP alleles located in gene regions.
19. A method in accordance with claim 18 wherein each of the
100,000 pairs of SNP alleles are spaced apart by about 10 kilobases
within gene regions.
20. A method in accordance with claim 13 wherein providing the
graphical user interface includes providing an interface configured
to receive, from the consumer, criteria relating to at least one
gene region containing the at least one SNP.
21. A method in accordance with claim 20 wherein the criteria
relating to the at least one gene region containing the at least
one SNP comprises excluding assays for SNPs located in 10 kilobases
at 5' end and 10 kilobases at 3' end of the gene region.
22. A method in accordance with claim 13, wherein said providing
the graphical user interface includes providing an interface
configured to receive, from the consumer, criteria relating to
minor allele frequency.
23. A method in accordance with claim 4 wherein the graphical user
interface is configured to receive an order for at least one gene
expression assay.
24. A method in accordance with claim 23 wherein the graphical user
interface is configured to receive an order for at least one gene
expression assay from a group of at least 10,000 gene expression
assays.
25. A method in accordance with claim 23 wherein said providing a
graphical user interface for ordering assays includes providing an
interface configured to receive, from the consumer, criteria
relating to at least one expressed transcript or portion
thereof.
26. A method in accordance with claim 1, wherein providing a user
interface configured to receive a request for design of one or more
custom assays and an order for said custom assays comprises
providing a graphical user interface configured to receive a
request for design of one or more custom assays and an order for
said custom assays.
27. A method in accordance with claim 26 wherein providing a user
interface configured to receive an order for one or more stock
assays comprises providing a graphical user interface configured to
receive an order for one or more stock assays.
28. A method in accordance with claim 1, wherein said user
interface configured to receive orders for custom assays includes a
file-receiving interface configured to receive from the consumer a
submission file containing information suitable for use in
designing at least one of said custom assays.
29. A method in accordance with claim 28, wherein said
file-receiving interface is configured to receive from the consumer
a submission file containing sequence information relating to the
target of the custom assay requested by the consumer.
30. A method in accordance with claim 28, wherein said
file-receiving interface is configured to receive from the consumer
a submission file containing sequence information relating to
target coordinates of the custom assay requested by the
consumer.
31. A method in accordance with claim 29, wherein said
file-receiving interface is configured to receive from the consumer
a submission file containing information relating to the identity
of the consumer requesting a custom assay.
32. A method in accordance claim 28, further comprising providing a
submission file builder configured to assist the consumer in
preparing said submission file for ordering custom assays.
33. A method in accordance claim 32 wherein the file builder
provides for electronically validating at least a portion of the
submission file.
34. A method in accordance with claim 33, wherein the electronic
validation comprises detecting typographical errors in the
submission file.
35. A method in accordance with claim 34 further comprising
prompting the user to correct detected typographical errors in the
submission file.
36. A method in accordance with claim 33 wherein the electronic
validation comprises generating an error log providing information
related to whether the submission file is properly formatted.
37. A method in accordance with claim 32, wherein the submission
file builder includes a sequence checker to verify correctness of
at least a portion of the information contained in the submission
file.
38. A method in accordance with claim 37, further comprising
providing an electronic shopping basket configured to store an
order received from the consumer, said file submission program
being operable to upload the submission file to said shopping
basket.
39. A method in accordance with claim 26 wherein the assays
configured to detect presence of genetic material are assays
configured to detect presence of at least one SNP allele.
40. A method in accordance with claim 39 wherein providing a user
interface configured to receive orders for assays includes
providing an interface configured to receive, from the consumer,
criteria relating to at least one gene region containing the at
least one SNP.
41. A method in accordance with claim 40 wherein the criteria
relating to the at least one gene region containing the at least
one SNP comprises excluding assays for SNPs located in 10 kilobases
at 5' end and 10 kilobases at 3' end of the gene region.
42. A method in accordance with claim 39, wherein providing a user
interface configured to receive orders for assays includes
providing an interface configured to receive, from the consumer,
criteria relating to minor allele frequency.
43. A method in accordance with claim 26 wherein assays configured
to detect presence of genetic material are assays configured to
detect expression of at least one gene.
44. A method in accordance with claim 1 wherein said delivering to
a consumer at least one assay further comprises delivering
information concerning said assay.
45. A method in accordance with claim 44 wherein said delivering
information concerning said assay comprises delivering at least one
datasheet.
46. A method in accordance with claim 44 wherein delivering
information concerning said assay comprises delivering said
information on a machine-readable medium.
47. A method in accordance with claim 46 wherein said delivering
information concerning said assay further comprises delivering at
least one datasheet.
48. A method in accordance with claim 46 wherein said
machine-readable medium is a compact disk.
49. A method in accordance with claim 1 wherein said delivering to
the consumer at least one custom or stock assay comprises
delivering the at least one custom or stock assay in a single
tube.
50. A method in accordance with claim 49 wherein said delivering to
the consumer at least one custom or stock assay in a single tube
comprises delivering to the consumer at least one probe and two
primers.
51. A method in accordance with claim 50 wherein the at least one
custom or stock assay in a single tube is a SNP assay comprising a
separate probe for each of two alleles and two primers.
52. A method in accordance with claim 50 wherein the probe
comprises at least one fluorophore and at least one fluorescence
quencher.
53. A method in accordance with claim 52 wherein the fluorescence
quencher is a non-fluorescent fluorescence quencher.
54. A method in accordance with claim 52 wherein the probe further
comprises at least one minor groove binder.
55. A method in accordance with claim 50 wherein said delivering to
the consumer at least one custom or stock assay in a single tube
further comprises delivering at least one custom or stock assay in
a single tube and PCR reagents.
56. A method in accordance with claim 50 wherein said delivering to
the consumer at least one custom or stock assay in a single tube
further comprises delivering to the consumer at least one custom or
stock assay in a single tube and a universal master mix, said
universal master mix comprising at least one salt, a buffer, and a
DNA polymerase.
57. A method in accordance with claim 49 wherein the single tube
further comprises a bar code identifier.
58. A method in accordance with claim 57 wherein the bar code is a
two-dimension bar code
59. A method in accordance with claim 49 wherein the single tube
further comprises an identifier which is a human-readable Assay
number
60. A method in accordance with claim 1 further comprising
manufacturing assays.
61. A method in accordance with claim 60 further comprising
performing pre-processing selection, designing primers and probes,
and performing in silico quality control prior to said
manufacturing.
62. A method in accordance with claim 61 wherein the assay is a
gene expression assay and wherein each said user interface
configured to receive orders for assays includes an interface
configured to receive, from the consumer, criteria relating to at
least one expressed transcript or portion thereof.
63. A method in accordance with claim 62 wherein said performing
pre-processing selection comprises identifying optimal sequence
regions which do not contain any single nucleotide polymorphisms or
repeat sequences.
64. A method in accordance with claim 63 wherein identifying
optimal sequence regions comprises utilizing at least one method
selected from the group consisting of masking single nucleotide
polymorphisms and repeat sequences in the at least one expressed
transcript or portion thereof to avoid designing probes and primers
thereon, mapping the at least one expressed transcript or portion
thereof against at least two genomic databases to identify
discrepancies to avoid designing probes and primers thereon,
identifying exon-exon boundaries for expressed transcripts of
multi-exon genes in order to design probes or primers thereon, and
combinations thereof.
65. A method in accordance with claim 64 wherein identifying
optimal sequence regions comprises masking repeat sequences
selected from the group consisting of di-nucleotide repeats,
tri-nucleotide repeats, Alu restriction site repeats, long
interspersed nuclear elements, and short interspersed nuclear
elements.
66. A method in accordance with claim 64 wherein said probes and
primers are designed in accordance with criteria selected from the
group consisting of avoiding inclusion of single nucleotide
polymorphisms or repeat sequences in probe and primer sequences,
avoiding inclusion of regions of discrepancy between at least two
genomic databases in probe and primer sequence, constructing either
or both of probes and primers on exon-exon boundaries for
multi-exon genes, and combinations thereof.
67. A method in accordance with claim 62 wherein said designing
probes and primers comprises utilizing specifications selected from
the group consisting of T.sub.m, GC content, buffer and salt
conditions, oligonucleotide concentration in assay, low secondary
structure of oligonucleotide, amplicon size, and low incidence of
primer-dimer formation.
68. A method in accordance with claim 61 wherein said performing in
silico quality control comprises determining quality of designed
probes and primers utilizing scoring methods selected from the
group consisting of transcript BLAST scoring, genome BLAST scoring,
scoring size of intron across which a probe spans for multi-exon
genes, and combinations thereof.
69. A method in accordance with claim 61 further comprising
manufacturing designed probes and primers having pre-selected
scoring criteria.
70. A method in accordance with claim 69 wherein said pre-selected
scoring criteria comprises assigning high transcript BLAST scoring
for matching to self and no other transcript, assigning high genome
BLAST scoring for matching to self and no other genome region and
assigning high scoring for intron size greater than 10 kilobases
and wherein a high assay design scoring is assigned for designed
assays scoring all three of high transcript BLAST scoring, high
genome BLAST scoring and high intron size scoring.
71. A method in accordance with claim 61 wherein the assay is a SNP
assay and wherein each said user interface configured to receive
orders for assays is configured to receive, from the consumer,
criteria relating to at least one gene region containing at least
one SNP.
72. A method in accordance with claim 71 wherein said performing
pre-processing selection comprises identifying optimal sequence
regions which contain neither repeat sequences nor any SNPs other
than a SNP for which the assay is designed.
73. A method in accordance with claim 72 wherein said identifying
optimal sequence regions comprises using one or more methods
selected from the group consisting of masking any SNPs other than
the at least one SNP for which the assay is to be designed and
repeat sequences in the at least one gene region to avoid
constructing probes and primers thereon, mapping the at least one
SNP against at least two genomic databases to identify
discrepancies to avoid constructing probes and primers thereon, and
combinations thereof.
74. A method in accordance with claim 73 wherein said identifying
optimal sequence regions comprises masking repeat sequences
selected from the group consisting of di-nucleotide repeats,
tri-nucleotide repeats, Alu restriction site repeats, long
interspersed nuclear elements, and short interspersed nuclear
elements.
75. A method in accordance with claim 73 wherein said probes and
primers are designed in accordance with criteria selected from the
group consisting of avoiding the inclusion of any SNPs other than
the at least one SNP for which the assay is to be designed,
avoiding the inclusion of regions of discrepancy between at least
two genomic databases in probe and primer sequence, and
combinations thereof.
76. A method in accordance with claim 70 wherein designing probes
and primers comprises utilizing specifications selected from the
group consisting of T.sub.m, GC content, buffer and salt
conditions, oligonucleotide concentration in assay, low secondary
structure of oligonucleotide, amplicon size and low incidence of
primer-dimer formation.
77. A method in accordance with claim 71 wherein said performing in
silico quality control comprises determining the quality of
designed probes and primers by genome BLAST scoring.
78. A method in accordance with claim 77 further comprising
manufacturing designed probes and primers having pre-selected
scoring criteria.
79. A method in accordance with claim 78 wherein pre-selected
scoring criteria comprises assigning high genome BLAST scoring for
matching to self and no other genome region.
80. A method in accordance with claim 60 further comprising quality
control testing of the manufactured assays according to
pre-selected quality control criteria.
81. A method in accordance with claim 80 wherein quality control
testing comprises one or more testing procedures selected from the
group consisting of synthesis yield testing, analytical quality
control testing, functional testing, validation testing, and
combinations thereof, wherein each of the one or more testing
procedures is performed according to pre-selected quality control
criteria.
82. A method in accordance with claim 81 wherein synthesis yield
testing comprises testing the manufactured assays using PAGE or
HPLC.
83. A method in accordance with claim 81 wherein the pre-selected
quality control criteria for synthesis yield testing is about 90%
(w/w) product yield.
84. A method in accordance with claim 83 wherein the pre-selected
quality control criteria for synthesis yield testing is about 95%
(w/w) product yield.
85. A method in accordance with claim 81 wherein analytical quality
control testing comprises testing the manufactured assays using
mass spectrometry.
86. A method in accordance with claim 85 wherein the pre-selected
quality control criteria for synthesis yield testing is such that
determined mass is not more than 5% greater or lesser than
calculated mass.
87. A method in accordance with claim 86 wherein the pre-selected
quality control criteria for synthesis yield testing is such that
determined mass is not more than 2% greater or lesser than
calculated mass.
88. A method in accordance with 81 wherein the manufactured assays
are SNP assays and functional testing comprises performing PCR
reactions of manufactured assays against from about 10 to about 20
genomic DNA samples.
89. A method in accordance with claim 88 wherein the pre-selected
quality control criteria for functional testing comprises detecting
presence of both alleles.
90. A method in accordance with claim 81 wherein the manufactured
assay is a gene expression assay and functional testing comprises
performing designed assay RT-PCR.
91. A method in accordance with claim 90 wherein the manufactured
assay is a multi-exon gene expression assay and the pre-selected
quality control criteria for functional testing comprises
detectable amplification of transcript in accordance with assay
design in absence of detectable amplification of genomic DNA.
92. A method in accordance with claim 90 wherein the manufactured
assay is a single exon gene expression assay and the pre-selected
quality control criteria for functional testing comprises
detectable amplification of transcript in accordance with assay
design in absence of detectable amplification of non-transcribed
genomic DNA.
93. A method in accordance with claim 81 wherein the manufactured
assay is a SNP assay and validation testing comprises performing
designed assay PCR against about 90 human genomic samples.
94. A method in accordance with claim 93 wherein the pre-selected
quality control criteria for validation testing comprises detecting
a minor allele frequency of at least 10%.
95. A method in accordance with claim 94 wherein the pre-selected
quality control criteria for validation testing comprises detecting
a minor allele frequency of at least 15%.
96. A method in accordance with claim 81 wherein the manufactured
assay is a gene expression and validation testing comprises
performing designed assay PCR against a pool of at least about 10
human cDNA samples.
97. A method in accordance with claim 96 wherein the human cDNA
samples are from different individuals.
98. A method in accordance with claim 96 wherein the human cDNA
samples are from different cell lines.
99. A method in accordance with claim 96 wherein the pre-selected
quality control criteria for validation testing comprises detection
of amplified transcript at a threshold of less than 35 PCR
cycles.
100. A method in accordance with claim 59 wherein said
manufacturing comprises high-throughput manufacturing.
101. A system for providing to a consumer, assays configured to
detect presence or expression of genetic material, said system
comprising: a web-based user interface configured to receive an
order for one or more stock assays; a web-based user interface
configured to receive a request for design of one or more custom
assays and an order for said custom assays; and a system for
delivering to the consumer at least one custom or stock assay in
response to an order for said one custom or stock assay placed by
the consumer.
102. A system in accordance with claim 101, further comprising a
gene web-based gene exploration platform configured to provide
information to assist a consumer in selecting one or both of a
stock assay and a custom assay.
103. A system in accordance with claim 102 wherein said information
is genomic and biomedical information from at least one public or
private source.
104. A system in accordance with claim 101, wherein the user
interface configured to receive an order for stock assays comprises
a graphical user interface.
105. A system in accordance with claim 104, further comprising a
graphical user interface configured for the consumer to perform at
least one search for at least one information item used to identify
genetic material for a stock assay.
106. A system in accordance with claim 105, wherein the at least
one information item used to identify the genetic material is a
gene identification item selected from the group consisting of gene
symbol, gene name, RefSeq accession number, Panther function,
Panther process, GO function, GO process, GO identifier, Applied
Biosystems identifier, Celera gene identifier (hCG), Celera
transcript identifier (hCT), Celera protein identifier (hCP),
LocusLink identifier, GenBank nucleotide identifier, GenBank
protein identifier, species identifier, chromosome identifier,
haplotype identifier, cytoband identifier, RefSeq GI identifier,
and combinations thereof.
107. A system in accordance with claim 105, wherein said at least
one search comprises a batch search.
108. A system in accordance with claim 105, wherein the at least
one information item comprises a gene classification search.
109. A system in accordance with claim 108, wherein the gene
classification search comprises a molecular function search.
110. A system in accordance with claim 108, wherein the gene
classification search comprises a biological process search.
111. A system in accordance with claim 104, further comprising a
web-based user interface configured to provide reference
information to the consumer concerning genetic material that is
detectable by an assay that is ordered by the consumer.
112. A system in accordance with claim 111, wherein the reference
information is selected from the group consisting of RefSeq
identifier, LocusLink gene name, molecular function, biological
process, Celera identification number, gene location, and
combinations thereof.
113. A system in accordance with claim 104 wherein the graphical
user interface is configured to receive an order for at least one
SNP assay.
114. A system in accordance with claim 113 wherein the graphical
user interface is configured to receive an order for at least one
SNP assay from a group of at least 40,000 SNP assays.
115. A system in accordance with claim 114 wherein each SNP assay
is configured to detect presence of one of at least 40,000 pairs of
SNP alleles located in gene regions.
116. A system in accordance with claim 115 wherein each of the
40,000 pairs of SNP alleles are spaced a part by about 10 kilobases
within gene regions.
117. A system in accordance with claim 114 wherein the graphical
user interface is configured to receive an order for at least one
SNP assay from a group of at least 100,000 SNP assays.
118. A system in accordance with claim 116 wherein each SNP assay
is configured to detect presence of one of at least 100,000 pairs
of SNP alleles located in gene regions.
119. A system in accordance with claim 118 wherein each of the
100,000 pairs of SNP alleles are spaced apart by about 10 kilobases
within gene regions.
120. A system in accordance with claim 113 wherein providing the
graphical user interface includes providing an interface configured
to receive, from the consumer, criteria relating to at least one
gene region containing the at least one SNP.
121. A system in accordance with claim 120 wherein the criteria
relating to the at least one gene region containing the at least
one SNP comprises excluding assays for SNPs located in 10 kilobases
at 5' end and 10 kilobases at 3' end of the gene region.
122. A system in accordance with claim 113, wherein said providing
the graphical user interface includes providing an interface
configured to receive, from the consumer, criteria relating to
minor allele frequency.
123. A system in accordance with claim 114 wherein the graphical
user interface is configured to receive an order for at least one
gene expression assay.
124. A system in accordance with claim 123 wherein the graphical
user interface is configured to receive an order for at least one
gene expression assay from a group of at least 10,000 gene
expression assays.
125. A system in accordance with claim 123 wherein said graphical
user interface for ordering assays includes providing an interface
configured to receive, from the consumer, criteria relating to at
least one expressed transcript or portion thereof.
126. A system in accordance with claim 101, wherein said user
interface configured to receive a request for design of one or more
custom assays and an order for said custom assays comprises a
graphical user interface configured to receive a request for design
of one or more custom assays and an order for said custom
assays.
127. A system in accordance with claim 126 wherein the user
interface configured to receive an order for one or more stock
assays comprises a graphical user interface configured to receive
an order for one or more stock assays.
128. A system in accordance with claim 101, wherein said user
interface configured to receive orders for custom assays includes a
file-receiving interface configured to receive, from the consumer,
a submission file containing information suitable for use in
designing at least one of said custom assays.
129. A system in accordance with claim 128, wherein said
file-receiving interface is configured to receive from the consumer
a submission file containing sequence information relating to the
target of the custom assay requested by the consumer.
130. A system in accordance with claim 129, wherein said
file-receiving interface is configured to receive from the consumer
a submission file containing sequence information relating to the
target coordinates of the custom assay requested by the
consumer.
131. A system in accordance with claim 128, wherein said
file-receiving interface is configured to receive from the consumer
a submission file containing information relating to the identity
of the consumer requesting a custom assay.
132. A system in accordance claim 128, further comprising a
submission file builder configured to assist the consumer in
preparing said submission file for ordering custom assays.
133. A system in accordance claim 132 wherein the file builder
provides for electronically validating at least a portion of the
submission file.
134. A system in accordance with claim 133, wherein the electronic
validation comprises detecting typographical errors in the
submission file.
135. A system in accordance with claim 134 further comprising a
system configured to prompt the user to correct detected
typographical errors in the submission file.
136. A system in accordance with claim 133 wherein the electronic
validation comprises generating an error log providing information
related to whether the submission file is properly formatted.
137. A system according to claim 132, wherein the submission file
builder includes a sequence checker to verify correctness of at
least a portion of the information contained in the submission file
for which the custom assay is to be designed.
138. A system according to claim 137, further comprising an
electronic shopping basket configured to store an order received
from the consumer, said file submission program being operable to
upload the submission file to said shopping basket.
139. A system in accordance with claim 126 wherein the assays
configured to detect presence of genetic material are assays
configured to detect presence of at least one SNP allele.
140. A system in accordance with claim 139 wherein the user
interface configured to receive orders for assays includes an
interface configured to receive, from the consumer, criteria
relating to at least one gene region containing the at least one
SNP.
141. A system in accordance with claim 140 wherein the criteria
relating to the at least one gene region containing the at least
one SNP comprises excluding assays for SNPs located in 10 kilobases
at 5' end and 10 kilobases at 3' end of the gene region.
142. A system in accordance with claim 139, wherein the user
interface configured to receive orders for assays includes an
interface configured to receive, from the consumer, criteria
relating to minor allele frequency.
143. A system in accordance with claim 126 wherein assays
configured to detect presence of genetic material are assays
configured to detect expression of at least one gene.
144. A system in accordance with claim 101 wherein said system for
delivering to a consumer at least one assay further comprises a
system for delivering information concerning said assay.
145. A system in accordance with claim 144 wherein said system for
delivering information concerning said assay comprises a system for
delivering at least one datasheet.
146. A system in accordance with claim 144 wherein said system for
delivering information concerning said assay comprises a system for
delivering said information on a machine-readable medium.
147. A system in accordance with claim 146 wherein said system for
delivering information concerning said assay further comprises a
system for delivering at least one datasheet.
148. A system in accordance with claim 146 wherein said
machine-readable medium is a compact disk.
149. A system in accordance with claim 101 wherein said system for
delivering for the consumer at least one custom or stock assay
comprises a system for delivering the at least one custom or stock
assay in a single tube.
150. A system in accordance with claim 149 wherein said at least
one custom or stock assay in a single tube comprises at least one
probe and two primers.
151. A system in accordance with claim 150 wherein the at least one
custom or stock assay in a single tube is a SNP assay comprising a
separate probe for each of two alleles and two primers.
152. A system in accordance with claim 150 wherein the probe
comprises at least one fluorophore and at least one fluorescence
quencher.
153. A system in accordance with claim 152 wherein the fluorescence
quencher is a non-fluorescent fluorescence quencher.
154. A system in accordance with claim 152 wherein the probe
further comprises at least one minor groove binder.
155. A system in accordance with claim 150 wherein said system for
delivering for the consumer at least one custom or stock assay
further comprises a system for delivering for the consumer at least
one custom or stock assay in a single tube and PCR reagents.
156. A system in accordance with claim 155 wherein said system for
delivering to the consumer at least one custom or stock assay
further comprises a system for delivering to the consumer at least
one custom or stock assay in a single tube and a universal master
mix, said universal master mix comprising at least one salt, a
buffer, and a DNA polymerase.
157. A system in accordance with claim 149 wherein the single tube
further comprises a bar code identifier.
158. A system in accordance with claim 157 wherein the bar code is
a two-dimension bar code.
159. A system in accordance with claim 149 wherein the single tube
further comprises an identifier which is a human-readable Assay
number
160. A system in accordance with claim 101 further comprising a
facility for manufacturing assays.
161. A system in accordance with claim 160 further comprising a
system for performing pre-processing selection, a system for
designing primers and probes, and a system for performing in silico
quality control prior to said manufacturing.
162. A system in accordance with claim 161 wherein the assay is a
gene expression assay and wherein each said user interface
configured to receive orders for assays includes an interface
configured to receive, from the consumer, criteria relating to at
least one expressed transcript or portion thereof.
163. A system in accordance with claim 161 wherein said system for
performing pre-processing selection comprises a component for
identifying optimal sequence regions which do not contain any
single nucleotide polymorphisms or repeat sequences.
164. A system in accordance with claim 163 wherein the component
for identifying optimal sequence regions comprises components
selected from the group consisting of a component for masking
single nucleotide polymorphisms and repeat sequences in the at
least one expressed transcript or portion thereof to avoid
designing probes and primers thereon, a component for mapping the
at least one expressed transcript or portion thereof against at
least two genomic databases to identify discrepancies to avoid
designing probes and primers thereon, a component for identifying
exon-exon boundaries for expressed transcripts of multi-exon genes
in order to design probes or primers thereon and combinations
thereof.
165. A system in accordance with claim 164 wherein the component
for identifying optimal sequence regions comprises a component for
masking repeat sequences selected from the group consisting of
di-nucleotide repeats, tri-nucleotide repeats, Alu restriction site
repeats, long interspersed nuclear elements, and short interspersed
nuclear elements.
166. A system in accordance with claim 164 wherein said probes and
primers are designed in accordance with criteria selected from the
group consisting of avoiding the inclusion of single nucleotide
polymorphisms or repeat sequences in probe and primer sequences,
avoiding the inclusion of regions of discrepancy between at least
two genomic databases in probe and primer sequence, constructing
either or both of probes and primers on exon-exon boundaries for
multi-exon genes, and combinations thereof.
167. A system in accordance with claim 162 wherein said system for
designing probes and primers utilizes specifications selected from
the group consisting of T.sub.m, GC content, buffer and salt
conditions, oligonucleotide concentration in assay, low secondary
structure of oligonucleotide, amplicon size and low incidence of
primer-dimer formation.
168. A system in accordance with claim 161 wherein said system for
performing in silico quality control comprises a component for
determining the quality of designed probes and primers utilizing
scoring systems selected from the group consisting of transcript
BLAST scoring, genome BLAST scoring, scoring the size of intron
across which a probe spans for multi-exon genes and combinations
thereof.
169. A system in accordance with claim 161 further comprising a
system for manufacturing designed probes and primers having
pre-selected scoring criteria.
170. A system in accordance with claim 169 wherein said
pre-selected scoring criteria comprises high transcript BLAST
scoring for matching to self and no other transcript, high genome
BLAST scoring for matching to self and no other genome region and
high scoring for intron size greater than 10 kilobases and wherein
high assay design scoring comprises high scoring for all three of
high transcript BLAST scoring, high genome BLAST scoring and high
intron size scoring.
171. A system in accordance with claim 161 wherein the assay is a
SNP assay and wherein each said user interface configured to
receive orders for assays is configured to receive, from the
consumer, criteria relating to at least one gene region containing
at least one SNP.
172. A system in accordance with claim 171 wherein said system for
performing pre-processing selection comprises a component for
identifying optimal sequence regions which contain neither repeat
sequences nor any SNPs other than a SNP for which the assay is
designed.
173. A system in accordance with claim 172 wherein said component
for identifying optimal sequence regions comprises systems selected
from the group consisting of masking any SNPs other than the at
least one SNP for which the assay is to be designed and repeat
sequences in the at least one gene region to avoid a component for
designing probes and primers thereon, mapping the at least one SNP
against at least two genomic databases to identify discrepancies to
avoid constructing probes and primers thereon, and combinations
thereof.
174. A system in accordance with claim 173 wherein said identifying
optimal sequence regions comprises masking repeat sequences
selected from the group consisting of di-nucleotide repeats,
tri-nucleotide repeats, Alu restriction site repeats, long
interspersed nuclear elements, and short interspersed nuclear
elements.
175. A system in accordance with claim 173 wherein said probes and
primers are designed in accordance with criteria selected from the
group consisting of avoiding the inclusion of any SNPs other than
the at least one SNP for which the assay is to be designed,
avoiding the inclusion of regions of discrepancy between at least
two genomic databases in probe and primer sequence, and
combinations thereof.
176. A system in accordance with claim 170 wherein probes and
primers are designed utilizing specifications selected from the
group consisting of T.sub.m, GC content, buffer and salt
conditions, oligonucleotide concentration in assay, low secondary
structure of oligonucleotide, amplicon size and low incidence of
primer-dimer formation.
177. A system in accordance with claim 171 wherein said system for
performing in silico quality control comprises a system for
determining the quality of designed probes and primers by genome
BLAST scoring.
178. A system in accordance with claim 177 further comprising a
system configured to manufacture designed probes and primers having
pre-selected scoring criteria.
179. A system in accordance with claim 178 wherein pre-selected
scoring criteria comprises high genome BLAST scoring for matching
to self and no other genome region.
180. A system in accordance with claim 160 further comprising a
system configured to perform quality control testing of the
manufactured assay according to pre-selected quality control
criteria.
181. A system in accordance with claim 180 wherein quality control
testing comprises testing systems are selected from the group
consisting of a synthesis yield testing system, an analytical
quality control testing system, a functional testing system, a
validation testing system and combinations thereof wherein each of
the one or more testing systems is performed according to
pre-selected quality control criteria.
182. A system in accordance with claim 181 wherein the synthesis
yield testing system comprises a system for testing the
manufactured assay using PAGE or HPLC.
183. A system in accordance with claim 181 wherein the pre-selected
quality control criteria for the synthesis yield testing system is
about 90% (w/w) product yield.
184. A system in accordance with claim 183 wherein the pre-selected
quality control criteria for the synthesis yield testing system is
about 95% (w/w) product yield.
185. A system in accordance with claim 181 wherein the analytical
quality control testing system comprises a system for testing the
manufactured assays using mass spectrometry.
186. A system in accordance with claim 185 wherein the pre-selected
quality control criteria for synthesis yield testing is such that
determined mass is not more than 5% greater or lesser than
calculated mass.
187. A system in accordance with claim 186 wherein the pre-selected
quality control criteria for the synthesis yield testing system is
such that determined mass is not more than 2% greater or lesser
than calculated mass.
188. A system in accordance with 181 wherein the manufactured
assays are SNP assays and the system for functional testing
comprises a system for performing PCR reactions of manufactured
assays against from about 10 to about 20 genomic DNA samples.
189. A system in accordance with claim 188 wherein the pre-selected
quality control criteria for the functional testing system
comprises detection presence of both alleles.
190. A system in accordance with claim 181 wherein the manufactured
assay is a gene expression assay and system for functional testing
comprises a system for performing designed assay RT-PCR.
191. A system in accordance with claim 190 wherein the manufactured
assay is a multi-exon gene expression assay and the pre-selected
quality control criteria for functional testing comprises
detectable amplification of transcript in accordance with assay
design in absence of detectable amplification of genomic DNA.
192. A system in accordance with claim 190 wherein the manufactured
assay is a single exon gene expression assay and the pre-selected
quality control criteria for functional testing comprises
detectable amplification of transcript in accordance with assay
design in absence of detectable amplification of non-transcribed
genomic DNA.
193. A system in accordance with claim 191 wherein the manufactured
assay is a SNP assay and the system for validation testing
comprises a system for performing designed assay PCR against about
90 human genomic samples.
194. A system in accordance with claim 193 wherein the pre-selected
quality control criteria for the system for validation testing
comprises detecting a minor allele frequency of at least 10%.
195. A system in accordance with claim 194 wherein the pre-selected
quality control criteria for the system for validation testing
comprises detecting a minor allele frequency of at least 15%.
196. A system in accordance with claim 181 wherein the manufactured
assay is a gene expression and the system for validation testing
comprises a system for performing designed assay PCR against a pool
of at least about 10 human cDNA samples.
197. A system in accordance with claim 196 wherein the human cDNA
samples are from different individuals.
198. A system in accordance with claim 196 wherein the human cDNA
samples are from different cell lines.
199. A system in accordance with claim 196 wherein the pre-selected
quality control criteria for the system for validation testing
comprises detection of amplified transcript at a threshold of less
than 35 PCR cycles.
200. A system in accordance with claim 159 wherein said
manufacturing comprises high-throughput manufacturing.
201. A method for constructing a system for providing to a
consumer, assays configured to detect presence or expression of
genetic material, said method comprising: providing a web-based
user interface configured to receive an order for one or more stock
assays; providing a web-based user interface configured to receive
a request for design of one or more custom assays and an order for
said custom assays; and providing a system for delivering to the
consumer at least one custom or stock assay in response to an order
for said one custom or stock assay placed by the consumer.
202. A method in accordance with claim 201 further comprising
providing a web-based gene exploration platform configured to
provide information to assist a consumer in selecting one or both
of a stock assay and a custom assay.
203. A method in accordance with claim 202 wherein said information
is genomic and biomedical information from at least one public or
private source.
204. A method in accordance with claim 201, wherein providing a
user interface configured to receive an order for stock assays
comprises providing a graphical user interface.
205. A method in accordance with claim 204, further comprising
providing a graphical user configured interface for the consumer to
perform at least one search for at least one information item used
to identify genetic material for a stock assay.
206. A method in accordance with claim 204, wherein the at least
one information item used to identify the genetic material is a
gene identification item selected from the group consisting of gene
symbol, gene name, RefSeq accession number, Panther function,
Panther process, GO function, GO process, GO identifier, Applied
Biosystems identifier, Celera gene identifier (hCG), Celera
transcript identifier (hCT), Celera protein identifier (hCP),
LocusLink identifier, GenBank nucleotide identifier, GenBank
protein identifier, species identifier, chromosome identifier,
haplotype identifier, cytoband identifier, RefSeq GI identifier,
and combinations thereof.
207. A method in accordance with claim 204, wherein said at least
one search comprises a batch search.
208. A method in accordance with claim 204, wherein the at least
one information item comprises a gene classification search.
209. A method in accordance with claim 208, wherein the gene
classification search comprises a molecular function search.
210. A method in accordance with claim 209, wherein the gene
classification search comprises a biological process search.
211. A method in accordance with claim 204, further comprising
providing a system for supplying reference information to the
consumer concerning genetic material that is detectable by an assay
that is ordered by the consumer.
212. A method in accordance with claim 211, wherein the reference
information is selected from the group consisting of RefSeq
identifier, LocusLink gene name, molecular function, biological
process, Celera identification number, gene location, and
combinations thereof.
213. A method in accordance with claim 205 wherein the graphical
user interface is configured to receive an order for at least one
SNP assay.
214. A method in accordance with claim 213 wherein the graphical
user interface is configured to receive an order for at least one
SNP assay from a group of at least 40,000 SNP assays.
215. A method in accordance with claim 214 wherein each SNP assay
is configured to detect presence of one of at least 40,000 pairs of
SNP alleles located in gene regions.
216. A method in accordance with claim 215 wherein each of the
40,000 pairs of SNP alleles are spaced apart by about 10 kilobases
within gene regions.
217. A method in accordance with claim 214 wherein the graphical
user interface is configured to receive an order for at least one
SNP assay from a group of at least 100,000 SNP assays.
218. A method in accordance with claim 217 wherein each SNP assay
is configured to detect presence of one of at least 100,000 pairs
of SNP alleles located in gene regions.
219. A method in accordance with claim 218 wherein each of the
100,000 pairs of SNP alleles are spaced apart by about 10 kilobases
within gene regions.
220. A method in accordance with claim 213 wherein providing the
graphical user interface for ordering assays includes providing an
interface configured to receive, from the consumer, criteria
relating to at least one gene region containing the at least one
SNP.
221. A method in accordance with claim 220 wherein the criteria
relating to the at least one gene region containing the at least
one SNP comprises excluding assays for SNPs located in 10 kilobases
at 5' end and 10 kilobases at 3' end of the gene region.
222. A method in accordance with claim 213, wherein said providing
the graphical user interface for ordering assays includes providing
an interface configured to receive, from the consumer, criteria
relating to minor allele frequency.
223. A method in accordance with claim 214 wherein the graphical
user interface is configured to receive an order for at least one
gene expression assay.
224. A method in accordance with claim 223 wherein the graphical
user interface is configured to receive an order for at least one
gene expression assay from a group of at least 10,000 gene
expression assays.
225. A method in accordance with claim 223 wherein said providing a
user interface for ordering assays includes providing an interface
configured to receive, from the consumer, criteria relating to at
least one expressed transcript or portion thereof.
226. A method in accordance with claim 201, wherein providing a
user interface configured to receive a request for design of one or
more custom assays and an order for said custom assays comprises
providing a graphical user interface configured to receive a
request for design of one or more custom assays and an order for
said custom assays.
227. A method in accordance with claim 226 wherein providing a user
interface configured to receive an order for one or more stock
assays comprises providing a graphical user interface configured to
receive an order for one or more stock assays.
228. A method in accordance with claim 201, wherein said user
interface configured to receive orders for custom assays includes a
file-receiving interface configured to receive, from the consumer,
a submission file containing information suitable for use in
designing at least one of said custom assays.
229. A method in accordance with claim 228, wherein said
file-receiving interface is configured to receive from the consumer
a submission file containing sequence information relating to the
target of the custom assay requested by the consumer.
230. A method in accordance with claim 229, wherein said
file-receiving interface is configured to receive from the consumer
a submission file containing sequence information relating to
target coordinates of the custom assay requested by the
consumer.
231. A method in accordance with claim 228, wherein said
file-receiving interface is configured to receive from the consumer
a submission file containing information relating to the identity
of the consumer requesting a custom assay.
232. A method in accordance claim 228, further comprising providing
a submission file builder configured to assist the consumer in
preparing said submission file for ordering custom assays.
233. A method in accordance claim 232 wherein the file builder
provides for electronically validating at least a portion of the
submission file.
234. A method in accordance with claim 233, wherein the electronic
validation comprises detecting typographical errors in the
submission file.
235. A method in accordance with claim 234 further comprising a
providing a prompt for the user to correct detected typographical
errors in the submission file.
236. A method in accordance with claim 233 wherein the electronic
validation comprises generating an error log providing information
related to whether the submission file is properly formatted.
237. A method in accordance with claim 232, wherein the submission
file builder includes a sequence checker to verify correctness of
at least a portion of the information contained in the submission
file for which the custom assay is to be designed.
238. A method for providing assays to a consumer as set forth in
claim 237, further comprising a shopping basket for storing an
order generated by the consumer, said file submission program being
operable to upload the submission file to said shopping basket.
239. A method in accordance with claim 226 wherein assays
configured to detect presence of genetic material are assays to
detect presence of at least one SNP allele.
240. A method in accordance with claim 239 wherein providing a user
interface configured to receive orders for assays includes
providing an providing an interface configured to receive, from the
consumer, criteria relating to at least one gene region containing
the at least one SNP.
241. A method in accordance with claim 240 wherein the criteria
relating to the at least one gene region containing the at least
one SNP comprises excluding assays for SNPs located in 10 kilobases
at 5' end and 10 kilobases at 3' end of the gene region.
242. A method in accordance with claim 239, wherein providing a
user interface configured to receive orders for assays includes
providing an interface configured to receive, from the consumer,
criteria relating to minor allele frequency.
243. A method in accordance with claim 226 wherein assays
configured to detect presence of genetic material are assays
configured to detect expression of at least one gene.
244. A method in accordance with claim 201 wherein said system
delivering to a consumer at least one assay further comprises
delivering information concerning said assay.
245. A method in accordance with claim 244 wherein said system for
delivering information concerning said assay comprises delivering
at least one datasheet.
246. A method in accordance with claim 244 wherein said system for
delivering information concerning said assay comprises delivering
said information on a machine-readable medium.
247. A method in accordance with claim 246 wherein said system for
delivering information concerning said assay further comprises a
system for delivering at least one datasheet.
248. A method in accordance with claim 246 wherein said
machine-readable medium is a compact disk.
249. A method in accordance with claim 201 wherein said system for
delivering to the consumer at least one custom or stock assay
comprises a system for delivering the at least one custom or stock
assay in a single tube.
250. A method in accordance with claim 249 wherein the at least one
custom or stock assay in a single tube comprises at least one probe
and two primers.
251. A method in accordance with claim 250 wherein the at least one
custom or stock assay in a single tube is a SNP assay comprising a
probe for each of two alleles and two primers.
252. A method in accordance with claim 250 wherein the probe
comprises at least one fluorophore and at least one fluorescence
quencher.
253. A method in accordance with claim 252 wherein the fluorescence
quencher is a non-fluorescent fluorescence quencher.
254. A method in accordance with claim 252 wherein the probe
further comprises at least one minor groove binder.
255. A method in accordance with claim 250 wherein said delivering
to the consumer at least one custom or stock assay in a single tube
further comprises delivering at least one custom assay in a single
tube and PCR reagents.
256. A method in accordance with claim 255 wherein said delivering
to the consumer at least one custom or stock assay in response to
an order for said one custom or stock assay placed by the consumer
further comprises delivering to the consumer one custom or stock
assay in a single tube and universal master mix, said universal
master mix comprising at least one salt, a buffer, and a DNA
polymerase.
257. A method in accordance with claim 249 wherein the single tube
further comprises a bar code identifier.
258. A method in accordance with claim 257 wherein the bar code is
a two-dimension bar code.
259. A method in accordance with claim 249 wherein the single tube
further comprises an identifier which is a human-readable Assay
number.
260. A method in accordance with claim 201 further comprising
providing a facility for manufacturing assays.
261. A method in accordance with claim 260 further comprising
providing a system for performing pre-processing selection, a
system for designing primers and probes, and a system for
performing in silico quality control prior to said
manufacturing.
262. A method in accordance with claim 261 wherein the assay is a
gene expression assay and wherein each said user interface
configured to receive orders for assays includes providing an
interface configured to receive, from the consumer, criteria
relating to at least one expressed transcript or portion
thereof.
263. A method in accordance with claim 262 wherein said performing
pre-processing selection comprises identifying optimal sequence
regions which do not contain any single nucleotide polymorphisms or
repeat sequences.
264. A method in accordance with claim 263 wherein identifying
optimal sequence regions comprises utilizing at least one method
selected from the group consisting of masking single nucleotide
polymorphisms and repeat sequences in the at least one expressed
transcript or portion thereof to avoid designing probes and primers
thereon, mapping the at least one expressed transcript or portion
thereof against at least two genomic databases to identify
discrepancies to avoid designing probes and primers thereon,
identifying exon-exon boundaries for expressed transcripts of
multi-exon genes in order to design probes or primers thereon and
combinations thereof.
265. A method in accordance with claim 264 wherein identifying
optimal sequence regions comprises masking repeat sequences
selected from the group consisting of di-nucleotide repeats,
tri-nucleotide repeats, Alu restriction site repeats, long
interspersed nuclear elements, and short interspersed nuclear
elements.
266. A method in accordance with claim 264 wherein said probes and
primers are designed in accordance with criteria selected from the
group consisting of avoiding inclusion of single nucleotide
polymorphisms or repeat sequences in probe and primer sequences,
avoiding inclusion of regions of discrepancy between at least two
genomic databases in probe and primer sequence, constructing either
or both of probes and primers on exon-exon boundaries for
multi-exon genes and combinations thereof.
267. A method in accordance with claim 262 wherein said system for
designing probes and primers utilizes specifications selected from
the group consisting of T.sub.m, GC content, buffer and salt
conditions, oligonucleotide concentration in assay, low secondary
structure of oligonucleotide, amplicon size and low incidence of
primer-dimer formation.
268. A method in accordance with claim 261 wherein said system for
performing in silico quality control comprises a system for
determining quality of designed probes and primers utilizing
scoring methods selected from the group consisting of transcript
BLAST scoring, genome BLAST scoring, scoring the size of intron
across which a probe spans for multi-exon genes, and combinations
thereof.
269. A method in accordance with claim 261 further comprising
providing a system for manufacturing designed probes and primers
having pre-selected scoring criteria.
270. A method in accordance with claim 269 wherein said
pre-selected scoring criteria comprises assigning high transcript
BLAST scoring for matching to self and no other transcript,
assigning high genome BLAST scoring for matching to self and no
other genome region and assigning high scoring for intron size
greater than 10 kilobases and wherein a high assay design scoring
is assigned for designed assays scoring all three of high
transcript BLAST scoring, high genome BLAST scoring and high intron
size scoring.
271. A method in accordance with claim 261 wherein the assay is a
SNP assay and wherein each said user interface configured to
receive orders for assays is configured to receive, from the
consumer, criteria relating to at least one gene region containing
at least one SNP.
272. A method in accordance with claim 271 wherein said system for
performing pre-processing selection comprises a component for
identifying optimal sequence regions which contain neither repeat
sequences not any SNPs other than a SNP for which the assay is
designed.
273. A method in accordance with claim 272 wherein said component
for identifying optimal sequence regions comprises using one or
more methods selected from the group consisting of a component for
masking any SNPs other than the at least one SNP for which the
assay is to be designed and repeat sequences in the at least one
gene region to avoid constructing probes and primers thereon, a
component for mapping the at least one SNP against at least two
genomic databases to identify discrepancies to avoid constructing
probes and primers thereon, and combinations thereof.
274. A method in accordance with claim 273 wherein said component
for identifying optimal sequence regions comprises a component for
masking repeat sequences selected from the group consisting of
di-nucleotide repeats, tri-nucleotide repeats, Alu restriction site
repeats, long interspersed nuclear elements, and short interspersed
nuclear elements.
275. A method in accordance with claim 273 wherein said probes and
primers are designed in accordance with criteria selected from the
group consisting of avoiding the inclusion of any SNPs other than
the at least one SNP for which the assay is to be designed,
avoiding the inclusion of regions of discrepancy between at least
two genomic databases in probe and primer sequence, and
combinations thereof.
276. A method in accordance with claim 270 wherein the system for
designing probes and primers comprises a system for utilizing
specifications selected from the group consisting of T.sub.m, GC
content, buffer and salt conditions, oligonucleotide concentration
in assay, low secondary structure of oligonucleotide, amplicon size
and low incidence of primer-dimer formation.
277. A method in accordance with claim 271 wherein said system for
performing in silico quality control comprises a system for
determining the probes and primers by genome BLAST scoring.
278. A method in accordance with claim 277 further comprising a
system for manufacturing designed probes and primers having
pre-selected scoring criteria.
279. A method in accordance with claim 278 wherein pre-selected
scoring criteria comprises assigning high Genome BLAST scoring for
matching to self and no other genome region.
280. A method in accordance with claim 260 further comprising
quality control testing of the manufactured assays according to
pre-selected quality control criteria.
281. A method in accordance with claim 280 wherein quality control
testing comprises one or more testing procedures selected from the
group consisting of synthesis yield testing, analytical quality
control testing, functional testing, validation testing and
combinations thereof wherein each of the one or more testing
procedures is performed according to pre-selected quality control
criteria.
282. A method in accordance with claim 281 wherein the system for
synthesis yield testing comprises a system for testing the
manufactured assays using PAGE or HPLC.
283. A method in accordance with claim 281 wherein the pre-selected
quality control criteria for synthesis yield testing is about 90%
(w/w) product yield.
284. A method in accordance with claim 283 wherein the pre-selected
quality control criteria for synthesis yield testing is about 95%
(w/w) product yield.
285. A method in accordance with claim 281 wherein analytical
quality control testing comprises testing the manufactured assays
using mass spectrometry.
286. A method in accordance with claim 285 wherein the pre-selected
quality control criteria for synthesis yield testing is such that
determined mass is not more than 5% greater or lesser than
calculated mass.
287. A method in accordance with claim 286 wherein the pre-selected
quality control criteria for synthesis yield testing is such that
determined mass is not more than 2% greater or lesser than
calculated mass.
288. A method in accordance with 281 wherein the manufactured
assays are SNP assays and functional testing comprises performing
PCR reactions of manufactured assays against from about 10 to about
20 genomic DNA samples.
289. A method in accordance with claim 288 wherein the pre-selected
quality control criteria for functional testing comprises detecting
presence of both alleles.
290. A method in accordance with claim 281 wherein the manufactured
assay is a gene expression assay and functional testing comprises
performing designed assay RT-PCR.
291. A method in accordance with claim 290 wherein the manufactured
assay is a multi-exon gene expression assay and the pre-selected
quality control criteria for functional testing comprises
detectable amplification of transcript in accordance with assay
design in absence of detectable amplification of genomic DNA.
292. A method in accordance with claim 290 wherein the manufactured
assay is a single exon gene expression assay and the pre-selected
quality control criteria for functional testing comprises
detectable amplification of transcript in accordance with assay
design in absence of detectable amplification of non-transcribed
genomic DNA.
293. A method in accordance with claim 281 wherein the manufactured
assay is a SNP assay and system for validation testing comprises a
system for performing designed assay PCR against about 90 human
genomic samples.
294. A method in accordance with claim 293 wherein the pre-selected
quality control criteria for validation testing comprises detecting
a minor allele frequency of at least 10%.
295. A method in accordance with claim 294 wherein the pre-selected
quality control criteria for validation testing comprises detecting
a minor allele frequency of at least 15%.
296. A method in accordance with claim 281 wherein the manufactured
assay is a gene expression and the system for validation testing
comprises a system for performing designed assay PCR against a pool
of at least about 10 human cDNA samples.
297. A method in accordance with claim 296 wherein the human cDNA
samples are from different individuals.
298. A method in accordance with claim 296 wherein the human cDNA
samples are from different cell lines.
299. A method in accordance with claim 296 wherein the pre-selected
quality control criteria for the system for validation testing
comprises a system for detection of amplified transcript at a
threshold of less than 35 PCR cycles.
300. A method in accordance with claim 259 wherein said
manufacturing comprises high-throughput manufacturing.
301. A kit comprising: one or more assays for detecting presence or
expression of genomic material, wherein at least one assay is in a
single tube and wherein the at least one assay in a single tube
comprises at least one probe, a forward primer and a reverse
primer.
302. A kit in accordance with claim 301 further comprising an
information source comprising at least one member of the group
consisting of an E-datasheet, an assay information file, at least
one printed datasheet and combinations thereof.
303. A kit in accordance with claim 301 wherein the assay is a SNP
assay.
304. A kit in accordance with claim 301 wherein the assay is gene
expression assay.
305. A kit in accordance with claim 303 wherein the assay is a SNP
assay comprising one probe for each of two alleles and two
primers.
306. A kit in accordance with claim 305 wherein the probe comprises
at least one fluorophore and at least one fluorescence
quencher.
307. A kit in accordance with claim 306 wherein the fluorescence
quencher is a non-fluorescent fluorescence quencher.
308. A kit in accordance with claim 307 wherein the probe further
comprises at least one minor groove binder.
309. A kit in accordance with claim 301 further comprising PCR
reagents or RT-PCR reagents.
310. A kit in accordance with claim 301 further comprising
universal master mix, said universal master mix comprising at least
one salt, a buffer, and a DNA polymerase.
311. A kit in accordance with claim 301 wherein the single tube
further comprises a bar code identifier.
312. A kit in accordance with claim 311 wherein the bar code
identifier is a two dimensional bar code identifier.
313. A kit in accordance with claim 301 wherein the single tube
further comprises a human-readable assay number.
314. A kit in accordance with claim 301 wherein the kit comprises a
plurality of assays each of which is in a single tube to constitute
a plurality of tubes.
315. A kit in accordance with claim 314 further comprising a rack
configured to hold said plurality of tubes.
316. A kit in accordance with claim 315 wherein the rack has a
bar-code identification.
317. A kit in accordance with claim 301 which comprises at least
one printed datasheet containing information on the assay.
318. A kit in accordance with claim 301 which comprises at least
one machine readable medium containing information on the
assay.
319. A kit in accordance with claim 318 which comprises at least
one datasheet containing information on the assay.
320. A kit in accordance with claim 318 wherein the machine
readable medium is a compact disk.
321. A method for building a submission file useful for designing
and ordering at least one of SNP genotyping assays and gene
expression assays, said assays comprising at least one probe, a
forward primer and a reverse primer, said method comprising:
providing a graphical user interface configured to receive, from a
consumer, information relating to assay design said information
comprising information related to at least one target sequence,
wherein said information does not include information selected from
the group consisting of sequence of the at least one probe,
sequence of the forward primer, sequence of the reverse primer and
combinations thereof.
322. A method in accordance with claim 321 further comprising:
electronically validating at least a portion of the information
relating to the at least one target sequence and generating
validating information related to said validating; and saving the
information relating to the at least one target sequence and the
validating information in a submission file.
323. A method in accordance with claim 322, further comprising
uploading the saved submission file to a web-based assay ordering
system.
324. A method in accordance with claim 323 wherein said electronic
validating comprises detecting typographical errors in a target
sequence.
325. A method in accordance with claim 322, further comprising
prompting the consumer to correct detected typographical errors in
the target sequence when such errors are present.
326. A method in accordance with claim 322 further comprising
generating an error log providing information related to whether
the target sequence is properly formatted.
327. A system for recommending genomic products and services to a
consumer, the products and services being used to detect presence
or expression of genetic material in a biological sample, the
system comprising: a first source of information regarding at least
one of presence and expression of genetic material in biological
samples; a second source of information regarding products and
services for analyzing genetic material; and an interface system
communicating with said first source of information and said second
source of information and operable to recommend to the consumer
certain products and services in response to inquires to said first
source of information by the consumer.
328. A system in accordance with claim 327 further comprising a
web-based interface configured to provide access to the first
source of information by the consumer.
329. A system in accordance with claim 327 wherein the first source
of information includes information regarding at least one SNP.
330. A system in accordance with claim 329 wherein the first source
of information further comprises information regarding identity of
the at least one SNP.
331. A system in accordance with claim 327 wherein the first source
of information further comprises information regarding identity of
at least one bi-allelic SNP.
332. A system in accordance with claim 327 wherein the first source
of information further comprises information regarding identity of
at least one bi-allelic SNP located in a gene region.
333. A system in accordance with claim 327 wherein the first source
of information further comprises information regarding identity of
each of a group of at least about 40,000 bi-allelic SNPs locate in
gene regions.
334. A system in accordance with claim 327 wherein the first source
of information further comprises information regarding identity of
each of a group of about 40,000 bi-allelic SNPS located in gene
regions and spaced apart by about 10 kilobases within the gene
regions.
335. A system in accordance with claim 327 wherein the first source
of information further comprises information regarding identity of
at least about 40,000 bi-allelic SNPs having a minor allele
frequency of at least about 10%.
336. A system in accordance with claim 327 wherein the first source
of information further comprises information regarding a population
within which the at least about 40,000 bi-allelic SNP have a minor
allele frequency of at least 10%.
337. A system in accordance with claim 327 wherein the first source
of information further comprises information regarding the identity
of at least about 40,000 bi-allelic SNPs having a minor allele
frequency of at least about 15%.
338. A system in accordance with claim 327 wherein the first source
of information further comprises information regarding identity of
each of a group of at least about 100,000 bi-allelic SNPs locate in
gene regions.
339. A system in accordance with claim 338 wherein the first source
of information further comprises information regarding identity of
each of a group of at least about 100,000 bi-allelic SNPS located
in gene regions and spaced apart by about 10 kilobases within the
gene regions.
340. A system in accordance with claim 338 wherein the first source
of information further comprises information regarding the identity
of each of at least about 100,000 bi-allelic SNPs having a minor
allele frequency of at least 10%.
341. A system in accordance with claim 340 wherein the first source
of information further comprises information regarding a population
within which the at least about 100,000 bi-allelic SNP have a minor
allele frequency of at least 10%.
342. A system in accordance with claim 337 wherein the first source
of information further comprises information regarding a population
within which the at least about 40,000 bi-allelic SNP have a minor
allele frequency of at least 15%.
343. A system in accordance with claim 327 wherein the first source
of information further comprises information regarding at least one
expressed gene.
344. A system in accordance with claim 343 wherein the first source
of information further comprises information regarding identity of
the at least one expressed gene.
345. A system in accordance with claim 344 wherein the information
regarding the identity of at least one expressed gene one gene
comprises information regarding the identity of each of a group of
at least about 10,000 expressed genes.
346. A system in accordance with claim 344 wherein the first source
of information further comprises information regarding exons and
introns of the at least one expressed gene.
347. A system in accordance with claim 344 wherein the first source
of information further comprises information regarding intron-exon
junction.
348. A system in accordance with claim 347 wherein the first source
of information further comprises information regarding intron
length at the intron-exon junction.
349. A system in accordance with claim 327 further comprises a
web-based interface configured to provide access to the first
source of information by the consumer.
350. A system in accordance with claim 327 wherein the second
source of information further comprises information regarding SNP
assays.
351. A system in accordance with claim 327 wherein the second
source of information further comprises information regarding
instruments for performing PCR or RT-PCR reactions.
352. A system in accordance with claim 327 wherein the second
source of information further comprises information regarding
laboratory information management systems.
353. A system in accordance with claim 352 wherein the information
regarding laboratory information management systems further
comprises in-formation regarding devices configured for use in a
laboratory information management system.
354. A method for providing to a consumer, assays configured to
detect presence or expression of genetic material, said method
comprising: providing a web-based user interface configured to
receive a request for design of one or more custom assays and an
order for said custom assays; and delivering to the consumer at
least one custom assay in a single tube in response to an order for
said at least one custom assay placed by the, consumer, wherein
said assay comprises at least one probe, a forward primer and a
reverse primer.
355. A method in accordance with claim 354, further comprising
providing a web-based gene exploration platform configured to
assist a consumer in selecting a custom assay.
356. A method in accordance with claim 355 wherein said information
comprises genomic and biomedical information from at least one
public or private source.
357. A method in accordance with claim 354, wherein providing a
user interface configured to receive a request for design of one or
more custom assays and an order for said custom assays comprises
providing a graphical user interface configured to receive a
request for design of one or more custom assays and an order for
said custom assays.
358. A method in accordance with claim 354, wherein said user
interface configured to receive orders for custom assays includes a
file-receiving interface configured to receive, from the consumer,
a submission file containing information suitable for use in
designing at least one of said custom assays.
359. A method in accordance with claim 358, wherein said
file-receiving interface is configured to receive from the consumer
a submission file containing sequence information relating to the
target of the custom assay requested by the consumer.
360. A method in accordance with claim 359, wherein said
file-receiving interface is configured to receive from the consumer
a submission file containing sequence information relating to
target coordinates of the custom assay requested by the
consumer.
361. A method in accordance with claim 358, wherein said file
receiving interface is configured to receive from the consumer a
submission file containing information relating to the identity of
the consumer requesting a custom assay.
362. A method in accordance claim 358, further comprising providing
a submission file builder configured to assist the consumer in
preparing said submission file for ordering custom assays.
363. A method in accordance claim 362 wherein the file builder
provides for electronically validating at least a portion of the
submission file.
364. A method in accordance with claim 363, wherein the electronic
validation comprises detecting typographical errors in the
submission file.
365. A method in accordance with claim 364 further comprising
prompting the consumer to correct detected typographical errors in
the submission file.
366. A method in accordance with claim 363 wherein the electronic
validation comprises generating an error log providing information
related to whether the submission file is properly formatted.
367. A method in accordance with 362, wherein the submission file
builder includes a sequence checker to verify correctness of at
least a portion of the information contained in the submission
file.
368. A method in accordance with claim 367, further comprising
providing an electronic shopping basket configured to store an
order received from the consumer, said file submission program
being operable to upload the submission file to said shopping
basket.
369. A method in accordance with claim 356 wherein the assays
configured to detect presence of genetic material are assays to
configured to detect presence of at least one SNP allele.
370. A method in accordance with claim 369 wherein providing a user
interface configured to receive orders for assays includes
providing an interface configured to receive, from the consumer,
criteria relating to at least one gene region containing the at
least one SNP.
371. A method in accordance with claim 370 wherein the criteria
relating to the at least one gene region containing the at least
one SNP comprises excluding assays for SNPs located in 10 kilobases
at 5' end and 10 kilobases at 3' end of the gene region.
372. A method in accordance with claim 369, wherein providing a
user interface configured to receive orders for assays includes
providing an interface configured to receive, from the consumer,
criteria relating to minor allele frequency.
373. A method in accordance with claim 356 wherein assays
configured to detect presence of genetic material are assays
configured to detect expression of at least one gene.
374. A method in accordance with claim 354 wherein said delivering
to a consumer at least one assay further comprises delivering
information concerning said assay.
375. A method in accordance with claim 374 wherein said delivering
information concerning said assay comprises delivering at least one
datasheet.
376. A method in accordance with claim 374 wherein delivering
information concerning said assay comprises delivering said
information on a machine-readable medium.
377. A method in accordance with claim 376 wherein said delivering
information concerning said assay further comprises delivering at
least one datasheet.
378. A method in accordance with claim 376 wherein said
machine-readable medium is a compact disk.
379. A method in accordance with claim 354 wherein said delivering
to the consumer at least one custom assay comprises delivering the
at least one custom assay in a single tube.
380. A method in accordance with claim 379 wherein said delivering
to the consumer at least one custom assay in a single tube
comprises delivering to the consumer at least one probe and two
primers.
381. A method in accordance with claim 380 wherein the custom assay
in a single tube is a SNP assay comprising a separate probe for
each of two alleles and two primers.
382. A method in accordance with claim 380 wherein the probe
comprises at least one fluorophore and at least one fluorescence
quencher.
383. A method in accordance with claim 382 wherein the fluorescence
quencher is a non-fluorescent fluorescence quencher.
384. A method in accordance with claim 382 wherein the probe
further comprises at least one minor groove binder.
385. A method in accordance with claim 380 wherein said delivering
to the consumer at least one custom assay in a single tube further
comprises delivering at least one custom assay in a single tube and
PCR reagents.
386. A method in accordance with claim 380 wherein said delivering
to the consumer at least one custom assay in a single tube further
comprises delivering to the consumer at least one custom assay in a
single tube and a universal master mix, said universal master mix
comprising at least one salt, a buffer, and a DNA polymerase.
387. A method in accordance with claim 379 wherein the single tube
further comprises a bar code identifier.
388. A method in accordance with claim 387 wherein the bar code is
a two-dimension bar code
389. A method in accordance with claim 379 wherein the single tube
further comprises an identifier which is a human-readable Assay
number
390. A method in accordance with claim 354 further comprising
manufacturing assays.
391. A method in accordance with claim 390 further comprising
performing pre-processing selection, designing primers and probes,
and performing in silico quality control prior to said
manufacturing.
392. A method in accordance with claim 391 wherein the assay is a
gene expression assay and wherein said user interface configured to
receive orders for assays includes an interface configured to
receive, from the consumer, criteria relating to at least one
expressed transcript or portion thereof.
393. A method in accordance with claim 392 wherein said performing
pre-processing selection comprises identifying optimal sequence
regions which do not contain any single nucleotide polymorphisms or
repeat sequences.
394. A method in accordance with claim 393 wherein identifying
optimal sequence regions comprises utilizing at least one method
selected from the group consisting of masking single nucleotide
polymorphisms and repeat sequences in the at least one expressed
transcript or portion thereof to avoid designing probes and primers
thereon, mapping the at least one expressed transcript or portion
thereof against at least two genomic databases to identify
discrepancies to avoid designing probes and primers thereon,
identifying exon-exon boundaries for expressed transcripts of
multi-exon genes in order to design probes or primers thereon and
combinations thereof.
395. A method in accordance with claim 394 wherein identifying
optimal sequence regions comprises masking repeat sequences
selected from the group consisting of di-nucleotide repeats,
tri-nucleotide repeats, Alu restriction site repeats, long
interspersed nuclear elements, and short interspersed nuclear
elements.
396. A method in accordance with claim 394 wherein said probes and
primers are designed in accordance with criteria selected from the
group consisting of avoiding inclusion of single nucleotide
polymorphisms or repeat sequences in probe and primer sequences,
avoiding inclusion of regions of discrepancy between at least two
genomic databases in probe and primer sequence, constructing either
or both of probes and primers on exon-exon boundaries for
multi-exon genes and combinations thereof.
397. A method in accordance with claim 392 wherein said designing
probes and primers comprises utilizing specifications selected from
the group consisting of T.sub.m, GC content, buffer and salt
conditions, oligonucleotide concentration in assay, low secondary
structure of oligonucleotide, amplicon size and low incidence of
primer-dimer formation.
398. A method in accordance with claim 391 wherein said performing
in silico quality control comprises determining quality of designed
probes and primers utilizing scoring methods selected from the
group consisting of transcript BLAST scoring, genome BLAST scoring,
scoring size of intron across which a probe spans for multi-exon
genes, and combinations thereof.
399. A method in accordance with claim 391 further comprising
manufacturing designed probes and primers having pre-selected
scoring criteria.
400. A method in accordance with claim 399 wherein said
pre-selected scoring criteria comprises assigning high transcript
BLAST scoring for matching to self and no other transcript,
assigning high genome BLAST scoring for matching to self and no
other genome region and assigning high scoring for intron size
greater than 10 kilobases and wherein a high assay design scoring
is assigned for designed assays scoring all three of high
transcript BLAST scoring, high genome BLAST scoring and high intron
size scoring.
401. A method in accordance with claim 391 wherein the assay is a
SNP assay and wherein said user interface configured to receive
orders for assays is configured to receive, from the consumer,
criteria relating to at least one gene region containing at least
one SNP.
402. A method in accordance with claim 401 wherein said performing
pre-processing selection comprises identifying optimal sequence
regions which contain neither repeat sequences nor any SNPs other
than a SNP for which the assay is designed.
403. A method in accordance with claim 402 wherein said identifying
optimal sequence regions comprises using one or more methods
selected from the group consisting of masking any SNPs other than
the at least one SNP for which the assay is to be designed and
repeat sequences in the at least one gene region to avoid
constructing probes and primers thereon, mapping the at least one
SNP against at least two genomic databases to identify
discrepancies to avoid constructing probes-and primers thereon, and
combinations thereof.
404. A method in accordance with claim 403 wherein said identifying
optimal sequence regions comprises masking repeat sequences
selected from the group consisting of di-nucleotide repeats,
tri-nucleotide repeats, Alu restriction site repeats, long
interspersed nuclear elements, and short interspersed nuclear
elements.
405. A method in accordance with claim 403 wherein said probes and
primers are designed in accordance with criteria selected from the
group consisting of avoiding the inclusion of any SNPs other than
the at least one SNP for which the assay is to be designed,
avoiding the inclusion of regions of discrepancy between at least
two genomic databases in probe and primer sequence, and
combinations thereof.
406. A method in accordance with claim 400 wherein designing probes
and primers comprises utilizing specifications selected from the
group consisting of T.sub.m, GC content, buffer and salt
conditions, oligonucleotide concentration in assay, low secondary
structure of oligonucleotide, amplicon size and low incidence of
primer-dimer formation.
407. A method in accordance with claim 401 wherein said performing
in silico quality control comprises determining the quality of
designed probes and primers by genome BLAST scoring.
408. A method in accordance with claim 407 further comprising
manufacturing designed probes and primers having pre-selected
scoring criteria.
409. A method in accordance with claim 408 wherein pre-selected
scoring criteria comprises assigning high Genome BLAST scoring for
matching to self and no other genome region.
410. A method in accordance with claim 390 further comprising
quality control testing of the manufactured assays according to
pre-selected quality control criteria.
411. A method in accordance with claim 410 wherein quality control
testing comprises one or more tests selected from the group
consisting of synthesis yield testing, analytical quality control
testing, functional testing, validation testing and combinations
thereof, wherein each of the one or more tests is performed
according to pre-selected quality control criteria.
412. A method in accordance with claim 411 wherein synthesis yield
testing comprises testing the manufactured assays using PAGE or
HPLC.
413. A method in accordance with claim 411 wherein the pre-selected
quality control criteria for synthesis yield testing is about 90%
(w/w) product yield.
414. A method in accordance with claim 413 wherein the pre-selected
quality control criteria for synthesis yield testing is about 95%
(w/w) product yield.
415. A method in accordance with claim 411 wherein analytical
quality control testing comprises testing the manufactured assays
using mass spectrometry.
416. A method in accordance with claim 415 wherein the pre-selected
quality control criteria for synthesis yield testing is such that
determined mass is not more than 5% greater or lesser than
calculated mass.
417. A method in accordance with claim 416 wherein the pre-selected
quality control criteria for synthesis yield testing is such that
determined mass is not more than 2% greater or lesser than
calculated mass.
418. A method in accordance with 411 wherein the manufactured
assays are SNP assays and functional testing comprises performing
PCR reactions of manufactured assays against from about 10 to about
20 genomic DNA samples.
419. A method in accordance with claim 418 wherein the pre-selected
quality control criteria for functional testing comprises detecting
presence of both alleles.
420. A method in accordance with claim 411 wherein the manufactured
assay is a gene expression assay and functional testing comprises
performing designed assay RT-PCR.
421. A method in accordance with claim 420 wherein the manufactured
assay is a multi-exon gene expression assay and the pre-selected
quality control criteria for functional testing comprises
detectable amplification of transcript in accordance with assay
design in absence of detectable amplification of genomic DNA.
422. A method in accordance with claim 420 wherein the manufactured
assay is a single exon gene expression assay and the pre-selected
quality control criteria for functional testing comprises
detectable amplification of transcript in accordance with assay
design in absence of detectable amplification of non-transcribed
genomic DNA.
423. A method in accordance with claim 411 wherein the manufactured
assay is a SNP assay and validation testing comprises performing
designed assay PCR against about 90 human genomic samples.
424. A method in accordance with claim 423 wherein the pre-selected
quality control criteria for validation testing comprises detecting
a minor allele frequency of at least 10%.
425. A method in accordance with claim 424 wherein the pre-selected
quality control criteria for validation testing comprises detecting
a minor allele frequency of at least 15%.
426. A method in accordance with claim 410 wherein the manufactured
assay is a gene expression and validation testing comprises
performing designed assay PCR against a pool of at least about 10
human cDNA samples.
427. A method in accordance with claim 426 wherein the human cDNA
samples are from different individuals.
428. A method in accordance with claim 426 wherein the human cDNA
samples are from different cell lines.
429. A method in accordance with claim 426 wherein the pre-selected
quality control criteria for validation testing comprises detection
of amplified transcript at a threshold of less than 35 PCR
cycles.
430. A method in accordance with claim 390 wherein said
manufacturing comprises high-throughput manufacturing.
431. A method for providing to a consumer, assays configured to
detect presence or expression of genetic material, said method
comprising: providing a web-based user interface configured to
receive an order one or more stock assays; and delivering to the
consumer at least one stock assay in a single tube in response to
an order for said at least one stock assay placed by the consumer
wherein said assay comprises at least one probe, a forward primer
and a reverse primer.
432. A method in accordance with claim 431, further comprising
providing a web-based gene exploration platform configured to
provide information to assist a consumer in selecting a stock
assay.
433. A method in accordance with claim 432 wherein said information
is genomic and biomedical information from at least one public or
private source.
434. A method in accordance with claim 431, wherein providing a
user interface configured to receive an order for stock assays
comprises providing a graphical user interface.
435. A method in accordance with claim 434, further comprising
providing a graphical user interface configured for the consumer to
perform at least one search for at least one information item used
to identify genetic material for a stock assay.
436. A method in accordance with claim 435, wherein the at least
one information item used to identify the genetic material is a
gene identification item selected from the group consisting of gene
symbol, gene name, RefSeq accession number, Panther function,
Panther process, GO function, GO process, GO identifier, Applied
Biosystems identifier, Celera gene identifier (hCG), Celera
transcript identifier (hCT), Celera protein identifier (hCP),
LocusLink identifier, GenBank nucleotide identifier, GenBank
protein identifier, species identifier, chromosome identifier,
haplotype identifier, cytoband identifier, RefSeq GI identifier,
and combinations thereof.
437. A method in accordance with claim 435, wherein said at least
one search comprises a batch search.
438. A method in accordance with claim 435, wherein the at least
one information item comprises a gene classification search.
439. A method in accordance with claim 438, wherein the gene
classification search comprises a molecular function search.
440. A method in accordance with claim 438, wherein the gene
classification search comprises a biological process search.
441. A method in accordance with claim 434, further comprising
providing reference information to the consumer concerning genetic
material that is detectable by an assay that is ordered by the
consumer.
442. A method in accordance with claim 441, wherein the reference
information is selected from the group consisting of RefSeq
identifier, LocusLink gene name, molecular function, biological
process, Celera identification number, gene location, and
combinations thereof.
443. A method in accordance with claim 434 wherein the graphical
user interface is configured to receive an order for at least one
SNP assay.
444. A method in accordance with claim 443 wherein the graphical
user interface is configured to receive an order for at least one
SNP assay from a group of at least 40,000 SNP assays.
445. A method in accordance with claim 444 wherein each SNP assay
is configured to detect presence of one of at least 40,000 pairs of
SNP alleles located in gene regions.
446. A method in accordance with claim 445 wherein each of the
40,000 pairs of SNP alleles are spaced apart by about 10 kilobases
within gene regions.
447. A method in accordance with claim 443 wherein the graphical
user interface is configured to receive an order for at least one
SNP assay from a group of at least 100,000 SNP assays.
448. A method in accordance with claim 447 wherein each SNP assay
is configured to detect presence of one of at least 100,000 pairs
of SNP alleles located in gene regions.
449. A method in accordance with claim 448 wherein each of the
100,000 pairs of SNP alleles are spaced apart by about 10 kilobases
within gene regions.
450. A method in accordance with claim 443 wherein providing the
graphical user interface includes providing an interface configured
to receive, from the consumer, criteria relating to at least one
gene region containing the at least one SNP.
451. A method in accordance with claim 450 wherein the criteria
relating to the at least one gene region containing the at least
one SNP comprises excluding assays for SNPs located in 10 kilobases
at 5' end and 10 kilobases at 3' end of the gene region.
452. A method in accordance with claim 443, wherein said providing
the graphical user interface includes providing an interface
configured to receive, from the consumer, criteria relating to
minor allele frequency.
453. A method in accordance with claim 434 wherein the graphical
user interface is configured to receive an order for at least one
gene expression assay.
454. A method in accordance with claim 453 wherein the graphical
user interface is configured to receive an order for at least one
gene expression assay from a group of at least 10,000 gene
expression assays.
455. A method in accordance with claim 453 wherein said providing a
graphical user interface for ordering assays includes providing an
interface configured to receive, from the consumer, criteria
relating to at least one expressed transcript or portion
thereof.
456. A method in accordance with claim 431 wherein said delivering
to a consumer at least one assay further comprises delivering
information concerning said assay.
457. A method in accordance with claim 456 wherein said delivering
information concerning said assay comprises delivering at least one
datasheet.
458. A method in accordance with claim 456 wherein delivering
information concerning said assay comprises delivering said
information on a machine-readable medium.
459. A method in accordance with claim 458 wherein said delivering
information concerning said assay further comprises delivering at
least one datasheet.
460. A method in accordance with claim 458 wherein said
machine-readable medium is a compact disk.
461. A method in accordance with claim 431 wherein said delivering
to the consumer at least one stock assay comprises delivering the
at least one stock assay in a single tube.
462. A method in accordance with claim 461 wherein said delivering
to the consumer at least one stock assay in a single tube comprises
delivering to the consumer at least one probe and two primers.
463. A method in accordance with claim 462 wherein the at least one
custom or stock assay in a single tube is a SNP assay comprising a
separate probe for each of two alleles and two primers.
464. A method in accordance with claim 462 wherein the probe
comprises at least one fluorophore and at least one fluorescence
quencher.
465. A method in accordance with claim 464 wherein the fluorescence
quencher is a non-fluorescent fluorescence quencher.
466. A method in accordance with claim 464 wherein the probe
further comprises at least one minor groove binder.
467. A method in accordance with claim 462 wherein said delivering
to the consumer at least one stock assay in a single tube further
comprises delivering at least one stock assay in a single tube and
PCR reagents.
468. A method in accordance with claim 462 wherein said delivering
to the consumer at least one stock assay in a single tube further
comprises delivering to the consumer at least one stock assay in a
single tube and a universal master mix, said universal master mix
comprising at least one salt, a buffer, and a DNA polymerase.
469. A method in accordance with claim 461 wherein the single tube
further comprises a bar code identifier.
470. A method in accordance with claim 469 wherein the bar code is
a two-dimension bar code
471. A method in accordance with claim 461 wherein the single tube
further comprises an identifier which is a human-readable Assay
number
472. A method in accordance with claim 431 further comprising
manufacturing assays.
473. A method in accordance with claim 472 further comprising
performing pre-processing selection, designing primers and probes,
and performing in silico quality control prior to said
manufacturing.
474. A method in accordance with claim 473 wherein the assay is a
gene expression assay and wherein each said user interface
configured to receive orders for assays includes an interface
configured to receive, from the consumer, criteria relating to at
least one expressed transcript or portion thereof.
475. A method in accordance with claim 474 wherein said performing
pre-processing selection comprises identifying optimal sequence
regions which do not contain any single nucleotide polymorphisms or
repeat sequences.
476. A method in accordance with claim 475 wherein identifying
optimal sequence regions comprises utilizing at least one method
selected from the group consisting of masking single nucleotide
polymorphisms and repeat sequences in the at least one expressed
transcript or portion thereof to avoid designing probes and primers
thereon, mapping the at least one expressed transcript or portion
thereof against at least two genomic databases to identify
discrepancies to avoid designing probes and primers thereon,
identifying exon-exon boundaries for expressed transcripts of
multi-exon genes in order to design probes or primers thereon and
combinations thereof.
477. A method in accordance with claim 476 wherein identifying
optimal sequence regions comprises masking repeat sequences
selected from the group consisting of di-nucleotide repeats,
tri-nucleotide repeats, Alu restriction site repeats, long
interspersed nuclear elements, and short interspersed nuclear
elements.
478. A method in accordance with claim 476 wherein said probes and
primers are designed in accordance with criteria selected from the
group consisting of avoiding inclusion of single nucleotide
polymorphisms or repeat sequences in probe and primer sequences,
avoiding inclusion of regions of discrepancy between at least two
genomic databases in probe and primer sequence, constructing either
or both of probes and primers on exon-exon boundaries for
multi-exon genes and combinations thereof.
479. A method in accordance with claim 474 wherein designing probes
and primers comprises utilizing specifications selected from the
group consisting of T.sub.m, GC content, buffer and salt
conditions, oligonucleotide concentration in assay, low secondary
structure of oligonucleotide, amplicon size and low incidence of
primer-dimer formation.
480. A method in accordance with claim 473 wherein said performing
in silico quality control comprises determining the quality of
designed probes and primers utilizing scoring methods selected from
the group consisting of transcript BLAST scoring, genome BLAST
scoring, scoring the size of intron across which a probe spans for
multi-exon genes and combinations thereof.
481. A method in accordance with claim 473 further comprising
manufacturing designed probes and primers having pre-selected
scoring criteria.
482. A method in accordance with claim 481 wherein said
pre-selected scoring criteria comprises assigning high transcript
BLAST scoring for matching to self and no other transcript,
assigning high genome BLAST scoring for matching to self and no
other genome region and assigning high scoring for intron size
greater than 10 kilobases and wherein a high assay design scoring
is assigned for designed assays scoring all three of high
transcript BLAST scoring, high genome BLAST scoring and high intron
size scoring.
483. A method in accordance with claim 473 wherein the assay is a
SNP assay and wherein each said user interface configured to
receive orders for assays is configured to receive, from the
consumer, criteria relating to at least one gene region containing
at least one SNP.
484. A method in accordance with claim 483 wherein said performing
pre-processing selection comprises identifying optimal sequence
regions which contain neither repeat sequences nor any SNPs other
than a SNP for which the assay is designed.
485. A method in accordance with claim 484 wherein said identifying
optimal sequence regions comprises using one or more methods
selected from the group consisting of masking any SNPs other than
the at least one SNP for which the assay is to be designed and
repeat sequences in the at least one gene region to avoid
constructing probes and primers thereon, mapping the at least one
SNP against at least two genomic databases to identify
discrepancies to avoid constructing probes and primers thereon, and
combinations thereof.
486. A method in accordance with claim 485 wherein said identifying
optimal sequence regions comprises masking repeat sequences
selected from the group consisting of di-nucleotide repeats,
tri-nucleotide repeats, Alu restriction site repeats, long
interspersed nuclear elements, and short interspersed nuclear
elements.
487. A method in accordance with claim 485 wherein said probes and
primers are designed in accordance with criteria selected from the
group consisting of avoiding the inclusion of any SNPs other than
the at least one SNP for which the assay is to be designed,
avoiding the inclusion of regions of discrepancy between at least
two genomic databases in probe and primer sequence, and
combinations thereof.
488. A method in accordance with claim 482 wherein designing probes
and primers comprises utilizing specifications selected from the
group consisting of T.sub.m, GC content, buffer and salt
conditions, oligonucleotide concentration in assay, low secondary
structure of oligonucleotide, amplicon size and low incidence of
primer-dimer formation.
489. A method in accordance with claim 482 wherein said performing
in silico quality control comprises determining the quality of
designed probes and primers by genome BLAST scoring.
490. A method in accordance with claim 489 further comprising
manufacturing designed probes and primers having pre-selected
scoring criteria.
491. A method in accordance with claim 480 wherein pre-selected
scoring criteria comprises assigning high Genome BLAST scoring for
matching to self and no other genome region.
492. A method in accordance with claim 472 further comprising
quality control testing of the manufactured assays according to
pre-selected quality control criteria.
493. A method in accordance with claim 492 wherein quality control
testing comprises one or more testing procedures selected from the
group consisting of synthesis yield testing, analytical quality
control testing, functional testing, validation testing and
combinations thereof, wherein each of the one or more testing
procedures is performed according to pre-selected quality control
criteria.
494. A method in accordance with claim 493 wherein synthesis yield
testing comprises testing the manufactured assays using PAGE or
HPLC.
495. A method in accordance with claim 493 wherein the pre-selected
quality control criteria for synthesis yield testing is about 90%
(w/w) product yield.
496. A method in accordance with claim 495 wherein the pre-selected
quality control criteria for synthesis yield testing is about 95%
(w/w) product yield.
497. A method in accordance with claim 493 wherein analytical
quality control testing comprises testing the manufactured assays
using mass spectrometry.
498. A method in accordance with claim 497 wherein the pre-selected
quality control criteria for synthesis yield testing is such that
determined mass is not more than 5% greater or lesser than
calculated mass.
499. A method in accordance with claim 498 wherein the pre-selected
quality control criteria for synthesis yield testing is such that
determined mass is not more than 2% greater or lesser than
calculated mass.
500. A method in accordance with 493 wherein the manufactured
assays are SNP assays and functional testing comprises performing
PCR reactions of manufactured assays against from about 10 to about
20 genomic DNA samples.
501. A method in accordance with claim 500 wherein the pre-selected
quality control criteria for functional testing comprises detecting
presence of both alleles.
502. A method in accordance with claim 493 wherein the manufactured
assay is a gene expression assay and functional testing comprises
performing designed assay RT-PCR.
503. A method in accordance with claim 502 wherein the manufactured
assay is a multi-exon gene expression assay and the pre-selected
quality control criteria for functional testing comprises
detectable amplification of transcript in accordance with assay
design in absence of detectable amplification of genomic DNA.
504. A method in accordance with claim 502 wherein manufactured
assay is a single exon gene expression assay and the pre-selected
quality control criteria for functional testing comprises
detectable amplification of transcript in accordance with assay
design in absence of detectable amplification of non-transcribed
genomic DNA.
505. A method in accordance with claim 493 wherein the manufactured
assay is a SNP assay and validation testing comprises performing
designed assay PCR against about 90 human genomic samples.
506. A method in accordance with claim 505 wherein the pre-selected
quality control criteria for validation testing comprises detecting
a minor allele frequency of at least 10%.
507. A method in accordance with claim 506 wherein the pre-selected
quality control criteria for validation testing comprises detecting
a minor allele frequency of at least 15%.
508. A method in accordance with claim 492 wherein the manufactured
assay is a gene expression and validation testing comprises
performing designed assay PCR against a pool of at least about 10
human cDNA samples.
509. A method in accordance with claim 508 wherein the human cDNA
samples are from different individuals.
510. A method in accordance with claim 508 wherein the human cDNA
samples are from different cell lines.
511. A method in accordance with claim 508 wherein the pre-selected
quality control criteria for validation testing comprises detection
of amplified transcript at a threshold of less than 35 PCR
cycles.
512. A method in accordance with claim 511 wherein said
manufacturing comprises high-throughput manufacturing.
513. A web portal configured to provide: an interface configured to
accept orders for one or more stock assays; an interface configured
to accept orders for one or more custom assays; a gene exploration
platform configured to provide information to assist a user in
selecting one or both of a stock assay and a custom assay.
514. A web site in accordance with claim 513 further configured to
provide links between said gene exploration platform and said
interface to accept orders for stock assays, and between said gene
exploration platform and said interface to accept orders for custom
assays.
515. A web site in accordance with claim 513 wherein said gene
exploration platform is further configured to provide access to a
set of genomic and biomedical data from at least one public or
private source.
516. A web site in accordance with claim 513 wherein said gene
exploration platform is configured to provide a user with at least
one member of the set consisting of: computational tools to view
and analyze gene structure and function; genome structure maps;
proteins classified by at least one of family, function, process,
and cellular location; and combinations thereof.
517. A web site in accordance with claim 513 wherein said gene
exploration platform is further configured to provide a chromosome
map report.
518. A web site in accordance with claim 513 wherein said gene
exploration platform is further configured to provide a scaffold
report.
519. A web site in accordance with claim 513 wherein said gene
exploration platform is further configured to provide a sequence
report.
520. A web site in accordance with claim 513 wherein said gene
exploration platform is further configured to provide a gene
list.
521. A web site in accordance with claim 513 wherein said gene
exploration platform is further configured to provide a chromosome
map display.
522. A web site in accordance with claim 513 wherein said gene
exploration platform is further configured to provide a biomolecule
report.
523. A web site in accordance with claim 522 wherein said
biomolecule report contains at least one view selected from the
group consisting of a protein view, an mRNA view, and a chromosome
view, and combinations thereof.
524. A web site in accordance with claim 513 wherein said gene
exploration platform is configured to provide a human gene mutation
database report.
525. A web site in accordance with claim 513 wherein said gene
exploration platform is configured to provide a genome navigation
facility whereby a user can navigate a genome by at least one of
searching a genome map or searching a genome assembly.
526. A web site in accordance with claim 513 wherein said gene
exploration platform is configured to provide a genome navigation
facility whereby a user can navigate a genome by searching by a
member of the group consisting of gene ID, gene symbol, and RefSeq
ID.
527. A web site in accordance with claim 513 wherein said gene
exploration platform is configured to provide a genome navigation
facility whereby a user can navigate a genome by searching by
cytogenetic band.
528. A web site in accordance with claim 513 wherein said gene
exploration platform is configured to provide a genome navigation
facility whereby a user can navigate a genome by searching by
position on a chromosome.
529. A web site in accordance with claim 513 wherein said gene
exploration platform is configured to provide a genome navigation
facility whereby a user can navigate a genome by searching for STS
markers.
530. A web site in accordance with claim 513 wherein said gene
exploration platform is configured to provide a genome navigation
facility whereby a user can navigate a genome by searching for a
region between two BACs.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional
Application No. 60/352,039, filed on Jan. 25, 2002, U.S.
Provisional Application No. 60/352,356, filed on Jan. 28, 2002,
U.S. Provisional Application No.60/369,127, filed on Apr. 1, 2002,
U.S. Provisional Application No. 60/369,657, filed on Apr. 3, 2002,
U.S. Provisional Application No. 60/370,921, filed on Apr. 9, 2002,
U.S. Provisional Application No. 60/376,171, filed on Apr. 26,
2002, U.S. Provisional Application No. 60/380,057, filed on May 6,
2002, U.S. Provisional Application No. 60/383,627, filed on May 28,
2002, U.S. Provisional Application No. 60/383,954, filed on May 29,
2002, U.S. Provisional Application No. 60/390,708, filed on Jun.
21, 2002, U.S. Provisional Application No. 60/394,115, filed on
Jul. 5, 2002, and U.S. Provisional Application No. 60/399,860,
filed on Jul. 31, 2002, all of which are hereby incorporated in
their entirety by reference.
FIELD
[0002] This application relates to methods for distributing
products and services, and more particularly, to methods for
placing, accepting, and filling orders for products and services,
especially biotechnological products and services.
BACKGROUND
[0003] With the completion of the first draft of the human genome
along with the sequencing of the genomes of other species, an
enormous amount of genomic resource data has become available. This
data has permitted extensive studies of gene expression as well as
studies of single nucleotide polymorphisms and their linkage to
disease conditions. However, these and other studies have been
limited by the need of researchers to spend substantial time,
money, and manual labor in the design of probes and primers for
experimental assays. Once designed, the researcher can synthesize
the probes and primers or order them from an oligonucleotide
synthesis facility or service. Only a limited number of studies can
be done given time constraints required for the individual
researcher to complete each of the tasks leading up to a particular
experiment, and, therefore, an overall provider of design,
manufacturing, and validation services for probes and primers would
be of significant value to the researcher.
SUMMARY
[0004] Accordingly, the present inventors have succeeded in
developing web-based systems for ordering assays, which, in various
embodiments, can comprise probes and primers. Included among
various of these systems are systems for ordering probes and
primers that have undergone design, manufacturing, and validation
procedures. In some of these various systems, the ordered probes
and primers are delivered to the researcher along with information
detailing various parameters associated with production of the
assay delivered.
[0005] Thus, in various configurations of the present invention,
there can be provided a method for supplying to a consumer assays
useful in obtaining structural genomic information, such as the
presence or absence of one or more single nucleotide polymorphisms
(SNPs), and functional genomic information, such as the expression
or amount of expression of one or more genes. As such, the assays
can be configured to detect the presence or expression of genetic
material in a biological sample. The method includes providing a
web-based user interface configured for receiving orders for stock
assays, providing a web-based user interface configured for
receiving requests for design of custom assays and for ordering
said assays, and delivering to the consumer at least one custom or
stock assay in response to an order for the one custom or stock
assay placed by the consumer. In certain other aspects, the present
invention can also be directed; to a system and to methods for
constructing a system for providing to a consumer assays configured
to detect presence or expression of genetic material.
[0006] In various configurations of the invention as described
above, the method can further include providing a web-based gene
exploration platform configured to provide information to assist a
consumer in selecting one or both of a stock assay and a custom
assay.
[0007] The present invention, in various configurations, can also
include a search resource provided to identify genetic material.
The search resource may provide one or more parameters identifying
gene structure or function for selection by the consumer. Assays
that detect the presence or expression of genetic material may
include assays for detecting SNPs or for detecting expressed genes.
In various configurations, the ordering interface can be configured
to receive criteria related to the SNP or to the expressed
transcript for which an assay is ordered
[0008] Stock SNP assays provided by the web-based user interface
can include, in some configurations, a large number of SNP assays,
for example, at least 40,000 SNP assays for detecting the at least
40,000 pairs of SNP alleles, or at least 100,000 SNP assays for
detecting the at least 100,000 pairs of SNP alleles. In some
configurations, SNP assays that can be ordered can b e assays for
SNPs that are known to be located in gene regions. In some
configurations, SNPs that can be detectable may be located at
intervals of about 10 kilobases (kb). Also in some configurations,
the SNPs have a minor allele frequency of about 10% in a population
(which may be, but is not necessarily, a human population).
[0009] Stock gene expression assays provided by the web-based user
interface can include, in some configurations assays for at least
about 10,000 or more expressed genes. In certain configurations,
gene expression assays for multi-exon genes can be made up of
probes and primers designed to lie on exon-exon boundaries to
preclude amplification of genomic DNA.
[0010] For SNP assays and gene expression assays, either or both of
pre-manufacturing quality control and post-manufacturing quality
control can be provided in some configurations of the present
invention. Pre-manufacturing quality control may include one or
more of pre-processing selection, designing primers and probes, and
performing in silico quality control. In the case of SNP assays,
pre-manufacturing controls may include identifying optimal sequence
regions which may not contain any SNPs or repeat sequences. In the
case of gene expression assays, the optimal sequence regions in
some configurations may not contain any SNPs other than a SNP for
which the assay is designed to detect, and also does not contain
any repeat sequences. The designing of primers and probes may
comprise, in some configurations, avoidance of non-optimal regions
as defined above as well as the use of specifications that optimize
PCR reaction conditions for the designed assay. Such specifications
include assay values for T.sub.m, GC content, buffer and salt
conditions, oligonucleotide concentration in assay, low secondary
structure of oligonucleotide, amplicon size and low incidence of
primer-dimer formation. In silico quality control can ensure that
probes and primers match target sequences but do not match other
sequences in the genome or other transcripts.
[0011] Post-manufacturing quality control provided in some
configurations includes one or more of synthesis yield testing,
analytical quality control testing, functional testing, and
validation testing.
[0012] In some configurations, assays can be shipped with a data
sheet which "may be a hard-copy datasheet or an electronic
datasheet, or both. The electronic datasheet may be in the form of
a CD-ROM or other suitable machine readable form. Assays that are
shipped can be identified, in some configurations, by identifiers
which can include a two-dimensional (2-D) barcode, and an assay
identification number. The assay components in certain
configurations include, in a single tube, two primers and a
TaqMan.RTM. probe. In the case of SNP assays, two primers and two
TaqMan.RTM. probes can be included, i.e., one TaqMan.RTM. probe for
each allele. In some configurations, the tubes also contain PCR
reagents for performing assays.
[0013] In certain configurations, the present invention provides an
assay kit. The kit contains at least one assay for detecting
presence or expression of genomic material. The kit also contains
an information source comprising an E-datasheet, an assay
information file, or at least one printed-copy datasheet or
combinations thereof.
[0014] Various configurations of the present invention also provide
a method for building a submission file useful for ordering at
least one of SNP genotyping assays and gene expression assays. The
method includes providing a graphical user interface configured to
accept, from a user, information relating to (a) recipient
identification, (b) assay amount, and (c) at least one target
sequence, electronically validating at least a portion of the
information relating to the target sequence; and saving the
information relating to recipient information, assay amount, and
target sequence to a file, wherein the information relating to
target sequence includes the validated information.
[0015] Various configurations of the present invention also provide
genomic products and services to a consumer. The products and
services provided can be used to detect presence or expression of
genetic material in biological sample. The system comprises a first
source of information regarding at least one of presence or
expression of genetic material in biological samples, a second
source of information regarding products and services for analyzing
genetic material and an interface system communicating with the
first source of information and the second source of information.
The system is able to recommend to the consumer certain processes
and services in response to inquires to said first source of
information by the consumer.
[0016] In various configurations, the present invention can provide
a web-based user interface configured to receive a request for
design of one or more custom assays and an order for said custom
assays; and deliver to the consumer at least one custom assay in a
single tube in response to an order for said at least one custom
assay placed by the consumer, wherein said assay comprises at least
one probe, a forward primer and a reverse primer.
[0017] In various configurations, the present invention can also
provide a web-based user interface configured to receive an order
one or more stock assays; and deliver to the consumer at least one
stock assay in a single tube in response to an order for said at
least one stock assay placed by the consumer wherein said assay
comprises at least one probe, a forward primer and a reverse
primer.
[0018] The present invention also provides a web portal configured
to provide an interface configured to accept orders for one or more
stock assays; an interface configured to accept orders for one or
more custom assays; a gene exploration platform configured to
provide information to assist a user in selecting one or both of a
stock assay and a custom assay.
BRIEF DESCRIPTION OF THE DRAWINGS
[0019] The present invention will become more fully understood from
the detailed description and the accompanying drawings,
wherein:
[0020] FIG. 1 is a block diagram representing one method of
providing assays to a consumer according to one of the various
embodiments of the present invention.
[0021] FIG. 2 is an exemplary window pane for navigating genome
information.
[0022] FIG. 3 is an exemplary window pane for a chromosome map
report.
[0023] FIG. 4 is an exemplary window pane for a scaffold
report.
[0024] FIG. 5 is an exemplary window pane for a sequence
report.
[0025] FIG. 6 is an exemplary window pane for a gene list.
[0026] FIG. 7 is an exemplary window pane for a chromosome map
display.
[0027] FIG. 8 is an exemplary window pane for a biomolecule
report.
[0028] FIG. 9 is an exemplary window pane for an mRNA view of a
biomolecule report.
[0029] FIG. 10 is an exemplary window pane for a chromosome view of
a biomolecule report.
[0030] FIG. 11 is an exemplary window pane for a human gene
mutation database report.
[0031] FIG. 12 is an exemplary window pane for a genome map
search.
[0032] FIG. 13 is an exemplary window pane for a genome assembly
search.
[0033] FIG. 14 is an exemplary window pane for a Panther protein
function-family browser.
[0034] FIG. 15 is an exemplary window pane for an ontology
investigation.
[0035] FIG. 16 is an exemplary window pane for an ontology keyword
results investigation.
[0036] FIG. 17 is an exemplary introductory window pane for
designing or selecting a genomic assay.
[0037] FIG. 18 is a block diagram representing the various
configurations of a computer system of the present invention that
is used for distributing biotechnology products to a consumer.
[0038] FIG. 19 is a flow chart representative of various method
configurations of the present invention that can perform by
computing system configurations such as those represented by FIG.
3, or by other computer system configurations.
[0039] FIG. 20 is an exemplary window pane providing instructions
to the user with respect to ordering custom assays according to one
of the various embodiments of the present invention.
[0040] FIG. 21 is a flow chart illustrating the manner in which the
user submits information for obtaining custom assays according to
one of the various embodiments of present invention.
[0041] FIG. 22 illustrates the contents of the header portion of a
submission file according to one of the various embodiments of the
present invention.
[0042] FIG. 23 is an illustration of a sequence record used for
obtaining custom SNP genotyping assays according to one of the
various embodiments of the present invention, showing sequence
AGTGAACGRGATAGGCKCTCCTGCCC (SEQ ID NO: 1), wherein R is A or G, and
K is G or T, in accordance with WIPO standard ST.25.
[0043] FIG. 24 is an illustration of a sequence record for
obtaining custom gene expression assay according to one of the
various embodiments of the present invention, showing sequence
AGTGAACGAGATAGGCAGCTCCTGCCCCAT- CCAAG (SEQ ID NO: 2).
[0044] FIG. 25 is a representation of a visual checklist for a SNP
submission file according to one of the various embodiments of the
present invention, showing sequences AGTGAACGRGATAGGCAKCTCCTGCCC
(SEQ ID NO: 1), TTACGGCCCTGAKGGGACTGCSATCATTTTCT (SEQ ID NO: 3),
and GAGTGGAGCAACANGCTTTCCGCAATTTAC (SEQ ID NO: 4), wherein R is A
or G, K is G or T, and N is A, C, G, or T in accordance with WIPO
standard ST.25.
[0045] FIG. 26 is an illustration of a visual checklist for a
submission file for gene expression assays according to one of the
various embodiments of the present invention, showing sequences
AGTGAACGAGATAGGCAGCTCCTGCCCCATCCAAG (SEQ ID NO: 2) and
TTACGGCCCTGAGGGGGACGMTCGATCATTTTCT (SEQ ID NO: 5).
[0046] FIG. 27 is a flow chart of the file builder program
according to one of the various embodiments of the present
invention.
[0047] FIG. 28 is an exemplary window pane which allows the user to
build a submission file when the using the file builder program
according to one of the various embodiments of the present
invention.
[0048] FIG. 29 is an exemplary window pane showing tutorial
information being displayed according to one of the various
embodiments of the present invention.
[0049] FIG. 30 is an exemplary window pane showing a demonstration
of the file builder program according to one of the various
embodiments of the present invention.
[0050] FIG. 31 is an exemplary window pane illustrating the
submission guidelines for obtaining custom assays according to one
of the various embodiments of the present invention.
[0051] FIG. 32 is a flow chart illustrating how the file builder
program issued according to one of the various embodiments of the
present invention.
[0052] FIG. 33 is an exemplary window pane which allows the user to
enter header line information for the submission file according to
one of the various embodiments of the present invention.
[0053] FIG. 34 is an exemplary window pane which permits the user
to enter information associated with a sequence record according to
one of the various embodiments of the present invention, showing
sequence ATTGCTGCTAATCGCCCCTATTAGCTTMGCCCGAGAAAGCCGCGATCG
TMGTCGCTAGCCCTMGA2TAGCTA- AGTCGTCGGTATCTAAAGCTCTGG ATCGTA (SEQ ID
NO: 6).
[0054] FIG. 35 is an exemplary window pane illustrating the manner
in which errors are brought to the attention of the user while the
file builder program is being executed according to one of the
various embodiments of the present invention, showing sequence
ATTGCTGCTMTCGCCCCTATTAGCTTAAGCCCGAGAAAGCCGCGATCG
TAAGTCGCTAGCCCTMGA2TAGCT- AAGTCGTCGGTATCTAAAGCTCTGG ATCGTA (SEQ ID
NO: 6).
[0055] FIG. 36 is an exemplary window pane generated after a
sequence is validated by the file builder program according to one
of the various embodiments of the present invention, showing
sequence ATTGCTGCTMTCGCCCCTATTAGCTTAAGCCCGAGAAAGCCGCGATCG
TAAGTCGCTAGCCCTMGATAGCTA- AGTCGTCGGTATCTAAAGCTCTGGA TCGTA (SEQ ID
NO: 7).
[0056] FIG. 37 is a representative window pane illustrating the
manner in which the submission file may be saved according to one
of the various embodiments of the present invention, showing
sequence ATTGCTGCTAATCGCCCCTATTAGCTTAAGCCCGAGAAAGCCGCGATCG
TMGTCGCTAGCCCTAAGATAGCT- AAGTCGTCGGTATCTAAAGCTCTGGA TCGTA (SEQ ID
NO: 7).
[0057] FIG. 38 is an exemplary window pane illustrating the display
of the file builder program after the sequence record has been
saved according to one of the various embodiments of the present
invention, showing sequence
ATTGCTGCTAATCGCCCCTATTAGCTTMGCCCGAGAMGCCGCGATCG
TMGTCGCTAGCCCTMGATAGCTMGTCGTCGGTATCTMAGCTCTGGA TCGTA (SEQ ID NO:
7).
[0058] FIG. 39 is an exemplary window pane illustrating the manner
in which the file builder program uploads information according to
one of the various embodiments of the present invention, showing
sequence ATTGCTGCTAATCGCCCCTATTAGCTTMGCCCGAGAAAGCCGCGATCG
TAAGTCGCTAGCCCTMGATAGCTM- GTCGTCGGTATCTAAAGCTCTGGA TCGTA (SEQ ID
NO: 7) partially obscured by a dialog box of a computer
program.
[0059] FIG. 40 is a block diagram representative of components and
data flow at various configurations of an assay design system.
[0060] FIG. 41 is a diagram representative of various
configurations of assay design program logic suitable for use in
assay designs system configurations represented by FIG. 40.
[0061] FIG. 42 is a diagram representative of various
configurations of reagent design procedures suitable for use in
assay design program logic configurations represented by FIG.
41.
[0062] FIG. 43 is a diagram representative of various
configurations of probe placing procedures suitable for use in
reagent design procedure configurations represented by FIG. 42.
[0063] FIG. 44 illustrates the BLAST results against a human genome
database showing gene NM.sub.--000217 which is a single-exon gene
and the primers (shaded arrows) and probe (shaded box) align
perfectly with the genomic DNA sequence, showing sequences
CCAGGGTGATGAAATAAGGAATGATGGCCACAA- TGTCNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTCCACGATGA AGAAGGGGTC (SEQ ID
NO: 8), and CCAGGGTGATGMATMGGAATGATGGCCACAATGTCTATGMGTTCATG
ATGTTTTTGMGMGTCCGTCTTGCTGGGGCAGGCGAAGAAGCGCACCA
CCAGCTCGAAGGAGAACCAGATGAT- GCACAGCGTTTCCACGATGAAGAA GGGGTC (SEQ ID
NO: 9).
[0064] FIG. 45 illustrates the BLAST results against a human genome
database showing gene NM.sub.--000216 which is a multi-exon gene
and the assay is designed over the exon 6-exon 7 boundary in which
the probe sequence is split between the two exons and over the
intervening intron is about 14 kb in length, showing sequences
TGTTGTTGGTTGCATGTGTCGATGTGAAG- TGMGTTGTGTTTGMTTCCA
CCTTTTCNNNNNNNNNNNNNNNGTTCTT (SEQ ID NO: 10), and
TGTTGTTGGTTGCATGTGTCGATGTGAAGTGMGTTGTGTTTGAATTCCA
CCTTTTCTAGTTTTCACMGCTGT- TCTT (SEQ ID NO: 11).
[0065] FIG. 46 illustrates a BLAST alignment of two primers and the
TaqMan.RTM. probe sequence against the transcript to which the
assay was designed, the primer sequences being indicated by shaded
arrows and the probe sequence indicated by the shaded box, showing
sequences TGATCGGGTCCATGAGCMNGATATGTACCAGATCATGNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNN- NNNNNNNNNNNNACTCACACTGGT CATCTCTGGCT (SEQ
ID NO: 12), and TGATCGGGTCCATGAGCMGGATATGTACCAGATCATGGACGAGATCAA
GGAAGGCATCCAGTACGTGTTCCA- GACCAGGAACCCACTCACACTGGTC ATCTCTGGCT (SEQ
ID NO: 13).
[0066] FIG. 47 illustrates a BLAST hit to a non-self transcript
showing an assay designed across exon 4-5 of NM.sub.--0002000 to
provide a perfect BLAST alignment to the self transcript (not
shown) with, however, a significant alignment to a second, non-self
transcript (NM.sub.--002159) in which each of the primers have a
single mismatch and the probe is a perfect match, showing sequences
GCTGATTCACATGCAAAGAGACATNNNNNNNNNNNNNGAA- AATTCCATG AAAAG (SEQ ID
NO: 14), GCTGATTCACATGAAAAGAGACATCATGGGTATAGMGAAAA- TTCCATGA AAAG
(SEQ ID NO: 15), GATTCA-CATGCMAGAGAC-ATNNNNNNNNNNNNNGAAA-ATT-
C-CAT-GA AAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNATGATTATGGAGGTTTGACTGGC (SEQ ID NO: 16)
and GAGACATCATGGGTATAGMGAAAATTCCATGAAAAGCATCATTCACATC
GAGM-TTTCCATTTTATGGGGAC- TATGGATCMATTATCTATATGACMTT
GATATCCTTAGTMTCATGGGGCATGATTATAGAGGTTTGACTGGC (SEQ ID NO: 17).
[0067] FIG. 48 illustrates the matching of the primers and probe
with NM.sub.--0002000.
[0068] FIG. 49 illustrates the significant matching of the primers
and probe with NM.sub.--0021590.
[0069] FIG. 50 is an exemplary window pane which may be used to
initiate collection of information for gene expression assays
according to one of the various embodiments of the present
invention.
[0070] FIG. 51 is a flow chart illustrating the manner in which the
user collects information for gene expression stock assays
according to one of the various embodiments of the present
invention.
[0071] FIG. 52 is an exemplary window pane illustrating ordering
information associated with obtaining stock assays for gene
expression according to one of the various embodiments of the
present invention.
[0072] FIG. 53 is an exemplary window pane illustrating the manner
in which documents are obtained relating to assays according to one
of the various embodiments of the present invention.
[0073] FIG. 54 is a flow chart illustrating the order in which the
user performs a search for gene expression assays according to one
of the various embodiments of the present invention.
[0074] FIG. 55 is a representative window pane illustrating the
manner in which the user agrees to terms and conditions of use for
searching assay information according to one of the various
embodiments of the present invention.
[0075] FIG. 56 is an exemplary window pane allowing the user to
search for a stock assays for gene expression according to one of
the various embodiments of the present invention.
[0076] FIG. 57 is an exemplary window pane allowing the user to
conduct a basic keyword search for gene expression assays according
to one of the various embodiments of the present invention.
[0077] FIG. 58 is an exemplary window pane allowing the user to
perform an advanced keyword search for gene expression assays
according to one of the various embodiments of the present
invention.
[0078] FIG. 59 is an exemplary window pane allowing the user to
conduct a batch identification search for gene expression assays
according to one of the various embodiments of the present
invention.
[0079] FIG. 60 is a flow chart illustrating the manner in which the
user conducts a classification search according to one of the
various embodiments of the present invention.
[0080] FIGS. 61-66 are exemplary window panes illustrating a
classification search for gene expression products performed
according to one of the various embodiments of the present
invention.
[0081] FIG. 67 is an exemplary window pane illustrating the output
of a search for gene expression assays according to one of the
various embodiments of the present invention.
[0082] FIG. 68 is an exemplary window pane illustrating the
information provided for a specific assay during a search for gene
expression assays according to one of the various embodiments of
the present invention.
[0083] FIG. 69 is an exemplary window pane which provides the user
with an overview of stock assays for SNP genotyping products.
[0084] FIG. 70 illustrates the manner in which the user obtains
information and orders stock assays for SNP genotyping according to
one of the various embodiments of the present invention.
[0085] FIG. 71 is an exemplary window pane used to conduct a basic
keyword search for selecting assays for SNP genotyping according to
one of the various embodiments of the present invention.
[0086] FIG. 72 is an exemplary window pane used to perform an
advance keyword search for searching SNP genotyping assays
according to one of the various embodiments of the present
invention.
[0087] FIG. 73 is an exemplary window pane which allows the user to
conduct a location search for a SNP genotyping assay according to
one of the various embodiments of the present invention.
[0088] FIG. 74 is an exemplary window pane allowing the user to
conduct a batch identification search for SNP genotyping assays
according to one of the various embodiments of the present
invention.
[0089] FIG. 75 is an exemplary window pane illustrating the output
of a search for SNP genotyping assays according to some
configurations of the present invention.
[0090] FIG. 76 is an exemplary window pane illustrating the output
for a specific assay after conducting a SNP genotyping assay search
according to one of the various embodiments of the present
invention.
[0091] FIG. 77 illustrates the manner in which the user may perform
a SNP genotyping search according to one of the various embodiments
of the present invention.
[0092] FIG. 78 illustrates an anion-exchange HPLC profile of a 0.2
.mu.mol 23-mer showing 90% of product is full-length DNA
molecule.
[0093] FIG. 79 illustrates a typical analyzed TaqMan.RTM. plate
showing four genotype clusters for a particular SNP, each data
point representing one sample plotted by intensity measures from
each of two fluorescent dyes such that clusters of points are
classified as being homozygous for either allele, heterozygous, or
no amplification.
[0094] FIG. 80 illustrates a pseudo-SNP resulting in all samples
appearing heterozygous.
[0095] FIG. 81 illustrates undesired genotype clustering attributed
to other unknown SNPs in the probes sequence.
[0096] FIG. 82 illustrates the results from samples all of which
are homozygous genotypes producing two clusters.
[0097] FIG. 83 illustrates the results from samples having a SNP
with no rare allele homozygotes producing three clusters.
[0098] FIG. 84 illustrates four clusters that are not well defined
resulting in the assay being deemed to fail to meet
specifications.
[0099] FIG. 85 illustrates allele frequency of SNPs tested for
validation.
[0100] FIG. 86 illustrates SNP assay manufacture and
validation.
[0101] FIG. 87 illustrates gene expression assay manufacture and
validation.
[0102] FIG. 88 illustrates an exemplary assay kit according to one
of the various embodiments of the present invention.
[0103] FIG. 89 illustrates a portion of the exemplary assay kit of
FIG. 72, specifically, a portion of a rack of single-tube assays,
illustrating human-readable identification numbers and
two-dimensional bar code on the assay tubes and an exemplary
illustration of the position of these identifying indicia on the
assay tubes.
DETAILED DESCRIPTION
[0104] Definitions:
[0105] Allele. One of several alternative forms of a gene or DNA
sequence at a specific chromosomal location (locus). At each
autosomal locus an individual possesses two alleles, one inherited
from the father and one from the mother.
[0106] Allele-specific Oligonucleotide (ASO). A synthetic
oligonucleotide, often about 20 bases long, which hybridizes to a
specific target sequence and whose hybridization can be disrupted
by a single base pair mismatch under carefully controlled
conditions. ASOs can be often labeled and used as allele-specific
hybridization probes. They can also be designed to act as
allele-specific primers in certain PCR applications.
[0107] Allelic association. Any significant association between
specific alleles at two or more neighboring loci.
[0108] Alternative splicing. The natural usage of different sets of
exons, to produce more than one product from a single gene.
[0109] Assay any of a number of nucleic acid assay systems (for
review see Kricka, Ann Clin Biochem. 39:114-129, 2002; Shi, Clin.
Chem. 47:164-172, 2001; Baner et al., Curr. Opin. Biotechnol.
12:11-15, 2001; Wittwer et al., U.S. Pat. No. 6,174,670, 2001). In
various embodiments an assay can comprise nucleobase polymers,
such, as, for example, oligonucleotides, which constitute one or
more probes and/or a forward and reverse primer. The assays can be
configured to detect the presence of a SNP, the expression of a
gene or the expression level of a gene. When using a TaqMan.RTM.
procedure, the assay includes a TaqMan.RTM. probe, a forward primer
and a reverse primer. See also "custom assay" and "stock
assay."
[0110] Alu repeat (or sequence). One of a family of about 750,000
interspersed sequences in the human genome that are thought to have
originated from the 7SL RNA gene.
[0111] Amplicon. A region defined by pairing of forward and reverse
primers around a target site.
[0112] Anticodon. A sequence of three consecutive bases in a tRNA
molecule that specifically binds to a complementary codon sequence
in mRNA.
[0113] Autocalling. The use of an automated system to make a
determination of genotype.
[0114] Bioinformatics. The collection, organization and analysis of
large amounts of biological data, using networks of computers and
databases.
[0115] BLAST. Basic Local Alignment Search Tool--Algorithms for
sequence searching. A fast technique for detecting subsequences
that match given query sequence. BLAST is a heuristic search
algorithm employed by computer programs to ascribe significance to
sequence findings using well-known statistical methods, for
example, a fast search algorithm to search DNA databases based upon
sequence similarities. (See, for example, Altschul et al. J Mol
Biol 215:403-10, 1990, Karlin et al., Proc. Nat'l Acad. Sci. USA
87: 2264-2268, 1990; Karlin et al., Proc. Nat'l Acad. Sci. USA 90:
5873-5877 1993; and Altschul et al., Nat. Genet. 6: 119-129 1994.)
A BLAST analysis, in this context, refers to comparing sequences
using a BLAST program such as blastp, blastn, blastx, tblastn,
tblastx (accessible on the internet at
http://www.ncbi.nim.nih.gov/BLAST/) or MPBLAST (Korf et al.,
Bioinformatics 16: 1052-1053 (2000). "BLASTING," in this context,
refers to comparing a sequence to sequences in a database, and
identifying sequences contained in the database that are similar or
identical to the sequence or its complement.
[0116] BLASTn. Search of a DNA sequence against a DNA sequence
database.
[0117] Calling. The process of determining a genotype.
[0118] cDNA. Complementary DNA--a single stranded DNA sequence that
was generated from and complementary to an mRNA sequence by reverse
transcription. cDNA sequences contain only genes that code for
protein (no non-coding DNA is included).
[0119] cDNA Library. A collection of single stranded DNA sequences
that represent DNA that is translated into protein. cDNA libraries
are generated from mRNA. They designed to represent the portion of
the genome that is present as mRNA in a given cell on its way to
synthesizing the proteins represented in that cell.
[0120] Centimorgan (cM). A unit of measure of recombination
frequency. One centimorgan is equal to a 1% chance that a marker at
one genetic locus will be separated from a marker at a second locus
due to crossing over in a single generation. In human beings, 1
centimorgan is equivalent, on average, to 1 million base pairs.
[0121] Common SNPs. SNPs which have a minor allele frequency equal
to or greater than a minimum percent of occurrence in an overall
population, e.g. a population of humans or, in certain subsets of
the overall population. Such subsets can include ethnically defined
subset population. This can be assessed using samples from mixed
populations or from specific populations such as Caucasian
populations or African American populations as are available from
repositories such as, for example, the Coriell Cell Repositories
(Coriell Institute for Medical Research, Camden, N.J.).
[0122] Conserved sequence. A base sequence in a DNA molecule (or an
amino acid sequence in a protein) that has remained essentially
unchanged throughout evolution.
[0123] Consumer. Encompasses customers and other users of the
products and services provided in configurations of the present
invention. Unless explicitly stated otherwise, it is permitted but
not required that configurations of the present invention
precondition distribution on receipt of a payment or a promise to
pay from the consumer for the distributed products or services. The
terms "consumer," "requester," "user" and "investigator" refer to
entities different from the supplier and distributor. The terms
"consumer," "requester," "user" and "investigator" are often used
interchangeably herein. However, in any given situation, it is
possible that the consumer, the requester, the user and/or the
investigator are different entities or individuals, which
themselves may (or may not) be related by agency. For example, the
consumer, requestor, user and investigator in one instance may be a
single individual engaged in research, such as at a college or
university. As another example, the consumer may be a medical
institution, the investigator may be a physician or researcher
employed by the medical institution, and the requestor may be an
assistant of the investigator. Also herein, the term "user" is
frequently used to refer to an entity (such as a consumer, a
requester, or an investigator) who can be accessing a computer
system.
[0124] Contig display name. The contig display name is the genome
assembly (GA) name as used in some configurations of gene
exploration systems.
[0125] Cryptic splice site. A sequence that resembles an authentic
splice junction site and which can, under certain circumstances,
participate in an RNA splicing reaction.
[0126] Custom assay. An assay that is designed from specifications
that are generally related to the target sequence, but that do not
contain information on the specific sequence of the probe or probes
and primers.
[0127] dbSNP rs#ID. A specific field for searching for a SNP
according to a dbSNP reference cluster ID.
[0128] dbSNP ss#ID. A specific field for searching for a SNP
according to a dbSNP assay ID.
[0129] Deletions can be generated by removal of a sequence of DNA,
the regions on either side being joined together.
[0130] Discriminator. A procedure in which the "A-statistic" is
used to screen out assemblies that are likely to be stacked regions
of repetitive sequence that can be from more than one area of the
genome.
[0131] Distribute. As used herein, the terms "distribute" and
"provide" may be used synonymously, and are intended to encompass
selling, marketing, or otherwise providing a product or
service.
[0132] Distributor. As used herein the terms "distributor,"
"provider" and "supplier" are used to refer to an entity or
entities that distributes and/or supplies products and/or services.
The terms "distributor," "provider," and "supplier" can encompass
sellers, marketers, and other providers of such products and
services. The distributor, supplier, and provider may refer to the
same entity, to two different entities, or to three different
entities. In the description herein, it may be generally assumed
that the manufacturer can be the supplier and distributor of the
assay-related products and services described herein. However, in
some configurations of the present invention, the distribution of
the assay-related products and services described herein may be
performed by an entity other than the manufacturer who supplies
them.
[0133] DNA sequence. The relative order of base pairs, whether in a
fragment of DNA, a gene, a chromosome, or an entire genome. See
base sequence analysis.
[0134] Domain. A discrete portion of a protein with its own
function and structure. The combination of domains in a single
protein determines its overall function. The domain of a chromosome
may refer either to a discrete structural entity defined as a
region within which a supercoiling can be independent of other
domains; or to an extensive region including an expressed gene that
can have a heightened sensitivity to degradation by the enzyme
DNAase I.
[0135] ENTREZ. NCBI's (National Center for Biotechnology
Information) search and retrieval system for their data sets. It
organizes GenBank sequences and links them to the literature
sources in which they originally appeared.
[0136] EST. Expressed Sequence Tag. A sampling of sequence from a
cDNA library. A short sequence of a cDNA clone for which a PCR
assay is available.
[0137] Euchromatin. The fraction of the nuclear genome that
contains transcriptionally active DNA and which, unlike
heterochromatin, adopts a relatively extended conformation.
[0138] Exon(s). The protein-coding sequences of genes. Exons only
comprise about 10% of the human genome. A segment of a gene that is
decoded to give a mRNA product or a mature RNA product. Individual
exons may contain coding DNA and/or noncoding DNA (untranslated
sequences). See introns.
[0139] FASTA (file or format). A DNA sequence format that begins
with a single line of text description that is less than 80
characters in length, followed by the DNA sequence file.
[0140] FASTA Search: A database search tool used to compare a
nucleotide or peptide sequence to a sequence database. The program
is based on the rapid sequence algorithm described by Lipman and
Pearson.
[0141] Fragments. Small sections of DNA.
[0142] Frameshift mutation. A mutation that alters the normal
translational reading frame of a DNA sequence.
[0143] GenBank. The public DNA sequence database maintained by the
National Center for Biotechnology Information (NCBI), part of the
National Library of Medicine.
[0144] Gene Exploration Platform (also referred to as Gene
Exploration System). A web-based user interface configured to
provide searchable information related to one or more genomes
and/or transcriptomes and/or proteomes.
[0145] Gene families. Groups of closely related genes that make
similar products.
[0146] Gene Ontology (GO). A controlled vocabulary for the
description of the molecular function, biological process and
cellular component of gene products which can be applied to all
eukaryotes. The GO terms can be used as search identifiers.
[0147] Gene prediction. The process of using computational methods
that search for known indicators of coding regions in the raw
genomic sequence. These indicators include codon use bias, lack of
stop codons, similarity of the translated protein sequence to known
proteins, upstream regulators, splice sites, start codon. The
outcome can be a set of exons that define a predicted gene.
[0148] Gene region. A linear stretch of genomic DNA which serves as
a functional gene region consisting of cis-acting regulatory
regions, transcribed regions, and intervening sequences as well as
10 kilobase pairs of 5' flanking sequence and 10 kilobase pairs of
3' flanking sequence.
[0149] Genomics. The study of the genetic material of an organism;
the sequencing and characterization of the genome and analysis of
the relationship between gene activity and cell function. The
genetic material includes exons, introns, regulatory sequences,
repeat elements and all other unidentified regions of the
genome.
[0150] GI. GenBank Identifier, a unique number assigned to protein
and nucleotide sequences in the GenBank database.
[0151] GT-AG rule. Rule that describes the presence of these
constant dinucleotides at the first two and last two positions of
introns of nuclear genes.
[0152] Haplotype. A series of alleles found at linked loci on a
single (paternal or maternal) chromosome.
[0153] Heterochromatin. A region of the genome, which remains
highly condensed throughout the cell cycle and shows little or no
evidence of active gene expression.
[0154] Homologies. Similarities in DNA or protein sequences between
individuals of the same species or among different species.
Homologous chromosomes: a pair of chromosomes containing the same
linear gene sequences, each derived from one parent. Homologous
chromosomes (homologs): two copies of the same type of chromosome
found in a diploid cell, one having being inherited from the father
and the other from the mother. Homologous genes (homologs): two or
more genes whose sequences can be significantly related because of
a close evolutionary relationship, either between species
(orthologs) or within a species (paralogs).
[0155] HSPs. High-scoring Segment Pairs; two sequence fragments of
arbitrary but equal length with an alignment that can be locally
maximal and for which the alignment score meets or exceeds a
threshold (cutoff) score. These can be generated by BLAST.
[0156] Informatics. The study of the application of computer and
statistical techniques to the management of information. In genome
projects, informatics includes the development of methods to search
databases quickly, to analyze DNA sequence information, and to
predict protein sequence and structure from DNA sequence data.
[0157] Introns. DNA sequences in genes, which have no
protein-coding function. Other non-coding regions include control
or regulatory sequences and intergenic regions whose functions are
unknown. Noncoding DNA separates neighboring exons eukaryote genes.
During gene expression, introns, like exons, can be transcribed
into RNA, but the transcribed intron sequences can be subsequently
removed by RNA splicing and are not present in mRNA.
[0158] Investigator. See "consumer."
[0159] Linkage map. A map of the relative positions of genetic loci
on a chromosome, determined on the basis of how often the loci are
inherited together. Distance is measured in centimorgans (cM).
[0160] Linker (or adaptor oligonucleotide). A double-stranded
oligonucleotide that can be ligated to a cloned DNA of interest in
order, for example, to facilitate its ability to be cloned.
[0161] Marker. An identifiable physical location on a chromosome
(e.g., restriction enzyme cutting site, gene) whose inheritance can
be monitored. Markers can be expressed regions of DNA (genes) or
some segment of DNA with no known coding function but whose pattern
of inheritance can be determined. See RFLP, restriction fragment
length polymorphism.
[0162] Master cluster. A "super cluster" that can be formed by
joining clusters and singletons that have representative clones
with significant matches (a Product Score of 40 or more) to the
same gene. The master cluster is named after the cluster (or
singleton) with the highest Product Score.
[0163] Mate pairs. A pair of reads that are in opposite
orientations and at a distance from each other approximately equal
to the insert length.
[0164] Messenger RNA (mRNA). RNA that serves as a template for
protein synthesis. See genetic code.
[0165] Missense mutation. A nucleotide substitution that results in
an amino acid change.
[0166] mRNA (Messenger RNA). The nucleic acid intermediate that can
be used to synthesize a protein. The mRNA corresponds to one strand
of the DNA and the sequence of the mRNA can be identical to the
sequence of the DNA, except for the replacement of a T (thymine)
with U (uracil).
[0167] Mutation frequency. Is the frequency at which a particular
mutant can be found in a population.
[0168] NCBI. The National Center for Biotechnology Information,
which can be accessed at the web site
http://www.ncbi.nlm.nih.gov.
[0169] Nonsense mutation. A mutation that occurs within a codon and
changes it to a stop codon.
[0170] Normalized library. A cDNA library from which most of the
highly expressed sequences have been removed in order to represent
a greater proportion of low-abundance messenger RNAs. Normalized
libraries are not an accurate reflection of a tissue's
gene-expression profile.
[0171] Nucleobase. Any nitrogen-containing heterocyclic moiety
capable of forming Watson-Crick hydrogen bonds in pairing with a
complementary nucleobase or nucleobase analog, e.g. a purine, a
7-deazapurine, or a pyrimidine. The present invention in some
configurations uses assays based upon probes that can be
polynucleotides or polymeric forms of other nucleobases such as
nucleic acid analogs. Typical nucleobases can be the naturally
occurring nucleobases adenine, guanine, cytosine, uracil, thymine,
and analogs (Seela, U.S. Pat. No. 5,446,139) of the naturally
occurring nucleobases, e.g. 7-deazaadenine, 7-deazaguanine,
7-deaza-8-azaguanine, 7-deaza-8-azaadenine, inosine, nebularine,
nitropyrrole (Bergstrom, (1995) J. Amer. Chem. Soc. 117:1201-09),
nitroindole, 2-aminopurine, 2-amino-6-chloropurine,
2,6-diaminopurine, hypoxanthine, pseudouridine, pseudocytosine,
pseudoisocytosine, 5-propynylcytosine, isocytosine, isoguanine
(Seela, U.S. Pat. No. 6,147,199), 7-deazaguanine (Seela, U.S. Pat.
No. 5,990,303), 2-azapurine (Seela, WO 01/16149), 2-thiopyrimidine,
6-thioguanine, 4-thiothymine, 4-thiouracil, O.sup.6-methylguanine,
N.sup.6-methyladenine, O.sup.4-methylthymine, 5,6-dihydrothymine,
5,6-dihydrouracil, 4-methylindole, pyrazolo[3,4-D]pyrimidines, "
PPG" (Meyer, U.S. Pat. Nos. 6,143,877 and 6,127,121; Gall, WO
01/38584), and ethenoadenine (Fasman (1989) in Practical Handbook
of Biochemistry and Molecular Biology, pp. 385-394, CRC Press, Boca
Raton, Fla.). Nucleobases that are nucleic acid analogs include
peptide nucleic acids in which the sugar/phosphate backbone of DNA
or RNA has been replaced with acyclic, achiral, and neutral
polyamide linkages. The 2-aminoethylglycine polyamide linkage with
nucleobases attached to the linkage through an amide bond has been
reported (see, for example, Buchardt, WO 92/20702; Nielsen (1991)
Science 254:1497-1500; Egholm (1993) Nature 365:566-68).
[0172] Open Reading Frame (ORF). A stretch of nucleotide sequence
with an initiation codon at one end, a series of triplet codons and
a termination codon at the other end: potentially capable of coding
for an as yet unidentified peptide or protein.
[0173] Ortholog. One of a set of homologous genes in different
species (e.g. SRY in humans and Sry in mice).
[0174] Panther. Celera Genomics's proprietary protein
classification software that allows hierarchical classification of
protein families and subfamilies to further aid in identifying
probable protein function. Panther facilitates target
identification and prioritization by allowing more accurate
predictions of protein function.
[0175] Paralog. One of a set of homologous genes within a single
species.
[0176] Pharmacogenomics. The study of the stratification of the
pharmacological response to a drug by a population based on the
genetic variation of that population.
[0177] Phrap. Developed by Phil Green at the University of
Washington, "Phil's Revised Assembly Program" is a tool for
assembling shot-gun sequenced DNA fragments.
[0178] PHYLIP. Program Package created by J. Felsenstein for
Phylogenicity.
[0179] Physical map. A map of the locations of identifiable
landmarks on DNA (e.g., restriction enzyme cutting sites, genes),
regardless of inheritance. Distance can be measured in base pairs.
The relative positions of regions can be determined by physical
measurements, such as by electron microscopy, restriction analysis,
or sequence determination. For the human genome, the
lowest-resolution physical map is the banding patterns on the 24
different chromosomes; the highest-resolution map would be the
complete nucleotide sequence of the chromosomes.
[0180] Point mutation. A mutation causing a small alteration in the
DNA sequence at a locus, often a single nucleotide change.
[0181] Polygenic character. A character determined by the combined
action of a number of genetic loci. Mathematical polygenic theory
assumes there can be very many loci, each with a small effect.
[0182] Polygenic disorders. Genetic disorders resulting from the
combined action of alleles of more than one gene (e.g., heart
disease, diabetes, and some cancers). Although such disorders can
be inherited, they depend on the simultaneous presence of several
alleles; thus the hereditary patterns can be usually more complex
than those of single-gene disorders.
[0183] Polymorphism. Difference in DNA sequence among individuals.
Genetic variations occurring in more than 1% of a population would
be considered useful polymorphisms for genetic linkage
analysis.
[0184] Precomputes. A series of computational analyses of Celera
Genomics data to public data. The analyses used include gene
prediction (GRAIL, Genscan, FgenesH), BLAST computes using several
public and proprietary datasets (nraa, CHGD, RefSeq) to show
similarity, and polishing of the BLAST results to find consensus
splice sites using SIM4 or Genewise with sequences that can be
highly similar to the genomic sequence.
[0185] Primer. A primer comprises a polymer of nucleobases, such
as, for example, an oligonucleotide, the sequence of which is
complementary to a target sequence, or to the complement of a
target sequence. In certain aspects, the 3' end of an
oligonucleotide primer can be extended by a DNA polymerase. The
primer is short relative to the target nucleic acid. A primer
sequence in some configurations comprises from about ten to about
fifty nucleotides, and in some configurations comprises from about
six, about eight, about ten, about thirteen up to about thirty
nucleotides and any length there between. In most cases, PCR
involves a forward primer and a reverse primer, which hybridize to
opposite strands in a target sequence.
[0186] Probe. A "probe" comprises an oligonucleotide that
hybridizes to a target sequence. In the TaqMan.RTM. assay
procedure, the probe hybridizes to a portion of the target situated
between the binding site of the two primers. A probe can further
comprise a reporter group moiety. In some configurations, the
reporter group moiety can be a fluorophore moiety. The reporter
group can be covalently attached directly to the probe
oligonucleotide, in some configurations to a base located at the
probe's 5' end or at the probe's 3' end. The reporter group may
also be attached to a minor groove binder (MGB), which can be
itself covalently attached to the probe (Afonina et al., Nucleic
Acids Research 25: 2657-2660 (1997); Kutyavin et al., Nucleic Acids
Research 28: 655-661 (2000)). The MGB is, in some configurations,
attached to the 3' end of the probe, either directly to the
oligonucleotide or else to the fluorophore moiety or to the
quencher moiety. A probe comprising a fluorophore moiety may also
further comprise a quencher moiety. The quencher moiety is, in some
configurations, a non-fluorescent quencher (NFQ). In some
configurations, in probes designed for SNP detection, the
fluorophore and the quencher can be attached to the oligonucleotide
on opposites sides of the SNP nucleotide. A probe comprises about
eight nucleotides, about ten nucleotides, about fifteen
nucleotides, about twenty nucleotides, about thirty nucleotides,
about forty nucleotides, or about fifty nucleotides. In some
configurations, a probe comprises from about eight nucleotides to
about fifteen nucleotides. As used herein, the use of the term "a
probe" (singular) is intended to include or refer to two bi-allelic
probes in the case of SNP assays, unless stated otherwise.
[0187] Proteome: The full set of proteins encoded by a genome.
[0188] Provide. See "Distribute."
[0189] Provider. See "Distributor."
[0190] Query. The DNA sequence used to search a database.
[0191] Radiation hybrid. A type of somatic cell hybrid in which
fragments of chromosomes of one cell type can be generated by
exposure to X-rays, and are subsequently allowed to integrate into
the chromosomes of a second cell type.
[0192] Real time. The term "real time" is always spelled out in
full. The abbreviation "RT," as used herein, always refers to
"reverse transcriptase."
[0193] Receptor. A molecule (usually a protein) that spans a cell
membrane and received extracellular signals and transmits them into
the cell.
[0194] Regional overlay. Celera regional overlays can be created
from Celera fragments and mate pair links, and external finished
clones and unordered contigs from unfinished clones, which are
referred to as BACs. The Celera Regional Assembler takes the
external data and uses Celera fragments and mate pairs to order and
orient the contigs within BACs, filling in gaps where possible.
[0195] Regulatory regions or sequences. A DNA base sequence that
controls gene expression.
[0196] Repetitive DNA. A set of nonallelic DNA sequences which show
considerable sequence homology.
[0197] Requestor. See "consumer."
[0198] Reverse transcriptase (RT). The abbreviation "RT" is used
herein exclusively as an abbreviation for "reverse transcriptase."
The term "real time" is always spelled out in full.
[0199] Scaffolds. Sets of contigs that can be ordered and oriented
using enforcing mate pairs.
[0200] Sequence homology. A measure of the similarity in the
sequence of two nucleic acids or two polypeptides.
[0201] Sequence tagged site (STS). Short (200 to 500 base pairs)
DNA sequence that has a single occurrence in the human genome and
whose location and base sequence are known. Detectable by
polymerase chain reaction, STSs can be useful for localizing and
orienting the mapping and sequence data reported from many
different laboratories and serve as landmarks on the developing
physical map of the human genome. Expressed sequence tags (ESTs)
can be STSs derived from cDNAs.
[0202] Significant complementarity. Includes complementarity
sufficient to interfere with the analysis of a target sequence.
Significant complementarity can comprise, in non-limiting example,
at least about 40% or greater sequence identity with the complement
of a target sequence.
[0203] Single Nucleotide Polymorphism (SNP). Replacement, loss, or
addition of one nucleotide (either A, C, G or T) in the DNA
sequence. There are probably several million SNPs throughout the
genome, and these alleles account for much of the variation seen in
the human population. These predominately biallelic polymorphisms
may exist in varying ratios in the population ranging from very
rare alleles (1-5% frequency) to common alleles (20-50%
frequency).
[0204] Splice acceptor site. The junction between the end of an
intron terminating in the dinucleotide AG, and the start of the
next exon.
[0205] Splice donor site. The junction between the end of an exon
and the start of the downstream intron, commencing with the
dinucleotide GT.
[0206] Stock assay. A pre-designed assay that does not require
custom design. In some configurations of the present invention, an
inventory of stock assays may be maintained from which users may
place orders.
[0207] Stringency. A parameter for filtering the results of a query
based on how closely related the sequences in a cluster must
be.
[0208] Subject. A DNA sequence that produces a match in a blast
search.
[0209] Supplier. See "Distributor."
[0210] SWISSPROT. European annotated non-redundant protein sequence
database; most highly annotated protein database.
[0211] TA. Transcript assembly. Celera assembly of public EST.
[0212] Tandem repeat sequences. Multiple copies of the same base
sequence on a chromosome; used as a marker in physical mapping.
[0213] Target. A biological sample comprising a nucleic acid. A
target can comprise as ingle-stranded or double-stranded nucleic
acid, and can comprise an RNA or a DNA. An RNA can be, in
non-limiting example, a messenger RNA (mRNA), a primary transcript,
a viral RNA, or a ribosomal RNA. A DNA can be, in non-limiting
example, a single-stranded DNA, a double-stranded DNA, a cDNA, a
viral DNA, an extrachromosomal DNA, or a mitochondrial DNA. A
skilled artisan will recognize from the context of usage whether a
target nucleic acid is single-stranded or double-stranded.
[0214] TBLASTn. A BLAST search of a protein sequence against a
nucleotide sequence database that has been translated in all six
frames.
[0215] Trace Files. The product of sequencing completed by the ABI
3700 Prism. After going through stringent quality control
processes, trace files can be then used as data input for
assembly.
[0216] Transcriptome. The full complement of activated genes,
mRNAs, or transcripts expressed from a genome.
[0217] TREMBL. Translated EMBL, a compilation of the EMBL DNA data
library.
[0218] UniGene database. A public database, maintained by NCBI,
which brings together sets of GenBank sequences that represent the
transcription products of distinct genes.
[0219] Unique clone. A sequence that has no match in GenBank or
other public databases.
[0220] Unique singleton. A clone that does not cluster and has no
match in the public databases.
[0221] UTR (untranslated region). Noncoding region found at the 5'
or 3' termini of mRNA.
[0222] Untranslated sequences. Noncoding sequences found at the 5'
and 3' termini of mRNA.
[0223] User. See "consumer."
[0224] Overview of Assays:
[0225] SNP Genotyping Assays:
[0226] In some configurations, the present invention includes
methods of providing investigators with assays useful for detecting
the presence of SNP alleles as well as assays useful for detection
or quantification of gene expression. The elucidation and
cataloguing of the sequences of genomes of various species,
particularly the human genome, including the identification in
public and/or private databases of more than 4,000,000 SNPs
distributed throughout the genome, as well as the identification
and cataloguing of a significant fraction of the approximately
30,000 expressed genes, provides the basis for establishing a
collection of validated assays for SNPs or gene expression. Such
assays can provide investigators with analytical tools for
investigating virtually any gene in a mapped genome.
[0227] In some configurations, SNP databases can be used to develop
assays that provide an investigator with the ability to analyze
samples for the presence of identified SNP alleles. Testing samples
from a particular individual allows SNP genotyping of that
individual. SNPs from public and/or private databases can be
selected for assay development. A number of approaches can be used
in constructing SNP databases that can be useful in SNP genotyping
(for review of SNP databases, see McCarthy et al., Nat. Biotechnol
1 8:505-508, 2000; Judson et al., Pharmacogenomics 3:379-391, 2002,
Miller et al., Hum. Mol. Genet. 10:2195-2198, 2001). In certain
aspects, a gene-based approach can be used. In a gene-based
approach, SNPs can be selected that reside on "gene regions." For
example, a gene region comprising a 60 kb sequence including 10 kb
upstream and 10 kb downstream from known functional sequences, can
in certain instances have at least seven identified SNPs associated
with it including at least one identified SNP that maps to a
location approximately 10 kb upstream to its 5'-most cis-acting
regulatory 'sequence, another identified SNP that maps to a
location approximately 10 kb downstream to its 3'-most cis-acting
regulatory or transcribed sequence, and at least 5 more identified
SNPs mapping therebetween. Within the gene region, the SNPs can be
selected such that they can be distributed across the gene region.
As such, the selected SNPs can be located about 5 kb apart, about
10 kb apart, about 15 kb apart, or more, or at any selected
separation distance between 5000 and 15000 bases, or at any
selected separation distance without limitation. The availability
of assays for SNP markers that can be spaced at intervals of
approximately 10 kb for a gene affords an investigator the
opportunity to obtain at least one SNP allele that can be used as a
marker for the gene. SNP markers can serve as markers for genotypes
or haplotypes and can be of value in investigating gene structure,
haplotype structure, inheritance studies, and the like.
[0228] In certain aspects of the present invention, the inventors
have focused on the selection of "common" SNPs. The minimum percent
of occurrence in a population or population subset depends upon the
requirements of a particular test and can be selected to be, in
certain instances, a bout 8%, about 10%, a bout 15%, a bout 20% or
greater or any value therebetween, or any selected frequency
without limitation, depending upon the assay requirements.
Particular minimum percent of occurrence values that can be
considered to be generally applicable can be in certain
embodiments, about 10% and in other embodiments, about 15%. In
certain configurations, known SNPs that have been cataloged in at
least one database can be subjected to a triage procedure to
produce a reduced set of SNPs. In addition, SNPs can be selected
whose minor alleles were observed in at least two distinct donors.
Unless a minor allele is reported in at least two individuals, a
SNP may be eliminated from further consideration for inclusion in
the set of SNPs. Sequences comprising the selected SNPs, as well as
sequences upstream and downstream from the SNPs, can be then
analyzed to determine their suitability for use in SNP assays. SNPs
deemed non-usable for assay development can be eliminated from
further consideration for inclusion in the set. In a subsequent
triage step, semi-empirical design quality control (QC) criteria
can be used to reduce the SNPs included in the set.
[0229] The following properties of a candidate SNP may be
considered in determining whether a candidate SNP is selected for
inclusion in the reduced set of SNPs: 1) the SNP maps within or
close to an annotated gene in a gene library, for example, within
one of about 30,000 Celera-annotated genes or within 10 kb of an
annotated gene; and 2) the SNP is spaced with respect to nearest
neighbor to provide at least three SNPs per gene on intervals
between SNPs of about 10 kb. Remaining gaps greater than about 10
kb in a gene region can be filled with at least two unscreened SNPs
per 10 kb.
[0230] Assays that pass this selection procedure can be then
validated in some configurations, based upon laboratory genotyping
results using a panel of genomic DNA from, for example, about 90
individuals. For example, the DNA panel comprises genomic DNA from
about 90 individuals representing a subset population of Caucasian
individuals and a subset population of individuals of African
American ancestry. Selected SNPs have a minor allele frequency of
at least 10% or greater or at least 15% or greater in at least one
population, or any selected minor allele frequency without
limitation.
[0231] SNP assays can include any SNP assay known in the art.
Methods for SNP detection include, in non-limiting example,
variations of the INVADER.TM. method of Third Wave Technologies,
and the TaqMan.RTM. method. In some configurations, assays can be
developed for use in a TaqMan.RTM. method for identifying a SNP
allele in a target sequence. The TaqMan.RTM. method uses two primer
oligonucleotides and a DNA polymerase for PCR sequence
amplification, as well as one or two probe oligonucleotides. For
SNP detection using a TaqMan method, one primer oligonucleotide
sequence maps to a site upstream from a target SNP sequence and a
second primer oligonucleotide sequence maps to a site downstream
from the target SNP sequence. A probe oligonucleotide sequence maps
to the SNP, and comprises one allele of the target SNP, a reporter
group moiety, which in some embodiments can be a fluorophore
moiety, a fluorescence quencher moiety, which can be in some
embodiments an NFQ moiety, and can also comprise an MGB moiety. In
TaqMan analyses using two probes, the second probe sequence also
maps to the SNP, and comprises an alternative allele of the target
SNP, a second reporter moiety (for example, a second fluorophore
moiety), a fluorescence quencher, and can also comprise an MGB.
When two probes are used, the fluorophores can be selected to be
distinguishable by virtue of their absorption or emission spectra.
In non-limiting example, the fluorophores VIC.TM. and FAM as
provided in kits by Applied Biosystems can be used as reporter
fluorophore moieties in a SNP assay. The probe can further comprise
an MGB. An MGB increases the melting temperature of a probe/target
hybrid without increasing probe length, thereby allowing shorter
probes to be used (Afonina et al., Nucleic Acids Research 25:
2657-2660 1997; Kutyavin et al., Nucleic Acids Research 28: 655-661
2000). In some configurations, the MGB moiety can be covalently
attached to the 3' end of the probe. The structure of the MGB can
be, in non-limiting example, a trimer of
1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate. This
oligopeptide binds double-stranded DNA in the minor groove, with a
high affinity for A-T-rich sequences in double stranded DNA.
Because the presence of an MGB increases the stability of hybrid
nucleic acids, oligonucleotide-MGB conjugates as short as 8-mers,
or G-C-rich 6-mers are able to form stable hybrids with
complementary sequences. These properties allow the use of probes
as short as six nucleotides. MGBs furthermore increase the
specificity of probe-target hybridization.
[0232] In the TaqMan.RTM. assay, each probe can be non-fluorescent
or poorly fluorescent in spite of the presence of a fluorophore
moiety, by virtue of the presence of the NFQ. However, during PCR
amplification of the TaqMan assay, a probe bound to a target SNP
can be digested by the polymerase, because of the enzyme's 5'
exonuclease activity. Because the PCR conditions can be selected
for high stringency hybridization, whereby a single nucleotide
mismatch between probe and target does not permit stable
hybridization, only probes perfectly complementary to the target
are digested by the polymerase. Thus, if two probes representing
alternative alleles of a SNP are used, only one probe will be
subject to digestion by the polymerase. Because digestion of a
probe releases a fluorophore from quenching by the quencher,
measurement of the absorption or emission wavelength of a sample
reveals which probe is digested by the polymerase, and hence, which
SNP allele is present in the sample. Because SNPs can be
heterozygous or homozygous, detection of absorption or emission
spectra of one or both fluorophores in a sample during or following
PCR amplification will reveal if the target sample is heterozygous
or homozygous. Fluorophore released from a quenched primer can be
quantified by any method known in the art. In some configurations,
a fluorimeter can be used. In some configurations, the fluorimeter
comprises a component of an integrated nucleic acid analysis
system, in non-limiting example, an ABI PRISM.RTM. 7900HT Sequence
Detection System.
[0233] In a SNP genotyping assay, two probes comprising identical
sequences except for the SNP allele nucleotide, different
fluorophores, and identical MGBs and NFQs can be used in various
embodiments. For a biallelic SNP assay, any two spectrally
distinguishable fluorophores for which the fluorescent signals can
be quenched by the non-fluorescent quencher are used. In a
non-limiting example, commercially available fluorophores, for
example VIC.TM. and FAM.TM. from Applied Biosystems, can be used as
probe labels in biallelic SNP genotyping.
[0234] In the design of an assay in various embodiments, at least
one potential probe oligonucleotide sequence, as well as potential
primer oligonucleotide sequences, can be analyzed in silico for
suitability in a PCR assay. An in silico analysis of an
oligonucleotide sequence can consider several criteria, such as, in
non-limiting example, the predicted melting temperature of a duplex
comprising the oligonucleotide sequence and its complement, the
absence of significant self-complementarity (e.g., the absence of
"hairpin loops"), the absence of significant complementarity with
any other oligonucleotide expected to be used in the assay (e.g.,
"primer-primer dimerization"), and the absence of significant
complementary with a genomic sequence outside of the target site.
In certain embodiments, a candidate oligonucleotide sequence can be
validated by "blasting" against the genome, and a candidate
sequence is selected for further development for use in an assay
only if its sequence appears no more than once in the genome.
[0235] Following in silico validation, each oligonucleotide
designed for an assay can be synthesized using organic synthesis
methods known in the art. The synthesis of probe oligonucleotides
also includes the covalent attachment of a reporter group, a
fluorescence quencher, and a minor groove binder.
[0236] Gene Expression Assays:
[0237] In some configurations of the present invention, information
in databases on expressed sequences can be used to develop assays
that provide an investigator with the ability to analyze a sample
for the presence and quantity of expressed RNA. In certain
configurations, a method is provided that permits an investigator
to obtain a validated assay to a known expressed gene. In some
configurations, assays can be designed for measuring gene
expression levels using reverse transcription coupled to the
polymerase chain reaction (Reverse Transcription-Polymeras- e Chain
Reaction, RT-PCR) (Sambrook et al., 2d Edition, Cold Spring Harbor
Laboratory Press, Cold Spring, N.Y. (1989)). In these
configurations, primer-or probe oligonucleotides comprising DNA
sequences corresponding to mRNA sequences (or the complement
thereof for a "reverse" primer sequence) can be designed and
validated. In some configurations, at least one probe or primer
spans an exon-exon boundary within a target mRNA (or cDNA) sequence
to diminish any contribution from genomic nucleic acids.
[0238] Once a target expressed gene has been determined or
designated, gene expression can be detected and quantified by the
investigator using an assay designed using any of a number of
methods. Thus, in some configurations, assays can be developed for
use in an RT-PCR analysis using the TaqMan.RTM. method for
quantifying a PCR-amplified cDNA of an target expressed mRNA. A
TaqMan.RTM. gene expression assay utilizes a pair of
oligonucleotide primers for PCR, as well as a probe
oligonucleotide. The primer oligonucleotides hybridize to different
sites within a double-stranded cDNA of an mRNA, in opposite
orientations. The probe oligonucleotide comprises a sequence that
hybridizes to a site between the primer hybridization sites. The
hybridization stringency conditions can be selected such that at
least one of the probe and primer oligonucleotides hybridizes
uniquely to the genome. In some configurations, at least one of the
probe and primer oligonucleotides comprises a sequence that spans
an exon-exon boundary, in order to minimize spurious signal
generated by contaminating genomic DNA acting as template. In some
configurations, the probe comprises a sequence that spans an
exon-exon boundary. The probe oligonucleotide further comprises a
reporter moiety, in some configurations a fluorophore, as well as a
fluorescence quencher, in some configurations an NFQ. Any
fluorophore which can be subject to quenching by a quencher may be
used as the reporter moiety. In non-limiting example, the
fluorophore VIC.TM., as provided in kits by Applied Biosystems, can
be used as a reporter fluorophore moiety in an RT-PCR gene
expression assay. The probe can further comprise an MGB. In some
configurations, the MGB moiety can be covalently attached to the 3'
end of the probe. The structure of the MGB can be, in non-limiting
example, a trimer of 1,2-dihydro-(3H)-pyrrolo[3,2-
-e]indole-7-carboxylate. Because the presence of an MGB increases
the stability of hybrid nucleic acids, oligonucleotide-MGB
conjugates as short as 8-mers, or G-C-rich 6-mers, are able to form
stable hybrids with complementary sequences, and therefore allow
the use of probes as short as six nucleotides. MGBs furthermore
increase the specificity of probe-target hybridization.
[0239] Either a one-step or two-step process configuration can be
used to analyze a sample for the presence or quantity of an RNA. In
some configurations, a one-step process configuration can be used
to detect and quantify an mRNA. In one-step process configurations,
a thermostable polymerase that exhibits reverse transcription, DNA
synthesis utilizing a DNA template, and 5'-to-3' exonuclease
activity, in non-limiting example recombinant Thermus thermophilus
DNA polymerase (rTth polymerase), can be used in a TaqMan.RTM.
analysis. Because rTth polymerase exhibits all enzyme activities
involving nucleic acids needed for an RT-PCR expression analysis,
an assay can be provided to an investigator comprising all of the
components for an RT-PCR analysis except for the target sample.
Thus, following an investigator's request, a pre-validated assay
can be sent to the investigator as a mixture in a single tube. The
investigator need only add a target sample to the mixture, then
subject the mixture to a standard thermal cycling protocol. In
certain alternative configurations, the oligonucleotides of an
assay can be supplied in a single tube, and the buffers, salts, and
thermostable polymerase can be supplied separately. As a result of
thermal cycling, fluorophore can be released if probes and primers
are hybridized to a cDNA target. Measurement of released
fluorophore provides a quantifiable signal, wherein fluorescence
intensity can be monotonically related to RNA concentration in the
target sample. Fluorophore released from a quenched primer can be
quantified by any method known in the art. In some configurations,
a fluorimeter can be used. In some configurations, the fluorimeter
comprises a component of an integrated nucleic acid analysis
system, in non-limiting example, an ABI PRISM.RTM. 7900HT Sequence
Detection System.
[0240] In yet other, "two-step" RT-PCR analysis configurations,
reverse transcription and PCR amplification can be conducted
separately. Reverse transcription can be catalyzed using a reverse
transcriptase, such as, in non-limiting example, a reverse
transcriptase from Avian Myeloblastosis Virus or Moloney Murine
Leukemia Virus. Second-strand synthesis, and amplification of cDNA
can be subsequently effected in a second step using a DNA
polymerase, such as, in non-limiting example, a heat-stable
polymerase such as Taq polymerase. The Taq polymerase can be, in
some configurations, a Taq polymerase that can be supplied
complexed with a heat-denaturable blocking agent, for example, an
antibody directed against the Taq polymerase, in order to prevent
elongation of an oligonucleotide prior to an initial heat
denaturation step at the start of a thermal cycling protocol.
[0241] In both SNP and gene expression assays, the assays can be
run under uniform conditions to allow high-throughput analyses of
samples. High-throughput capability lends itself to automation and
robotics, wherein hundreds or thousands of individual gene
expression analyses can be conducted within a single day. For
example, 384 samples can be analyzed simultaneously by setting up
384 separate RT-PCR assays on a single 384-well tray, and
conducting the reactions in a single thermal cycler apparatus.
Robotics can be used to facilitate the rapid and accurate handling
of the samples.
[0242] In various configurations, the invention includes provision
of an assay for analysis of a SNP or an expressed gene using PCR or
a variant or modification thereof. Variations of PCR include, for
example, the TaqMan.RTM. assay, in which a pair of primer
oligonucleotides and at least one probe oligonucleotide can be
hybridized to a target nucleic acid. The DNA polymerase, in
particular a heat stable DNA polymerase such as a taq polymerase,
catalyzes the hydrolysis of the probe as a result of the
polymerase's 5' to 3' exonuclease activity. If the probe comprises
both a fluorophore moiety as a reporter group and a quencher
moiety, such as a non-fluorescent quencher, hydrolysis of the probe
results in separation of the fluorophore and the quencher, leading
to an increase in the fluorescent signal obtainable from the
reporter group.
[0243] Various configurations of the present invention make
available to an investigator a system for obtaining validated
assays and protocols for studying SNPs and their connection with
disease or conditions as well as for studying the expression of
genes. The assays can be made available in large number and in a
standard format for performing tests involving SNPs or gene
expression. The present invention also provides a system for rapid
development of new assays, which can be based upon a specified
target sequence or gene region provided by the investigator.
[0244] In some configurations of the present invention, stock gene
expression products can be off-the-shelf quantitative gene
expression assays that have been built on the 5' nuclease chemistry
and that have been designed utilizing a bioinformatics pipeline
that performs BLAST and other sequence analysis using, for example,
either public or private data. An example of a database suitable
for use with some configurations of the present invention can be
the Celera Discovery System (CDS.TM.), which is an example of a
gene exploration system 19 (see FIG. 1). In some configurations,
assays can be formulated into a 20.times. mix, quality control
tested and functionally tested. Requestors can be provided with
exon junction information and information relating the assay target
sequence to the transcription sequence, and may, in some
configurations, be provided with or have the option of being
provided with the probe and primer sequence information as well as
the full transcription sequence information.
[0245] In contrast, in configurations supplying custom assays,
requesters can perform upfront BLAST or sequence analysis
themselves, if desired, and then provide a target sequence and
desired location or locations of a TaqMan.RTM. MGB probe to the
supplier. Configurations of the present invention then utilize a
suitable program such as, for example, Primer Express or a modified
version thereof (which may, for example, execute in batch mode) to
design the TaqMan.RTM. MGB probe and primer set. The primers and
probes can be quality control-tested by the supplier and then
formulated into a single-tube mix having, for example,
concentrations of 20.times., 60.times., or other concentrations. In
some configurations, requestors may select a concentration by
ordering specific part numbers. The supplier supplies requesters
with primer and TaqMan.RTM. MGB probe sequences.
[0246] Some configurations of the present invention provide both
"custom" and "stock" options, and provide one or more predesigned,
preformulated, quality control-tested assay in a single tube.
[0247] Web Based Portal System
[0248] According to various aspects of the system disclosed herein,
the user may be able to use a web based portal to order products
associated with conducting assays. The web based portal may be used
to order custom assays and/or stock assays. In this regard, the
user may initially navigate to the portal as shown in block 10 of
FIG. 1. The portal may be similar to that shown in FIG. 17,
although it will be understood that any other suitable portal may
be used. Once the user arrives at the portal, the user determines
the type of assay that is desired as represented by block 12. For
example, a user may desire to order a custom assay, a stock assay
that can be used for gene expression experiments, or a stock assay
that can be used for SNP genotyping experiments. It will be
understood, however, that this set of assays is only exemplary in
nature and may also include other assays and/or related
products.
[0249] Depending upon the type of assay which the user desires, the
processing may differ. For example, if the user desires to obtain a
custom assay, the system proceeds to obtain from the user
information which may be useful to deliver the custom assay to the
user as indicated by block 14. Similarly, if the user desires to
obtain an assay for gene expression experimentation, the system
proceeds to obtain the information which may be useful to generate
such an assay as represented by block 16. In addition, if the user
desires to obtain an assay for SNP genotyping, the system proceeds
to collect information useful to providing such an assay as
represented by block 18. Further, the user may desire to use the
gene exploration system as indicated by block 19. The gene
exploration system will be described below.
[0250] Gene Exploration System:
[0251] Some configurations of the present invention provide a gene
exploration system or platform 19, that allows the user to perform
in silico research which can assist the user in the process of
assay selection. Gene exploration system 19 can be accessed
directly from the portal 10 or from selection screens from custom
assay and/or stock assay blocks 14, 16, and 18. For example, if a
user has entered a custom or stock assay screen and wants to obtain
further genomic information about a given assay, or if a user
decides to perform further research prior to ordering a gene, an
appropriate entry link to the gene expression system can be
accessed.
[0252] Gene exploration platform 19 can provide access to a set of
genomic and biomedical data from public and/or private sources.
Some configurations provide integrated access to such data from
Celera, GenBank, and other public and private data sources.
Computational tools can also be provided to facilitate the viewing
and analyzing of gene structure and function, genome structure and
physical maps, and/or proteins classified by family, function,
process, and/or cellular location. An intuitive user interface can
be provided that organizes information for easy navigation and
analysis.
[0253] In certain configurations the gene exploration system, block
19, can provide the user with a link to a genome navigation page
such as that illustrated in FIG. 2. Several options can be provided
for genome navigation, including, for example, human, mouse, human
and mouse comparative genomics, protein classification, and
pharmacogenomics. For example, in some configurations, the genome
navigation option can be configured to provide users with the
capability to browse and search genome maps, genome assembly, and
genes data.
[0254] Protein classification option allows the user to browse
and/or search one or more protein information databases. Database
capabilities may include, for example, browsing and text searching
Celera PANTHER.TM. families and gene ontology classification
data.
[0255] The pharmacogenomics option available in some configurations
can provide the user with the ability to search against one or more
SNP databases, for example, the Celera Human SNP Reference Data
database.
[0256] A navigation bar can be provided in some configurations of
the present invention. The navigation bar provides access to one or
more features, such as a biomolecule library; a text search
(allowing the user to launch sequence analysis applications); a
sequence analysis (allowing the user to launch sequence analysis
applications); a workspace (allowing a user to start a new session
and delete, rename, import, and/or export sessions, and/or select
queries to delete and/or link with other queries, and perform
complex queries); a queue display (permitting the user to display
the status of his or her sequence analysis jobs and to retrieve the
results); an options display (providing, for example, a display of
user account information and/or display options); online help; and
logoff. Some configurations can limit the number of sessions
allowed to a user.
[0257] Some configurations of the present invention can provide a
research facility based upon genome assembly and annotation data
from one or more public and/or private databases. One or more of
these databases may be Celera databases, from which chromosome map
reports, scaffold reports, sequence reports, gene lists, chromosome
map displays and/or biomolecule reports are available.
[0258] A representative example of a chromosome map report as
provided in some configurations of the present invention is shown
in FIG. 3. This report lists the scaffolds on a chromosome.
Chromosome reports can be sorted by chromosome location in
ascending order in some configurations. For each scaffold, one or
more information items may be available, which may include a link
to a corresponding scaffold report; the scaffold's coordinates
and/or orientation on a reference chromosome axis; and/or the
scaffold's length. From a chromosome map report, some
configurations of the present invention provide access to the
chromosome map display.
[0259] In some configurations of the present invention, to retrieve
a chromosome map display, a user first searches a genome assembly
(for example, the Celera genome assembly) to retrieve all scaffolds
on a single chromosome. The user then clicks on a link to a
chromosome map report from a scaffold report. A representative
example of a scaffold report as provided in some configurations of
the present invention is shown in FIG. 4.
[0260] In some configurations of the present invention, sequence
reports can be provided. A representative example of a sequence
report as provided by some configurations of the present invention
is shown in FIG. 5. Sequence reports provided by some
configurations of the present invention display the location of a
genomic assembly segment on a reference chromosome axis and a
nucleotide consensus sequence (ungapped) in FASTA format.
[0261] Various configurations of the present invention make gene
lists available to users. A representative example of a gene list
as provided in some configurations of the present invention is
shown in FIG. 6. This gene list displays related information about
genome annotation data in (for example) a tabular format.
[0262] Gene list information in some configurations can include,
for example, one or more of the following items: gene ID,
transcript ID, protein ID, gene name (if assigned), gene symbol (if
assigned), gene alias (if assigned), reference sequence ID (if
present).
[0263] Some configurations of the present invention provide a
chromosome map display, as shown in FIG. 7. The chromosome map
display can provide a graphical overview of a reference genome. In
addition, it may provide access to one or more of the following: a
corresponding scaffold report, a corresponding biomolecule report,
and/or a corresponding gene list.
[0264] In some configurations a biomolecule report as provided as
illustrated in FIG. 8. This report can contain one or more of three
views: a protein view, an mRNA view, and a chromosome view. The
protein view (such as the one illustrated in FIG. 8) can display
one or more of the following information items for a selected
protein ID (for example, a selected Celera Protein ID): a
corresponding gene symbol, gene alias (if assigned), and/or gene
ID; a corresponding transcript ID (e.g., Celera transcript ID);
begin and/or end coordinates on the reference genome, and/or icons
that indicate orientation: forward strand, reverse strand, or
uncertain; a link to a human gene mutation database report, if
available; the gene ontology classification; a Panther protein
family classification; and/or protein domain hit identities.
[0265] The mRNA view (a representative example of which is shown in
FIG. 9) can display one or more of the following information items
for a selected transcript ID (for example, a selected Celera
Transcript ID): corresponding gene symbol, gene alias (if
assigned), and/or gene ID (e.g., Celera gene ID), begin and end
coordinates on the reference genome, which can include icons to
indicate the orientation; a link to a human gene mutation database
report, if available; a corresponding protein ID (e.g., Celera
Protein ID), the number of nucleotides and exons in the transcript;
a Panther protein family classification; a link to best hits
against one or more sequence databases (e.g., Celera and public
databases); evidence; and/or a link to transcribed sequence for all
exons.
[0266] The chromosome view (of which a representative example is
shown in FIG. 10) can display one or more of the following
information for a selected gene ID (for example, a selected Celera
gene ID): corresponding gene symbol and/or gene alias (if
available); begin and end coordinates on the reference genome,
which can include icons to illustrate the orientation; link to
human genome mutation database report, if available; corresponding
transcript ID (e.g., Celera transcript ID); corresponding protein
ID (e.g., Celera protein ID); and/or link to the gene sequence
(e.g., the Celera gene sequence).
[0267] In some configurations of the present invention, a human
gene mutation database (HGMD) report can be provided, as shown in
FIG. 11. An HGMD report may include one or more of the following:
corresponding gene name; link to corresponding OMIM record; links
to SNP results (e.g., links to Celera SNP results), which may be
made accessible only to subscribers; begin and end coordinates on
the reference genome, which may include icons to indicate the
orientation; HGMD classified mutation types; and/or mutations by
HGMD phenotypes.
[0268] Some configurations of gene exploration platform 19 allow
navigation of a genome by searching a genome map and/or by
searching a genome assembly. For example, to search by chromosome
number, some configurations allow a user to click on a "genome map"
link (shown in FIG. 2), and respond by serving a "Search Genome
Maps" web page, a representative example of which is shown in FIG.
11. In some configurations, a user can then select a chromosome
from the "whole chromosome viewer" pull-down list. After selecting
a chromosome from the pull-down list, the user can click "gene
list" to view the list of genes for the selected chromosome, or
click "map" to view the chromosome display.
[0269] In some configurations, the user can search by gene ID, gene
symbol, and/or RefSeq ID. To do so from the web page shown in FIG.
11, for example, the user can select one of a number of ID types
from a pull down list. The user can then type an ID for which to
search in a text box, for example, "hCG14571" and select a flanking
region from a pull-down list. A default value, for example, 0 Mb,
may be provided. The user may then click on "gene list" to view the
gene list results, or may click on "map" to view the chromosome
display for the specified ID.
[0270] Some configurations permit a user to perform a search by
cytogenetic band. In some of these configurations, the user can be
presented with a "Search Genome Maps" page such as that shown in
FIG. 12. The user can then type a begin value in the first "band"
text box and an end value in the "to band" text box. A flanking
region can be selected from the pull-down list, if desired. Next,
the user can click on "gene list" to view the list of genes that
exist between the two cytogenetic bands, or click on "map" to view
the chromosome display for the specified region. Some
configurations permit a user to perform a search for a single
cytogenetic band. For example, in the "Search Genome Maps" page
represented in FIG. 12, a user can type a value in the second
"band" text box, select a flanking region from the pull-down list,
and click "gene list" to view the gene list results, or click "map"
to view the chromosome display for the specified band.
[0271] Some configurations permit a user to search by position on a
chromosome. For example, in the "Search Genome Maps" page shown in
FIG. 12, the user can select a chromosome from a pull-down list,
type a begin value (e.g., in Mb) in the first "position" text box,
type an end value in the "to position" text box, select a flanking
region from the pull-down list (if desired), and click "gene list"
to view the list of genes that exist between the two positions, or
"map" to view the chromosome display for the selected region. In
some configurations, a user can specify a single position by
selecting a chromosome from the pull-down list, typing the desired
position in the second "position" text box, selecting a flanking
region from the pull-down list, and clicking on "gene list" or
"map."
[0272] Some configurations allow a user to search for STS markers
from, e.g., a radiation hybrid database (RHdb) or a database of
sequence tagged sites (dbSTS). To search for a region bounded by
two markers in some configurations, a user clicks on "genome maps"
(see FIG. 2), and, in the "Search Genome Maps" page that appears
(see FIG. 12), the user types an STS marker ID in the first
"marker" text box. Searches for RHdb IDs and dbSTS IDs can be
distinguished, in some configurations, by the user typing "RHn,"
where n can be the ID number, to search for an RHdb ID, or by the
user typing "dbSTSn" to search for a dbSTS ID. The user then types
an STS marker ID in the "to marker" text box, selects a flanking
region from the pull down list, if desired, and clicks on "gene
list" to view the list of genes that exist between the two STS
markers, or on "map" to view the chromosome display for the
selected region. In some configurations, to search for a single
marker, the user follows a similar procedure, except that the user
types the STS marker ID in the second "marker" text box and can be
required to select a flanking region.
[0273] Some configurations of the present invention allow a user to
search for a region between two BACs. For example, in the "Search
Genome Maps" page shown in FIG. 12, the user may type a BAC ID in
the first "BAC ID" text box, and a BAC ID in the "to BAC ID" text
box. The user can then select a flanking region from the pull-down
list, if desired. A default flanking region (e.g., 0 Mb) may be
provided. The user then clicks on "gene list" to view the list of
genes that exist between the two BACs, or on "map" to view the
chromosome display for the specified region. In some
configurations, the user may search for a single BAC by a similar
procedure, except that the BAC ID can be typed in the second "BAC
ID" text box.
[0274] Some configurations of the present invention provide a
capability that allows a user to search a genome assembly by
chromosome number or by genome assembly number to retrieve one or
more of the following: a chromosome map report that can displays
all scaffolds on a single chromosome; a scaffold report that can
display all genomic assembly segments associated with a single
scaffold; and/or a sequence report that can display a single
genomic assembly sequence segment.
[0275] For example, in some configurations, to retrieve a list of
all scaffolds on a single chromosome, the user can search by
chromosome number to generate a chromosome map report by clicking
on "genome assembly" on a page such as that illustrated in FIG. 2.
A "search genome assembly" web page such as that shown in FIG. 13
can be then served from the server to the user's web browser. The
user then selects a chromosome from the pull-down list. Optionally,
the user may select a size from the "scaffold lengths" pull-down
list to filter results, and/or the user may specify a target on the
chromosome by typing values in the "position" and "to position"
text boxes. After clicking "search," a chromosome map report
appears.
[0276] Some configurations allow the user to search by genome
assembly number to generate a scaffold report. For example, in the
"search genome assembly" web page of FIG. 13, a genome assembly
number can be typed into the "scaffold report" text box, and the
user clicks on "search." A scaffold report then appears.
[0277] Some configurations allow the user to search by genome
assembly number segment to generate a sequence report. For example,
in the "search genome assembly" of FIG. 13, the user can type a
genome assembly number segment in the sequence report text box and
click "search." A sequence report then appears.
[0278] Some configurations of the present invention provide the
user with the capability of finding genes by Panther families
protein classification. Thus, some configurations provide a Panther
protein function-family browser, which allows a user to perform one
or more of the following: browse functional categories and protein
families/subfamilies; text search functional categories or protein
families/subfamilies; create a gene list; view the Panther tree for
a given family; view the Panther multiple sequence alignment (MSA)
for a given family; and/or view the Panther "Partial" MSA for a
given family.
[0279] In some configurations, a Panther protein function-family
browser can be made available when the user clicks on "Panther
families" on the web page illustrated in FIG. 2. A representative
example of a Panther protein function-family browser screen is
shown in FIG. 14. This browser screen contains a "categories panel"
and a "families panel." The families panel can also show
subfamilies, as is illustrated in FIG. 14.
[0280] In various configurations, the browser may also provide
facilities for accepting text searches (for example, the user might
search for the text "kinase"), so that folders can be opened and
categories containing the search term can be made visible (and can
be highlighted, in some configurations). Some configurations also
provide a sub-family search.
[0281] Some configurations of the present invention provide a
Panther gene list. For example, a user can browse or text search to
select desired protein families/subfamilies in the families panel,
and go to a gene list listing all proteins assigned to the selected
families/subfamilies. Various sorting and modification options can
be provided, and export facilities can be provided (e.g., exporting
the list to the user's local disk in a format suitable for other
uses).
[0282] A Panther tree viewer can be provided in some configurations
of the present invention. Panther distance trees allow users to
explore the relationships between sequences in a particular family,
and may also show some of the information used to annotate the
families and subfamilies. In various exemplary configurations, the
tree viewer has two panels that can be mapped to each other. One
panel graphically displays the relationship between the different
sequences. An attribute table contains one row for each sequence in
the tree, and each column displays a different attribute of the
sequence, such as the GenBank accession number for the sequence;
the brief definition line parsed out of, for example, a SwissProt
or GenBank record; the organism from which the sequence was
derived; and/or links to open relevant abstracts from PubMed. In
some configurations, the page also links to MSA views, and/or
highlights selected subfamilies.
[0283] Some configurations also provide the user with a Panther MSA
viewer. This viewer can be useful because Panther MSAs are used in
producing Panther distance trees, and therefore, the
family/subfamily classification. In some configurations, there can
be two viewer modes: full MSA, which can include all publicly
available sequences in the family that are related closely enough
to produce an informative multiple alignment; and partial MSA,
which shows the alignment only for the currently selected
subfamilies. In some configurations, the MSA view can be divided
into subfamilies in the same ordering as in the tree, so that the
most closely related sequences appear closest to one another in the
alignment. Also, some configurations of MSA viewers have two
panels: an information panel, and an MSA panel. The information
panel can contain information about each subfamily and sequence.
This information may include hyperlinks to more detailed
information. The MSA panel can display the multi-sequence
alignment, which can be generated by aligning the sequences to the
family hidden Markov model (HMM).
[0284] A Panther HMM alignment view can be provided. This view
shows the query sequence aligned to the consensus sequence for the
HMM. Also, a Panther family/subfamily hits view can be provided
that shows all the Panther family/subfamily HMMs that hit a query
sequence with a score better than a certain threshold.
[0285] In some configurations, certain genes (e.g., Celera genes)
can be found by gene ontology protein classification. These
configurations may provide either or both of a text search or a
"drill down" search, for example.
[0286] To perform a text search in some configurations, a user
clicks on "gene ontology" on the page illustrated in FIG. 2. An
"ontology" page then appears. A representative example of an
ontology page used in some configurations of the present invention
is shown in FIG. 15. The user then types a search string into the
ontology keyword text box and clicks on "find." An "ontology
keyword results" page can be then generated and served to the
user's browser. A representative example of an "ontology keyword
results" page as can be produced in some configurations of the
present invention is shown in FIG. 16. The user may then click on a
link to drill down to the gene ontology (GO) classification list
for that result. The user may continue to drill down until he or
she accesses the desired category that also has a corresponding
gene list link.
[0287] In some configurations, a user may drill down gene ontology
classifications. For example, in some configurations, from the
"ontology" page of FIG. 15, the user may select a species and a GO
classification. The user can then drill down until he or she
accesses the desired category that also has a link to a gene
list.
[0288] In some configurations, GenBank human nucleotide sequences
can be mapped to the human genome assembly (e.g., the Celera human
genome assembly) using a combination of BLASTN and a modified
version of the SIM4 algorithm. Also, some configurations map public
sequences using repetitive hits (e.g., a sequence that maps to
greater than 10 locations on the genome), orphans (e.g., a sequence
fails to map to a genome), and best hit (e.g., if a sequence maps
to between 2 to 10 locations, an attempt can be made to identify
the best mapping.
[0289] Some configurations of the present invention provide
browsing capabilities that permit a user to map public IDs (e.g.,
GenBank accession) to a human genome project (e.g., the Celera
human genome) by searching a mapping database. In some
configurations, for example, an ID mapper provides searching
capabilities for one or more mapping databases, which may include
GenBank DNA, GenBank mRNA, dbEST, and/or RefSeq.
[0290] In some configurations, text searches of data may also be
performed by a user. For example, both Celera and non-Celera data
may be searched by text.
[0291] Various configurations of the present invention can also
include facilities for performing sequence analysis. For example,
one or more of the following protein analysis types may be provided
and made accessible to the user's browser window: BLASTP; TBLASTN;
TFASTA; FASTA; PSI-BLAST; and/or HMMPFAM. Also, one or more of the
following nucleotide analysis types may be provided and made
accessible to the user's browser window: BLASTN; BLASTX; and/or
TBLASTX.
[0292] Some configurations of the present invention provide
workspaces that allow a user to start a new session, delete an
entire session and its results, delete selected query results,
rename a session, import session results, export session results,
copy query results from one session to a different session, and/or
perform additional queries from existing queries. For example,
results can be exported to the user's local hard disk memory and
re-imported for use later.
[0293] Computational System
[0294] In various configurations of the present invention and
referring to FIG. 18, a computing system 20 comprising a plurality
of computers 22, 26 may be utilized to distribute information,
products and services such as the custom assays and/or stock assays
described above, to a user or consumer 28. A first computer 22
(i.e., a distributor computer) on a computer network 24 (e.g., a
public network, such as the Internet) interacts with a consumer 28
using a second computer 26 (i.e., a consumer computer) to obtain
information that can be associated with a human or nonhuman target
DNA (or RNA) sequence, which may include SNP and/or exon locations,
i.e., the sequence itself, the SNP and/or exon locations
themselves, or other information from which these items may be
determined such as, for example, a gene name, accession number,
etc. In some configurations, this interaction can be initiated by
consumer 28 typing a uniform resource locator (URL) into a web
browser running on consumer computer 26 and downloading a hypertext
mark-up language (HTML) or other type of web page serving as a web
portal (such as to which the user navigates in block 10 of FIG. 1)
from a server 30 running on distributor computer 22.
[0295] The web page displayed on consumer computer 26 may include
various types of introductory and sales information, provide a
login for authorized user/purchasers, and solicit the DNA (or RNA)
sequence and other information, as is necessary or desirable. In
some configurations, the initial web page can be one of several web
pages provided by server 30 that interact with consumer 28 to
obtain information. For example, in some configurations, the
initial web page accessed by consumer 28 can be a corporate web
site that provides information for consumer 28 as well as a form in
which consumer 28 types identifying information using consumer
computer 26. Distributor computer 22 receives the information
entered by consumer 28 and sent by consumer computer 26 via
computer network 24.
[0296] In some configurations, distributor computer 22 verifies the
identity of consumer 28 and his or her qualifications to access a
sales page and to purchase assays from the distributor. For
example, this verification may be performed by a web application
server 32 (for example, the IBM.RTM. WEBSPHERE.RTM. Application
Server available from International Business Machines Corporation,
Armonk N.Y.) running on distributor computer 22 with reference to a
consumer database 34 of qualified consumers and consumer
identifications. If consumer 28 cannot be verified or is not
qualified to make a purchase, this information may be returned by
web application server 32 and web page server 30 via computer
network 24 to consumer 28, and consumer 28 will not be allowed to
complete a purchase and/or to access additional information.
[0297] Custom Assays:
[0298] Referring to FIGS. 18 and 19, various configurations of the
present invention perform a method 44 for distributing a
biotechnology product to a consumer. More particularly, the method
includes utilizing a computer network 24 to interact at 46 with a
consumer 28 to obtain information associated with (i.e., indicative
of) at least one nucleic acid sequence. The target nucleic acid
sequence obtained from the consumer can be, for example, a target
RNA or DNA sequence, which itself may include an exon or a portion
thereof, and/or a single nucleotide polymorphism (SNP). The
information may further include information associated with a SNP
location and/or an exon location. The provided nucleic acid
sequence can be analyzed at 48 for format errors. If errors are
detected, further interaction at 46 may be performed to correct the
format errors. (In some configurations, prior to interacting at 46
with consumer 28 to obtain information comprising a nucleic acid
sequence, consumer 28 can be required to verify his or her identity
via computer network 24, and/or confirm his qualifications to place
an order.)
[0299] Upon obtaining information from consumer 28, various methods
of the present invention provide, at 50, a forward primer sequence,
a reverse primer sequence, and a probe sequence having specified
characteristics.
[0300] The forward primer sequence and the reverse primer sequence
together define an amplicon sequence. The amplicon lies within the
target nucleic acid sequence. The probe sequence can be
complementary to a portion of the amplicon sequence. Next, in
various configurations, one or more of the forward primer sequence,
the reverse primer sequence, and the probe sequence can be
validated at 52, using, for example, a genome database such as
database 40. Validation may include BLASTing of one or more of the
sequences, as described above. At least one assay can be
manufactured at 54. The manufactured assay comprises a forward
primer in accordance with the forward primer sequence, a reverse
primer in accordance with the reverse primer sequence, and a probe
in accordance with the probe sequence. In some configurations, the
forward primer sequence, the reverse primer sequence, and/or the
probe sequence can be a validated sequence from 52. The assay can
be shipped at 58 to consumer 28. Some configurations of the present
invention ship the assay in a single tube format with a
two-dimensional bar code. In some configurations, the probe in the
manufactured assay comprises a fluorescence quencher. The
fluorescence quencher can be a non-fluorescent dye. In some
configurations, the fluorescence quencher can be configured to
reduce background fluorescence and increase quenching efficiency.
The assay itself can be suitable for use in a sequence detection
system, such as, for example, a real-time PCR system.
[0301] Some configurations test, at 56, the manufactured forward
primer, the manufactured reverse primer, and/or the manufactured
probe before delivery to verify that the assay meets specified
characteristics. Tests at 56 may include, for example, performing
mass spectroscopy on the manufactured assay to determine that an
oligonucleotide sequence is correct, and/or performing a functional
test to determine that an amplification has occurred and at least
one allelic discrimination can be confirmed.
[0302] According to the various embodiments, if the user selects to
obtain a custom assay at block 14 as shown in FIG. 1 (and, in
configurations in which verification and/or qualification can be
required, the user is verified and qualified), a window pane can be
presented to the user which provides introductions to the user as
to the manner of submission of an order for a custom assay. A non
limiting example of one such window pane is shown in FIG. 20. In
this regard, the user may be requested to follow certain procedures
relating to: selecting the target sequence, assess the quality of
the sequence, prepare the submission file, format the sequence for
submission, prepare the order message, and submit~the order by
e-mail, by regular mail or over the internet. Each of these
elements will be more fully discussed below with reference to FIG.
21.
[0303] As shown in FIG. 21, the user may, according to the various
embodiments of the present invention, select the target sequence
(60) for which an assay is to be delivered. There can be various
factors which may be considered in selecting a target sequence.
These factors may include: biological significance of the sequence,
sequence length, sequence quality, uniqueness of sequence, and
repetitive elements. With respect to biological significance, it
will be appreciated that the quality assurance assays performed
during the manufacture of the primer and probe as discussed herein
may be used to determine whether the yielding content of the
primers and probe meets specifications. For this reason, it may be
desirable to initially determine whether the biological performance
of the assay will accomplish the desired result.
[0304] With respect to target sequence length, in certain
embodiments the length of the sequence can range from about 60
bases to about 5000 bases. However, larger and shorter sequences
may also be used. Short sequences (e.g., fewer than 300 bases) may
limit the number of potential assays that can be designed. For this
reason, in some configurations, a sequence length of approximately
600 bases can be submitted, though increasing the sequence length
may increase the number of possible assays. In addition, the
sequence may be selected such that the target site can be directed
towards the center of the submitted sequence.
[0305] In addition, a user can determine the quality of the
sequence (62), e.g., to determine whether the sequence is unique in
public databases when selecting the submission sequence. If there
are similar versions of the sequence in a public database, how
closely they agree can be a factor that can be used to determine
the quality of the sequence. If other versions of the target
sequence are different in public databases, it is possible to mask
the ambiguous bases using N's as described below. Examples of
databases with curated sequences include RefSeq
(http://www.ncbi.nim.nih.gov/LocusLink/refseq.html), which contains
mRNA sequences, and dbSNP (http://www.ncbi.nim.nih.gov/SNP), which
contains SNPs. The NCBI RefSeq project provides reference sequence
standards for the naturally occurring molecules of the central
dogma, from chromosomes to mRNAs to proteins.
[0306] When ambiguous bases are determined to exist, it may be
desirable to annotate the submission sequence to avoid ambiguous
bases in the regions of the sequence used for designing assays.
When an ambiguous base occurs, the ambiguous base may be
substituted with an N. For example, if the lowercase bases in the
sequence
[0307] ACGTGACGTGACGTGACGTGACGTGGATcGTGggggTCCT (SEQ ID NO: 18)
[0308] are ambiguous, the lowercase bases can be substituted as
follows:
[0309] ACGTGACGTGACGTGACGTGACGTGGATNGTGNNNNTCC (SEQ ID NO: 19)
[0310] It may be desirable to minimize the number of substitutions
of ambiguous bases with Ns. This is because the system does not
include Ns in the primer or probe and therefore sequences with Ns
reduces the number of available primer and probes from which to
select the optimal assay. In addition, it may also be desirable not
to have Ns that are too close to the target site. In this regard,
it may be desirable not to have Ns within five bases of the target
site when submitting sequences for gene expression assays, as well
as 2 bases of the target site when submitting sequences for SNP
assays. It will be understood, however, that a larger or smaller
separation between the target site and the location of Ns may be
used.
[0311] In various configurations, the user can, if desired, further
assess the quality of the sequence (62) by determining whether
unique primers and probes can be generated for the specific
sequence. Various methods may be used to determine whether unique
primers and probes may be manufactured. In one non-limiting example
for determining whether a unique primer and probe can be generated
for a DNA sequence a BLAST search tool can be used as follows. Such
a BLAST search tool can be useful for determining the uniqueness of
the target region. Using either the entire target sequence or a
portion thereof, e.g. 50 bp upstream and downstream from a SNP a
BLAST search can be performed (e.g. at the web site
hftp:H/www.ncbi.nlm.nih.gov/BLAST). The BLAST search can detect
regions with sequence similarities and repetitive elements.
[0312] After the sequence has undergone a BLAST search, the
sequence can be run through a program such as Repeat Masker to
detect common repetitive elements. Repeat Masker may be found at
http://repeatmasker.genome.washington.edu. If many regions with
similar sequences are located after running a program such as
Repeat Masker, a filter may be used to limit the number of regions
with similar sequences. For example, it may be useful to limit the
search to human genomic DNA for SNPs or mRNA/cDNA for gene
expression. It will be noted that the BLAT server at the University
of California, Santa Cruz carries out searches using assembled
genomic sequence. The BLAT server at the University of California,
Santa Cruz, is located at http://genome.ucsc.edu/golden
Path/octTracks. html.
[0313] In another non-limiting example a user can assess whether
useful probes and primers can be manufactured for a gene expression
assay by performing a BLAST search of a target region which
encompasses an exon-exon boundary. N's can be substituted for small
regions of repeats, SNPs, and ambiguous sequences. If the target
region is found not to be unique, a different exon-exon boundary
can be selected and a BLAST search performed on a target region
which encompasses the alternate exon-exon boundary.
[0314] After the target sequence has been selected but before the
submission file is prepared, the sequence data again can be
reviewed to determine whether sequence problems may cause failure
in the assay design. As discussed above, these problems may occur
if the sequences are too short, a low confidence in the sequence is
present, the sequence is of poor quality, there are masked bases,
too many Ns limit the design, and there are Ns too close to the
target site for the probe. Each of these issues are discussed
above.
[0315] After the user selects the target sequence at block 60, and
assesses the quality of the sequence at block 62, the user can
prepare the submission file which includes the relevant information
for ordering the assay, such as the target sequence data from which
the primers and probes can be designed. As a design choice,
programs utilized in configurations of the present invention may
impose formatting requirements on input data to simplify parsing of
the input data. For example, a submission file in some
configurations can contain a header line and one sequence record
for each assay, and some configurations may require the submission
file to be formatted in this manner. An example of a submission
file for a SNP assay (showing SEQ ID NO: 1, SEQ ID NO: 3, and SEQ
ID NO: 4) with the header line and sequence records formatting
according to exemplary formatting requirements can be as
follows:
1 >JohnSmith 9997865432 partnumber4332072 seq_000001
AGTGAACG[A/G]GATAGGCA[G/T]CTCCTGCCC 1=s33d, 2=s33g seq_000002
TTACGGCCCTGA[G/T]GGGACTGC[G/C]ATCATTTTCT 1=snlf,2=sn3a seq_000003
GAGTGGAGCAACA[TAGC/*]GCTTTCCGCAATTTAC 1=34d
[0316] Similarly, an example of a submission file for a gene
expression assay, including a header line and sequence records, can
be as follows (showing SEQ ID NO: 2, and SEQ ID NO: 5):
2 >JohnSmith 9997865432 partnumber4332079 seq_000004
AGTGAACGAGATAGGCAGCTCCTGCCCCATCCAAG 13=ml3, 20=txyz seq_000005
TTACGGCCCTGAGGGGGACGAATCGATCATTTTCT 15=tryk
[0317] According to various embodiments of the present invention,
user 28 may prepare the submission file manually. Alternatively,
user 28 may use a file builder program (described below) which
queries user 28 for relevant information, automatically
constructing the sequence file, and allows user 28 to upload the
sequence file through the portal. As shown in FIG. 21, user 28
makes this selection at block 64.
[0318] Manual Preparation of Submission File:
[0319] If user 28 selects to prepare the submission file manually
at 64, then user 28 prepares the submission file without using the
file builder program. The structure of the submissions file will
now be described. The contents of the submission file may vary
depending on whether the assay being designed is to be used for
creating a SNP genotyping assay or an assay which will be used for
gene expression.
[0320] As discussed above, the submission file may contain two
components: a header line and one or more sequence records. The
header line contains information regarding the individual ordering
the assay, and may have the same contents if user 28 orders one or
more SNP genotyping assays or one or more gene expression assays.
The header line of a submission file may contain one or more the
following fields: a greater-than (>) symbol (or another symbol
or token that can serve to identify the line as a header line of a
submission file), a name field, a telephone number field, and a
part number field. In some configurations, this formatting may be
imposed as a requirement. In addition, also as a design choice,
some configurations limit the header line to no more than 255
characters. The orientation of these fields in the header line is
as shown in the FIG. 22. Also in some configurations, as a design
choice, each sequence record may be limited to a single line
regardless of length.
[0321] To create a header consistent with these formatting
conventions, a standard text editor such as Microsoft.RTM.) Notepad
can be used. A greater-than symbol (>) can be entered as the
first character, followed by the contact name and phone number. A
part number can be then entered which is used to select the
parameters of the resulting assay. In some configurations, part
numbers can be assigned by the supplier that indicate a type of
assay and a scale of synthesis. The supplier may, but need not,
require separate submission files for each requested assay. In some
configurations, SNP human assays, SNP non-human assays, and gene
expression assays can be assigned different part numbers. Also in
some configurations, different part numbers can also be assigned
according to the scale of the assay. As a non-limiting example, in
some configurations in which SNP human assays, SNP non-human
assays, and gene expression assays are each supplied in three
different scales, a total of nine different part numbers can be
used.
[0322] A non-limiting example of part numbers and designations are
shown in the tables reproduced below:
3 SNP Human Assay Part Numbers Number of Reactions 5 .mu.L 25-.mu.L
Reaction Reaction Part Scale 96-Well 384-Well Number V-Scale 200
1,000 4331349 S-Scale 600 3,000 4332072 A-Scale 2,400 12,000
4332073
[0323]
4 SNP Non-Human Assay Part Numbers Number of Reactions 5 .mu.L
25-.mu.L Reaction Reaction Part Scale 96-Well 384-Well Number
V-Scale 200 1,000 4332077 S-Scale 600 3,000 4332075 A-Scale 2,400
12,000 4332076
[0324]
5 Gene Expression Assay Parts Numbers Number of Reactions 5 .mu.L
25-.mu.L Reaction Reaction Part Scale 96-Well 384-Well Number
V-Scale 140 360 4331348 S-Scale 300 750 4332078 A-Scale 1,160 2,900
4332079
[0325] It will be noted that in this example there can be only one
part number for each record. Accordingly, a separate submission
file can be created for each assay type or each scale which is
desired. A completed header line may be varied so long as the
general rules here are satisfied.
[0326] The sequence record contains the sequence data for designing
the primers and probes and may vary depending upon whether the
assay being requested is a SNP assay or a gene expression assay. If
the assay is a SNP assay, then the sequence record may have the
following fields as shown in FIG. 23: a record name field, a
sequence field, and a coordinate field which provides the position
and name for specific target site. The record name field may be a
unique name to identify the sequence record and may be limited to
no more than 10 characters in length as a design choice in some
configurations. Also as a design choice, the record name field may
be limited to containing only letters, numbers, underscore, hyphen
or period character combinations with no spaces or tabs. In the
example shown in FIG. 23, the record name is seq.sub.--000001. The
sequence field may be used to contain the nucleic acid sequence
with the SNP target site marked. In the example shown in FIG. 23,
there are two SNP target sites: [A/G] and [G/T]. Configurations of
the present invention can be permitted to require that the entries
in the sequence field are in 5' to 3' orientation, that they
contain no more than 5,000 characters, that there can be no tabs or
spaces in the field, and the only characters that appear are A, C,
G, T, or N, except where SNP or insertion or deletion target sites
are indicated. Insertion or deletion target sites are sometimes
referenced herein as "insertion/deletion" target sites or as
"indel" target sites. Although an exemplary configuration is
described that imposes these rules, other configurations may impose
more or less restrictive rules and/or different rules.
Configurations of the present invention can also be permitted to
convert all lower case letters to uppercase to simplify processing
of data.
[0327] Although other conventions may be used, configurations can
be permitted to require that SNP target sites be indicated with
square brackets around each site, with two sequences corresponding
to the individual alleles separated by a forward slash. For
example, ACAC[G/T]TCT can be denoted by two alleles: ACACGTCT or
ACACTTCT. Also, configurations can be permitted to require that
indel target sites be indicated with square brackets around each
site, and that, within the brackets, base(s) present be indicated,
followed by a forward slash and an asterisk, wherein the asterisk
indicates a deletion. For example, ACAC[GA/*]TC can denote two
alleles: ACACGATC or ACACTC. It will be noted that the indel target
sequence can in various embodiments contain 6 bases in addition to
the insertion/deletion base or bases.
[0328] Finally, the coordinate field identifies and names a marked
target site. Configurations can be permitted to require that the
target site be indicated in 5' to 3' order. Although other
conventions may be used, configurations can be permitted to require
that the coordinate field include the target site order position,
an equal (=) sign, and an alphanumeric target site name of no more
than four characters. Multiple coordinates may be specified in some
configurations, and it can be permissible for these configurations
to require that the coordinates be separated by commas without
spaces. For example, in the sequence record shown in FIG. 23, the
sequence record identifies two coordinates, one identifying each
target site. In this regard, "1=s33d" identifies the first SNP
target site from the 5' end, and resulting probe sequences can
include CGAGA and CGGGA. In addition, "2=s33g" identifies the
second SNP target site from the 5'end, and the resulting probe
sequences can include CAGCT and CATCT. It will be understood,
however, that the sequence record may contain any number of
different fields of many different lengths.
[0329] In some configurations, only one assay will be synthesized
for each record. The assay name associated with a particular assay
that can be ultimately synthesized may be defined by the record
name and coordinate. For example, in the sequence record shown in
FIG. 23, the assay name associated with record "seq.sub.--000001"
with the coordinate "1=s33d" may be "seq.sub.--00001-s33d". In
addition, the assay name associated with the record
"seq.sub.--000001" with the coordinate "2=sgg" may be
"seq.sub.--000001-s33g".
[0330] As discussed above, configurations of the present invention
can be permitted to require (or allow) that the format of a
sequence record for a gene expression assay vary from the sequence
record for a SNP genotyping assay. In this regard, the sequence
record for a gene expression assay can include three fields: a
record name field, a sequence field, and a coordinate field. The
record name field may be a unique name that can be used to identify
the sequence record. Configurations of the present invention can be
permitted to impose restrictions on the unique name, for example,
limiting it to no more than 10 characters. In the example of
sequence record for a gene expression assay shown in FIG. 24, the
record name is "seq.sub.--000004". The sequence field can be the
nucleic acid sequence with the target sites unmarked. The
coordinate field can be used to identify and name a gene expression
target site. A convention that can be used, and which can be
permitted to be imposed by some configurations of the present
invention, is that the coordinate field include the target site
nucleotide position, an equal sign and a target site name.
Configurations of the present invention can be permitted to impose
restrictions on the target site name, for example, that the name be
alphanumeric and no more than four characters. Various
configurations can allow multiple coordinates to be present and can
require, for example, that multiple coordinates be separated by
commas and no spaces. For example, in the sequence record shown in
FIG. 24, there are two coordinates one for each target site. In
this regard, "13=m13" identifies the 13.sup.th nucleotide from the
5' end, which is located at the center of the target sequence, and
the resulting probe sequence can include AGATAGGCAG (SEQ ID NO:
20). In addition, the coordinate "20=txyz" identifies the 20.sup.th
nucleotide from the 5' end, which is located at the center of the
target sequence, and the resulting probe sequence can include
CAGCTCCTGC (SEQ ID NO: 21). In this example, the txyz user-supplied
coordinate can be selected for assay design and this can be added
to the record name as a unique identifier to create a new record
name, e.g., seq.sub.--000004txyz.
[0331] Sequence field information can be (and in some
configurations, can be required to be) arranged in 5' to 3'
orientation and it can be permitted in some configurations to limit
the sequence field information to no more than about 5,000
characters. However, it is to be understood that the sequence field
may have (or may be allowed to have) more than 5,000 characters in
some configurations. By design choice, configurations may also
require that there be no spaces or tabs between the characters, and
that only permissible characters can be A, C, G, T, or N.
Configurations can be permitted to automatically convert lowercase
letters to uppercase, for example, for ease in processing.
[0332] Although not required, at least one coordinate in the
coordinate field of the sequence record can contain the target
position, an "equals" sign, and a target site name for each site.
It is permitted to require that the coordinate field contain no
spaces, and that multiple sites be separated by commas. As
discussed above, at least one coordinate can be required for each
sequence record. If a specific target site is not present, multiple
sites can be selected across the sequence.
[0333] When entering sequence records, the record name can be
entered according to the guidelines set forth above. A single space
or a tab may then be entered followed by the sequence data also
according to the guidelines discussed above. Another space or tab
can then be entered followed by the coordinate(s) also set forth
above, then the enter key can be depressed. These steps can be
repeated for each sequence record.
[0334] In some configurations, File >Save can be selected to
save the file as a text (i.e., ".txt") document. If Microsoft
Notepad is being used on a Microsoft WINDOWS.RTM. 2000 operating
system, ANSI encoding can be selected. Configurations of the
present invention can be permitted to impose restrictions on the
name selected for the saved file. For example, some configurations
can require file names of no more than eight alphanumeric
characters, and may require the extension .txt to be present.
[0335] After the file has been saved, a further check may be
performed to determine whether the submission file satisfies the
format requirement set forth in FIG. 25. A visual checklist for a
gene expression assay submission files is set forth in FIG. 26.
[0336] Once the submission file has been checked for errors and is
ready for submission, an order message can be prepared as indicated
by block 70. The order message contains order information which
includes the submission file and the part number listed in the
header of the submission file. If more than one submission file is
being submitted, the submission file and the corresponding part
number for each submission file can be present. In addition, the
order message can include either a purchase order number or credit
card information with the name as it appears on the card, the card
number and the expiration date. The order message can also contain
contact details such as name, e-mail address, phone number, address
and e-mail address of primary contact in case of difficulties with
the submitted file. Shipping information can also be provided which
can include identification of the person to receive shipment, for
example, that person's name, address (including room number,
building and department) and/or phone number. An invoice number and
identification of a purchasing agent or person to receive invoice
details may also be included, and such identification may include
that person's name, address, e-mail address and/or phone
number.
[0337] Once the submission files have been checked for errors, the
submission file can be submitted to the system either by e-mail, by
regular mail or by web access. If the order is to be sent by
e-mail, the submission file can be attached to the order message
and an indicia of the processing can be placed in the subject line
of message. For example, the text "CA" may be placed in subject
line to indicate that the order can be processed as a custom assay.
The e-mail message can then be sent to the facility conducting the
design process, for example an e-mail message sent to
custom.assay@Company.com.
[0338] If the order is being submitted by regular or express mail,
a copy of the order message can be included. The submission file
may be placed on a machine readable medium, for example, a 3.5 inch
floppy disk or CD ROM in a format readable on (for example)
Microsoft Windows operating systems. The order message and
submission file can be then submitted to the service using the
invention.
[0339] File Builder:
[0340] To assist user 28 in preparing a sequence for submission to
the custom assay system, various embodiments of the present
invention include a file builder program to prepare the submission
file as represented by block 74. The file builder program can be
used for submitting sequences for SNP genotyping assays and for
submitting sequences for gene expression assays. File builder
program configurations of the present invention can include a DNA
sequence checker as well as a text editor to facilitate building,
editing, and correcting new as well as validating imported sequence
submission files. Once the submission files are created using the
file builder program, the submission files can be uploaded over the
Internet to the system for synthesis or otherwise submitted. A file
builder program may be resident on consumer computer 26, or it may
be a web-based application or resident on the host computer.
[0341] Exemplary configurations of a file builder program will now
be described in greater detail with reference to FIG. 27 and FIG.
28. When user 28 initiates an exemplary configuration of a file
builder program at block 76, user 28 can select one or more options
to facilitate the building of a submission file. It will be
understood that options available in various file builder
configurations may vary from those described herein. However, in
some exemplary configurations, user 28 can initially select to
learn more about the file builder program at block 78. If user 28
selects to learn about the file builder program at block 78, user
28 can be directed toward a set of instructions which can be either
resident on consumer computer 26 or a web site that contains
information regarding custom assay submission guideline protocol as
indicated by block 80. An example of a window pane associated with
one such tutorial is represented in FIG. 29.
[0342] In some configurations, user 28 can also select an option of
viewing a file builder demonstration program at decision block 82.
The file builder demonstration program shows how user 28 can
complete the fields for preparing a submissions file using the file
builder program (as will be described below). In this regard, the
file builder demonstration program provides step-by-step
instructions regarding the use of the file builder program to
format an assay request. If user 28 selects to view a file builder
demonstration at decision block 82, file builder demonstration
program can be displayed for user 28 at block 84. As a design
choice, some configurations of the file builder demonstration
program may utilize Macromedia Flash. An exemplary window pane
generated by the file builder demonstration program is shown in
FIG. 30.
[0343] User 28 may also select to view the submission guidelines
for preparing the submission file as indicated by decision block
86. If user 28 selects to view the submission guidelines at
decision block 86, the file builder program displays at block 88 a
file containing the submission guidelines in a suitable display
format, one example of which is portable document format (PDF). An
exemplary window pane showing the submission guidelines displayed
at block 88 illustrated in FIG. 31.
[0344] User 28 can also select to build a submission file at
decision block 90. If user 28 selects to build a submission file at
decision block 90, user 28 can be directed to a series of window
panes at block 92 that allow user 28 to enter header line
information of the type described above. In this regard, user 28 at
block 100 of FIG. 32 selects the part number associated with the
SNP genotyping or gene expression assays. Additional information
about the assay can be included with the part number, including one
or more of the following: assay scale, e.g. V scale, A scale, or S
scale, target species, e.g. human or non-human, assay
concentration, and assay volume. In addition, user 28 can be
requested to provide a first name, last name, telephone number and
e-mail address of the person receiving the order. An example of a
window pane that may be used for this purpose is shown as FIG.
33.
[0345] After user 28 enters the relevant header file information at
block 100, the file builder program requests entry at block 102 of
a sequence name which can be the name given by user 28 to the
specific sequence. In addition, user 28 can also be requested to
provide a target sequence as indicated by block 104. Finally, user
28 also provides at block 106 the target coordinates. An exemplary
window pane for which this information can be entered, is shown in
FIG. 34.
[0346] After the sequence name, target sequence and target
coordinates have been entered, user 28 is able to validate the
sequence (i.e., check for formatting and typographical errors) at
block 108. User 28 may instruct the file builder program to
validate the sequence by clicking on a "validate" button, such as
that shown in FIG. 34. When user 28 chooses to validate the
sequence, the file builder program reviews the text of the sequence
for errors.
[0347] If the file builder program detects typographical errors in
the target sequence, some configurations generate a window pane
that indicates to user 28 that typographical errors are present. In
the example shown in FIG. 34, there were two errors present, the
number 2 and the number 5 being present in the sequence. The file
builder program can provide suitable output to bring the errors to
the attention of user 28, such as the output shown in FIG. 35. User
28 then has the option at block 110 of fixing either one or all of
the errors in the target sequence information provided to the file
builder program. After the target sequence errors have been
corrected in block 110, an error message log can be generated at
block 112 which further provides information on whether the
sequence is formatted properly as described above. If the error
message log indicates that there is an error in the formatting of
information, user 28 can then fix the formatting errors at block
114. If the file is formatted properly, the error message log can
indicate that the sequence record was validated. A non-limiting
example showing a window pane in which information provided by that
user 28 was successfully validated is shown in FIG. 36.
[0348] After the information from user 28 has been successfully
validated, the information can be saved to disk as indicated by
block 116 (see FIG. 37). It will be noted that the location at
which the file is saved can be displayed by the file builder
program, as can be the contents of the submission file (see FIG.
38).
[0349] By convention, files in some configurations can be saved
with a file extension of ".txt". After the file has been saved,
user 28 is able to upload the submission file at block 118 to the
system by clicking on or depressing an appropriate button. Before
or after user 28 has requested sequence information be uploaded to
the system, user 28 may be requested to provide appropriate
identification and password information. Configurations of the
present invention can be permitted to make such identification
mandatory. A non-limiting example of a window pane requesting such
identification information is shown in FIG. 39. After user 28 has
entered the appropriate identification and password information,
the file can be uploaded to the ecommerce web site store. Once the
submission file is uploaded to the store, user 28 may complete the
order process at block 120. In some configurations, user 28 logs
into the web site of the store using the same user identification
and password and then chooses to proceed to the electronic shopping
basket at which point the order can be displayed to user 28. User
28 can then review the order and continue shopping or proceed to
process the order. In some configurations, the user will have
identified more than one assay to be ordered and all of the
identified assays can be ordered and added to the shopping basket.
In addition, the user can place one or more assays in the shopping
basket and then return to continue shopping and subsequently place
one or more additional assays in the shopping basket.
[0350] In some configurations, if user 28 selects to process the
order, the store provides stored contact and shipping information
and asks that user 28 verify the information as well as provide any
special instructions. User 28 can then verify payment information
and place the order if all the information can be correct.
[0351] Returning to FIG. 18, in some configurations, a variant
configurator 36 (such as SELECTICA.RTM. Configurator.TM., available
from Selectica, Inc., San Jose, Calif.) interacts with consumer 28
via network 24 to produce a list of specified characteristics, as
discussed below. Configurator 36 can be essentially an automated
decision tree that produces the input for assay design program 38
and that ensures that input parameters to assay design program 38
are within bounds that can be handled by program 38. If there are
no errors, assay design program 38 then uses a lookup process, a
design process, or another suitable method to provide a forward
primer sequence, a reverse primer sequence, and a probe sequence
that have the specified characteristics.
[0352] Upon successful validation, oligo factory 42 accepts the
order from consumer 28, manufactures at least one assay having
components including a forward primer, a reverse primer and a probe
and ships the manufactured assay to the consumer. The forward
primer, reverse primer, and probe can be manufactured in accordance
with the validated sequences.
[0353] In some configurations and referring to FIG. 40, an assay
design system 122 can be provided as computer software that allows
automated, high-throughput design of assays such as, for example,
TaqMan.RTM. assays. The designed assays can in various embodiments,
include primers and probes for allelic discrimination and gene
expression assays in a batch format. This computer software can be
particularly useful when designing hundreds or thousands of assays.
Assay design program 38 can be a non-interactive pipeline of a
Igorithms for the design of TaqMan.RTM. or other probe and primer
reagents. In some configurations, heuristic rules can be utilized
in assay design program 38. Pre- and post-processing utility
programs and wrapper scripts can be utilized as components of the
complete assay design system 122.
[0354] In various configurations, input to assay design program 38
includes a parameter file 126 that specifies design rules and one
or more sequence data files 124. Output includes a log file 132
that reports system settings and attributes describing each
successful reagent design (including probe, primer, and amplicon
sequences). Additional output indicating a system status can be
reported to a display screen as the program is running, in some
configurations.
[0355] Sequence input file 124 can contain formatted and annotated
sequence data. Parameter file 126 can contain keyword-associated
settings that govern rules and scoring applied during designs.
Prior to attempting any designs, the format of supplied sequence
data can be checked at 128 for errors. If errors are found at 130
in the sequence data from input file 124, they can be reported to
an error log 140 and the process can be terminated.
[0356] In various configurations, assay design program 38 starts by
parsing parameter file 126 to set up rules and scoring schemes. If
initialization errors occur, they may be caused by conflicting
options or incorrect file names or formats. If there are any errors
encountered during the initialization phase, they can be reported
to log file 140 and assay design program 38 can then stop.
Following successful initialization, assay design program 38
sequentially attempts to design assay sets for each target site in
each sequence listed in the input sequence data from parameter file
126. As designs are processed, they can be recorded in a design log
file 132. Design attempts that fail can also be recorded in log
file 132. Design failures can occur when no acceptable set of
reagents satisfying all rules and scores can be found for a
sequence target.
[0357] If, at 134, there are no valid designs present in design log
file 132, this fact can be reported in error report 140. Otherwise,
following the core design process, design log file 132 may be used
to generate output sequence data in a number of different formats.
Log pick program 136 can perform this post-processing of design log
132 data to produce formatted outputs 138. A script can be
implemented utilizing the UNIX operating system to integrate the
whole system by tying together all of the processes shown in FIG.
40. The script can also log runs of process 122 and assign each
output batch a serial number for tracking purposes.
[0358] Separate design rules and constraints can be applied to
potential probes, primers, and amplicons. All designs resulting
from a given run share a common set of rules. Probe constraints
include limits on size (i.e., probe length), T.sub.m (target,
minimum, and maximum temperatures), internal loops (total and
contiguous matching bases in a "hairpin stem"), G+C content (i.e.,
combined G and C percentage), and runs of a given base, such as G.
Analogous constraints can also be separately applied to primers,
which have an additional limit on G+C at the 3' end (5 bases) of
the primers. Constraints applied to amplicons include length
(including primers), G+C content, and the number of ambiguous bases
(note that ambiguous bases are generally not allowed within probes
or primers). In addition, the primers defining amplicons can be
constrained to limit the maximal size of internal priming sites
(i.e., the number of contiguous matching bases starting at the 3'
end of one primer that complements any part of the other
primer).
[0359] For many of the constraints listed above, system 122 may
apply either a filter or a score. When applied as a filter, a
constraint will be either satisfied or not with the corresponding
design being either accepted or rejected. When applied as a score,
attributes may be given a graded value that reflects how "optimal"
a given design is. For example, a design with all constrained
attributes near optimum values will be favored over one with
attributes deviating from the optimum values. Scoring provides
finer tuning of the constraints that system 122 will use to
evaluate and select designs.
[0360] Logic flow representative of some configurations of assay
design program 38 is shown in more detail in FIG. 41. Upon starting
program 38 at 142, an initialization phase 144 reads parameter data
from parameter file 126 and sequence data from sequence data file
124. (As shown in FIG. 40, sequence data 124 may be checked for
errors at 128 and 130 before being read by assay design program
38.) Initialization 144 includes parsing parameter file 126 and
setting up for subsequent probe design. If any problems are
encountered at 146 as a result of initialization 144, assay design
program 38 reports a diagnostic message and stops at 150.
Otherwise, processing continues. In some configurations of the
present invention, most parameter file 126 options have default
values and may be superceded by command line options. Options
actually used during design can be reported in log file header 148,
which is or becomes part of design log 132 of FIG. 40.
[0361] Various configurations of assay design program 38 attempt to
acceptably design assay sets for each target site at 156. These
designs can be logged at 158. An attempt can be made to identify
acceptable designs at 160 for each input sequence record from
sequence data file 124. When records are exhausted at 152, assay
design program 38 is done at 150. Otherwise, for each record, each
target can be tried at 156 in the order listed. If no target
information is supplied, the sequence midpoint (if the sequence
contains no SNP annotations) or the first SNP (if annotated) can be
used as a target. When no targets are left for a given record at
154, assay design program 38 progresses at 152 to the next
record.
[0362] For target sites, some configurations of assay design
program 38 identify, at 160, successful and unsuccessful designs,
according to the design metrics and scoring metrics. If program 38
fails to design for a target, this fact along with the
corresponding unsuccessful design can be reported to log file 132
and the program progresses at 154 to the next target associated
with the record. If it succeeds to design for a target, the details
of the chosen record can be reported to log file 132. Normally, a
single successful design causes assay design program 38 to move to
the next record at 152. However, in some configurations, if an
option to evaluate all targets listed for each record is enabled,
assay design program 38 progresses, at 162, to the next target at
154 rather than to the next record at 152 following a successful
design.
[0363] Representative logic for designing reagents for a simple
target suitable for various configurations of procedure 156 is
shown in more detail in FIG. 42. Upon starting at 164, design for
record/target program 156 extracts design "windows" at 166, e.g.,
one or two subsequences around the target can be extracted. For SNP
targets, two separate windows can be extracted at 166 around the
SNP target site, one for each allele. In addition, any other SNP
that is known to be within the sequence of the window can be masked
by converting it to an N, which represents any nucleotide. For
non-SNP targets, a single subsequence window can be extracted at
166. Windows can be limited in size by the supplied input sequence
length or by the maximum allowable amplicon size. Problems
encountered at 168 during window extraction (for example, an
incorrectly formatted SNP annotation) cause a failure at 188. (In
general, failures in this and other procedures or functions may be
reported to the consumer and result in no product being shipped.
Failures resulting from data that is improper, inconsistent,
out-of-bounds, etc. need not be fatal. Thus, in various
configurations, the software can be configured to reset itself
after an order or failure therefore, to be ready for the next
order.)
[0364] If no problems are encountered, placement of probes can be
normally attempted next at 172, unless an option to design only
primers is enabled at 170, in which case, execution continues at
176. (A primer-only option may be enabled, for example, by a
command line option, such as "-op".) Probe placement at 172 yields
either one or two acceptable probes (non-SNP and SNP cases,
respectively), or not. If acceptable probes are not identified at
174, target design process 156 fails at 188. Otherwise, bounds can
be set for primers at 176.
[0365] In some configurations of the present invention, to set
primer bounds at 176, three sub-regions within the design window
can be defined. In cases in which probes can be designed (e.g.,
cases in which not only primers are designed), a central mask
region corresponding to coordinates of the probes can be defined.
Bounds for the mask region may be explicitly designed relative to
target site coordinates. For example, in some configurations, a
command line option (such as "-pm") can be used to specify that the
mask region is to be designed relative to target site coordinates.
In this case, the actual mask region can be the larger of the
specified bounds or the mask formed by the probes. Fixing the
central mask region determines the two sub regions where primers
may be designed. The "upstrand" sub-region begins at the start of
the window and extends to the start of the mask region. The
"downstrand" sub-region follows the mask and extends to the end of
the window. The three sub-regions of the window (i.e., upstrand,
mask, and downstrand) do not overlap.
[0366] With the uprstrand and downstrand sub-regions determined,
design procedure 156 attempts to collect a number of primers in
each sub-region at 178. Forward primers can be taken from the
upstrand region and reverse primers can be taken from the
downstrand region. Potential primers can be evaluated at each
nucleotide position starting from the coordinates closest to the
mask (i.e., the end and start coordinates of the upstrand and
downstrand regions, respectively). Such evaluation may, for
example, determine whether a potential primer is acceptable
according to standards known and recognized in the art. In some
configurations, design procedure 156 collects up to ten forward and
ten reverse primers, but by setting a command line option (such as
"-np"), the limit of ten can be changed to another number.
[0367] If at least one potential forward and one potential reverse
primer is not found at 180, design process 156 fails at 188. With
two lists of primers, design process 156 next attempts to identify
an acceptable forward/reverse pair at 182. If no acceptable primer
pair is identified at 184, design process 156 fails at 188.
Otherwise, a complete design has been found at 186.
[0368] The logic of a representative configuration of procedure 172
for placing probes in various configurations of the present
invention is shown in more detail in FIG. 43. When a design attempt
is begun at 188, a probe placement can be attempted. The logic
follows slightly different but similar paths depending upon a
determination of whether the target is a SNP site or a non-SNP site
at 190. For SNP sites, sample sequences on both alleles of both
strands can be considered at 194. For non-SNP sites, a
determination can be made at 192 as to whether both strands or only
a single strand is used at 194, 196, or 198. Explicit strands can
be then determined at 200 or 204 and non-target strand probes can
be eliminated at 202 or 206 to pick the best probe at 208 or 210.
Features that can be used to pick the best probe can be determined
on the basis of T.sub.m value and filter or score values. Minimal
target overlap can be an input parameter. For non-SNP targets this
value may be negative, allowing a larger sequence region to be
sampled. For SNP targets, the minimum value of target overlap can
be two bases, but the overlap may be increased. Probes targeting
both forward and reverse strands can be evaluated. Probes may not
start with G and normally the requirement that G content does not
exceed C content can be applied, but an option can be provided to
eliminate the G.ltoreq.C rule. In some configurations, and in some
cases, both forward and reverse strands can be considered
explicitly for T.sub.m delineation. If probe scoring is being
applied, the best scoring probe can be selected. Otherwise, the
constraint satisfying probe most overlapping the target site can be
selected. From this determination of whether a probe is acceptable
or not at 212 or 214, probes can be selected that pass, at 216, or
alternatively can be selected against, at 218, for failing the
criteria.
[0369] For SNP target sites, sequences corresponding to both
alleles (only bi-allelic SNP sites can be supported in some
configurations) can be explicitly constructed and the best probes
for both strands of both allele sequences can be identified as
described above. An acceptable pair of SNP probes must target the
same sequence strand. If acceptable probe pairs can be found for
both strands, the strand yielding the pair with the largest total
score can be selected. When input sequences have multiple SNP sites
denoted, the non-targeted SNP sites can be masked (i.e., set to
base N) when the sequences for each explicitly targeted allele are
constructed.
[0370] If no acceptable probe (or, for SNPs, no acceptable probe
pair) can be found for a given target, the system reports this fact
and attempts to continue, depending upon the number and format of
sequence targets supplied. If a single sequence is supplied as
input, failure to select a probe (or pair) results in a program
termination. If multiple target coordinates (or SNPs) are listed
for a given sequence, failure to place a probe at one target
coordinate causes probe placement process 172 to consider the next
listed coordinate until all listed targets are exhausted. For
multiple sequence input, failure to place a probe at any target
coordinate leads the program to address the next listed sequence
until all input sequences are exhausted. If there are multiple
targets for a given sequence, whether or not a probe can be placed
on any one individual target, all targets will be tested and the
best design chosen.
[0371] Once a probe (or probe pair) sequence is selected, a list of
upstream (forward) and downstream (reverse) primers can be
delineated starting immediately before and after the probe
position. These can be delineated via T.sub.m (in some
configurations using a different algorithm than used for probe
design), and filtered or scored. If SNP probe pairs can be being
designed, primers are delineated starting immediately before and
after the footprint corresponding to both SNP-targeting probe
positions. At least one forward and one reverse primer must be
identified. By default, up to ten forward and ten reverse primers
can be collected, but the number of upstream and downstream primers
may be changed, such as by using a command line switch. Failure to
identify any forward or any reverse primers results in probe
placement process 172 to report the problem and continue with the
next target coordinate or next sequence as described above.
[0372] Forward and reverse primers can be checked for pair-wise
compatibility and the corresponding amplicons can be filtered or
scored. The compatibility check can include screening the 3' ends
of the primers across the amplicon associated with a given primer
pairing. If too great a 3' match is identified, the primers may not
be paired. The pair of primers with the best score, by default, the
shortest amplicon, can be chosen in some configurations of the
present invention. Failure to select an acceptable primer pair
results in probe placement process 172 reporting the problem and
continuing as described above.
[0373] Acceptable designs comprising one or two probe sequences
(such as, for example, probe sequences that can be used to make
TaqMan.RTM. probes) together with corresponding forward and reverse
primer sequences can be recorded in the log file. Along with the
sequences, the coordinates, T.sub.m values, and scores may be
reported for each probe and primer. Any associated auxiliary data
(e.g., tracking information) loaded during sequence and target
input may be also reported to the log file when a successful design
is obtained. If no acceptable designs can be found for a target
sequence, only the target name may be recorded in the log file.
[0374] Stock Assays: Gene Expression
[0375] In some configurations, custom gene expression products
include off-the-shelf assays. In some configurations, assays can be
provided for 15,000 genes based upon the NCBI Reference Sequence
Database Project (RefSeq). In some configurations, off-the-shelf
assays can be provided for about 30,000 genes (i.e., every human
gene or almost every human gene). Various configurations use 5'
nuclease chemistry with TaqMan.RTM. MGB probes and/or operate with
universal formulation and thermal cycling parameters (for example,
in some of these configurations, 900 nM primers, 250 nM probe).
Some configurations provide assays designed utilizing a
bioinformatics pipeline that includes private and public data, such
as a combination of Celera data and Public data, or either private
data or public data alone.
[0376] Gene Expression Assay Preparation:
[0377] In some configurations, gene expression assays include two
unlabeled oligonucleotide primers and a single TaqMan.RTM. probe
(Livak et al., PCR Methods Appl 4:357-362) with an MGB, moiety.
Assay design can include transcript pre-processing, actual design
of the primers and probe and in silico quality control prior to
manufacturing the probe.
[0378] Pre-Processing: In some configurations, certain sequence
regions within the transcript can be identified in the
pre-processing step for designing the oligonucleotide primers and
probe for a 5' nuclease assay. For example, sequence regions may be
selected that do not contain any known single nucleotide
polymorphisms or repeat sequences. Also, 5' nuclease assays for
gene expression may be designed across exon-exon boundaries, and
thus, in some configurations, the position of each of the exon
boundaries within a multi-exon transcript can be determined prior
to the design of each assay.
[0379] In some configurations, transcript pre-processing begins
once a batch of transcripts is compiled into a multi-fasta file.
Repetitive and low complexity regions in each transcript can be
masked (i.e. nucleotides replaced by an N) in some configurations.
Repetitive sequences that can be masked include, for example,
simple repeats (di- and tri-nucleotide repeats), Alu restriction
site repeats, long interspersed nuclear elements (LINEs), and short
interspersed nuclear elements (SINEs).
[0380] Exon-exon boundaries can be identified by mapping the masked
transcripts to the human genome using alignment software. The
positions of each exon-exon boundary can be marked for each
multi-exon transcript, with single-exon transcripts being
identified as such. Mapping may be performed against the Celera
genome assembly, with supplemental mapping information provided by
public sequence data. If sequence discrepancies are found between
the public transcripts and the Celera genome during this step, the
discrepant bases may be masked.
[0381] In some configurations, in the final pre-processing step,
all known single nucleotide polymorphisms (SNPs) can be masked
after performing a BLAST analysis against a genomic database using
methods known in the art (see Altschul et al., J. Mol. Biol.
215:403-410, 1990). All of the known SNPs can be identified within
each transcript. Both the SNP-masking and sequence
discrepancy-masking steps can be useful in preventing
oligonucleotide primer and probe assays from being designed over
ambiguous or known variant nucleotide(s).
[0382] Assay Design: The gene expression assay design can be based
upon specifications as described above including optimal Tm
requirements, GC-content, buffer/salt conditions, oligonucleotide
concentrations, secondary structure, optimal amplicon size, and
reduction of primer-dimer formation. As noted above, each gene
expression assay can include, in some configurations, two unlabeled
oligonucleotide primers and a single TaqMan.RTM. probe. The
TaqMan.RTM. probes incorporate both an MGB and an NFQ at the 3' end
of the oligonucleotide. The use of MGB probes increases the
probability of designing an assay in traditionally difficult
sequence regions (e.g., AT-rich sequences). Additionally, the
relatively short MGB probes increase the probability that a probe
can be designed over every exon-exon boundary of a multi-exon
gene.
[0383] For transcripts from multi-exon genes an assay target
position can be selected at each exon-exon boundary. The probe
rather than one of the primers can be generally, but not always
placed over the exon-exon boundary to ensure that the primers bind
in two distinct exons. Placing the probe over the exon-exon
boundary ensures that the primers can be in two different exons,
and that fluorescent signal can be only generated from amplicons to
which the probe can specifically bind and be cleaved. Assays
designed over exon-exon boundaries can be designated by
Hs********_m*, where the "m" indicates multiple exons.
[0384] For single-exon genes, both the primers and probe must be
placed within the exon. Any assays that have the primers and probe
placed within a single exon can, therefore, be designated
Hs********_s*, where the "s" indicates a single exon. This
designation provides an indication to users that there can be the
potential to amplify contaminating genomic DNA in an RNA sample,
and thus the appropriate experimental design controls can be
implemented to avoid this problem.
[0385] For multi-exon genes, n-1 assays can be designed where n can
be the number of exons. For transcripts from single-exon genes,
multiple assays can also be designed by designating target
positions that can be dispersed across the entire length of the
transcript. The design of multiple assays for each transcript
provides two advantages: 1) it increases the probability that a
successful assay will emerge at the end of the entire design and
quality control process, and 2) having assays that can be designed
from the 5' to the 3' ends of every transcript provides great
flexibility in the choice of a high-quality assay at any position
on the transcript.
[0386] In Silico Quality Control: In some configurations, after
design, primer and probe sets are processed through a quality
control step. This process penalizes, and thus helps to screen out:
1) assay designs that are not highly specific for the gene of
interest, and 2) assay designs that may not accurately report the
quantitative expression results for a particular target (i.e., an
accurate threshold cycle (Ct) value) in a 5' nuclease assay.
[0387] In some configurations, the in silico quality control
comprises three major parts, and each step generates a penalty
score specific to a given assay design. A final penalty score for
each assay design comprises the sum of each of the three individual
penalty scores. The assay design with the lowest cumulative penalty
score for each transcript can be the assay that can be chosen for
manufacturing.
[0388] In some configurations, the three parts comprising the in
silico quality control process include:
[0389] 1) Transcript BLAST Scoring, which comprises determining the
degree of homology, through BLAST, between the assay and other
closely-related transcripts. A penalty can be assigned if an assay
detects any closely homologous transcript(s) other than the
intended target.
[0390] 2) Genome BLAST Scoring, which comprises determining the
degree of homology, through BLAST, between the assay and non-self
regions of genomic DNA (e.g. homologous genes and pseudogenes). A
penalty can be assigned if an assay hits a second (or greater
number) physical location on the genome in addition to the location
of the gene-of-interest.
[0391] 3) Determining the size of the intron across which the probe
spans (for assays to multi-exon genes). A penalty can be assigned
when the assay is designed across an exon-exon boundary that spans
a small intron (for example, <2 Kb).
[0392] In various configurations, for all BLAST searches, a quality
control query construct can be made by generating an amplicon
sequence that includes each of the two primers and the intervening
probe; the amplicon can be created by padding the specific number
of nucleotides between the primers and the probe with N's (FIG. 44
and FIG. 45).
[0393] 1) Transcript BLAST Scoring: The quality control query
construct for each 5' nuclease assay can be BLASTed against
transcript database(s) in some configurations to ensure that 1)
each primers/probe trio in the quality control query sequence
matches the target transcript sequence, and that 2) each assay can
be specific for the gene of interest and will not amplify
transcripts from other genes. Primers with homology to other genes
(with an intervening homologous probe) can produce an unwanted
fluorescent signal, and thus an artificially low Ct value. Primers
to homologous genes (without an intervening homologous probe) may
amplify homologous transcript(s) in addition to the target
transcript and cause competition for reagents in the PCR reaction,
resulting in an artificially high threshold cycle (Ct) value if the
competing homologous transcript is expressed at high levels. These
types of side reactions can skew the Ct for the gene of interest
and thus produce an erroneous quantitative result for the target
transcript. If homology exists, an assay can be assigned a penalty
score based on the degree of homology to other transcripts. In some
configurations, three sets of numbers can be reported in this
transcript BLAST step as described below.
[0394] (a) BLAST Hit to Self (Transcript_SelfHSP):
[0395] The high scoring pair (HSP) from this BLAST can produce a
match of 100% homology with self. This HSP represents the alignment
of the quality control query construct to the target transcript in
the transcript database, and shows a "0 0 0" (representing 0
mismatches in the forward primer sequence, 0 mismatches in the
probe sequence, and 0 mismatches in the reverse primer sequence)
result when BLASTed against the database from which the target
transcript was retrieved (FIG. 46). If the quality control query
construct has no hits against a particular transcript database,
then the mismatch can be reported as an artificially high mismatch
value (e.g., "50 50 50") and the assay can be flagged as being
problematic.
[0396] (b) Continuous BLAST Hits to Non-Self Transcripts
(Transcript_HomoHSP)
[0397] In this set of BLAST results the top non-self HSPs can be
reported (i.e. BLAST results to homologous transcripts). The
highest penalty can be assigned to the HSP that is the closest
homolog but that is not a perfect match to the quality control
query construct. If two HSPs have the same homology score to the
query construct, then the one with the higher homology to the probe
region can be chosen as the top hit.
[0398] This approach will skip all of the homologs that have a "0 0
0" match and will only report the top non-zero HSPs. Therefore, a
primer/probe set that can amplify alternative splice variants for
the same gene will not be penalized, since these
alternatively-spliced transcripts may be present as unique
transcripts within the database being queried. This step helps to
ensure that assays can be gene-specific, but not necessarily
transcript-specific.
[0399] Two or more highly homologous genes may end up with
identical assay design in regions where the genes have identical
sequence. In such a situation a transcript penalty can not be
assigned (because of the "0 0 0" match). Situations in which an
assay could detect transcripts from more that one gene can be
penalized in a downstream part of the in silico quality control
process when BLASTing can be done against the genome assembly (see
below). Designing the process in this manner facilitates
differentiation between an assay detecting an alternatively-spliced
variant of the same gene versus an assay that detects a transcript
from a different gene locus.
[0400] (c) Non-Continuous BLAST Hits to Non-Self Transcripts
(Transcript_HomoHIT):
[0401] In some configurations, a BLAST query can be performed to
analyze any alignments with high homology to each of the two
primers, but which come from non-continuous regions of a homologous
transcript. The quality control query construct hits two different
(non-contiguous) parts (HSPs) of a non-self transcript. This BLAST
result can be indicative of an amplicon from a homologous
transcript being of a different size than the target amplicon.
These BLAST results can be from two different HSPs (FIGS. 47, 48,
and 49). The higher the homology between the primers and the HIT,
the greater the penalty. A penalty can be assigned to minimize the
likelihood of non-specific amplification of transcripts other than
the target and thus competition for reagents in the PCR reaction
that could affect the threshold cycle (Ct) of the target of
interest.
[0402] 2) Genome BLAST Scoring: In some configurations, the same
quality control query construct that can be BLASTed against the
transcript databases can also be BLASTed against the human genome
assembly and the output can be reported in a similar manner. This
quality control step avoids missing homologous transcripts that may
not yet be known in transcript databases, facilitates, via genomic
alignment, the distinguishing of different genes from alternative
splice variants of the same gene, reduces amplification of
artifacts due to the possible presence of contaminating genomic DNA
in a total RNA sample, and penalizes those primers/probe that would
amplify pseudogenes in total RNA samples that contain contaminating
genomic DNA.
[0403] (a) Blast hit to self (Genome SelfHIT). As with the BLAST
search to align the primers and probe to the target sequence in the
transcript databases, similar BLAST searches can be used to align
the primers and probe to the unique gene in the genome to which
they were designed. For multi-exon genes the match must be
"0.times.0" for the primer/probe set to avoid a penalty. The two
zeros represent no mismatches between the forward and reverse
primer sequences and the genome sequence, and the fact that they
come from two different HSPs indicates that the primers can be on
two different exons, separated by an intron. The non-zero value of
X reflects the fact that the probe is interrupted by an intron, and
thus does not align itself to contiguous sequence in genomic DNA.
For single exon genes, the BLAST search alignment returns a value
of " 0 0 0 " because there are no intronic regions to interrupt the
probe sequences and lead to mismatches.
[0404] (b) Continuous BLAST hits to non-self gene(s)
(Genome_HomoHSP): The Genome_HomoHSP BLAST results identify genomic
regions that have high homology to the primers and probe, and can
amplify a PCR product of similar size to the target transcript from
contaminating genomic DNA present in an RNA template. This
situation can most often occur because of the presence of a
pseudogene in genomic DNA. This BLAST result identifies the HSP
with the highest homology to the amplicon, with the focus primarily
in the two primer regions. If two HSPs have the same degree of
homology in the primer sequences, then the HSP with a higher
homology to the probe region can be chosen as the top hit, and the
degree of mismatch in the primers and probe can be used to generate
the penalty. The higher the degree of homology between the primers
and probe and the HSP, the greater the penalty. This, in effect,
over-penalizing assays by assigning this genomic DNA penalty.
However, this penalty can be applied in order to maximize the
ability of an assay to accurately quantitate the target of interest
in RNA preparations that may be contaminated with genomic DNA.
[0405] (c) Non-continuous BLAST hits to non-self gene(s)
(Genome_HomoHIT): This genomic BLAST alignment identifies the
genomic sequences that have the highest homology to each of the
primers but come from two different HSPs. If the intervening
sequence between the two HSPs is short, then the penalty can be
high. This minimizes the chance of amplifying a non-target template
in an RNA preparation with genomic DNA contamination. If the
genomic interval between the two primers is large the penalty can
be smaller because it is unlikely the primers can actually produce
an amplicon from this type of secondary template.
[0406] As described above, there can be no penalty for non-self "0
0 0" hits in the transcript BLAST quality control step, and thus
the Genome_HomoHIT BLAST results can be used to penalize assays
that cannot discriminate between homologous genes. If two or more
highly homologous genes have identical assays designed (for
example, in a region where the two different genes have identical
sequence) then the assays can be penalized at this step. If the
Genome_HomoHIT results shows "0.times.0" hits at least one genomic
location in addition to self, then the assay can be assigned a
large penalty because it can be assumed that this second hit is to
a separate and distinct gene.
[0407] 3) Intron Size Scoring: The third part of the in silico
quality control scoring process can be the determination of intron
size for assays to multi-exon genes that have the probe spanning an
exon-exon boundary. Although a penalty for small intron size can be
integrated into the genome_HomoHIT rule, a separate rule also
penalizes primer/probe sets that span introns of small size. This
reduces the possibility of competition for reagents in RNA samples
contaminated with genomic DNA, and also decreases the chance of
amplifying incompletely spliced transcripts. The intron penalty can
be based on the size of the intron: the larger the intron, the
smaller the penalty.
[0408] Linking Assays to Transcripts:
[0409] A large number of BLAST searches against a variety of
databases can be performed during the assay design process, as
outlined above. In one non-limiting example, as many as about 100
BLAST results can be stored for each assay. The BLAST files that
can be loaded into TaqDB contain the mismatch information resulting
from the comparison of the primers and probe to these various
databases. When there is a BLAST file showing a perfect match
(0,0,0) to a transcript (this will, by definition, occur for the
transcript from which the assay was originally designed) then a
link can be created in the database between the assay and the
accession ID of that transcript. When there are additional
transcripts that perfectly match the primers and probe, they can
also be added to the database and "virtually" linked to that
particular assay. These links can be considered virtual because
they can be links to transcripts that the assay was not originally
designed to detect, but which it will detect. Alternative splice
forms of a particular gene are the most common source of virtual
links. Cross referencing all of the BLAST files with all of the
assays in this manner allows the creation of many-to-many
relationships between assays and transcripts, thus defining which
transcripts an assay may amplify. As a result of this process, an
assay can match multiple transcript accession IDs, for example,
multiple RefSeq entries. In addition, other BLAST files that
contain small mismatches can also be loaded into the database and
linked to the assay as BLAST quality control data.
[0410] The assay-to-many-transcripts relationships can be displayed
on the website online ordering system so that a researcher will
have information on all of the transcripts an assay will detect,
prior to purchasing the assay.
[0411] Remapping:
[0412] Transcript databases change over time inasmuch as new
transcripts are continually being discovered, and occasionally
entries that were originally thought to be transcripts can be found
to be faulty and can be purged. In certain configurations, in order
to keep the collection of assays current, BLAST searching can be
used to map the assays to the new set of transcripts after a new
transcript database is released (e.g., RefSeq is updated
approximately every four weeks). This process keeps the information
current through the identification of every known transcript that a
particular assay can amplify, and it also allows the removal of any
assay in the collection that no longer maps to the up-to-date
transcripts. An additional benefit of the remapping process is that
it is not necessary to design assays for every sequence in every
transcript database. Rather one can often find a link from an
existing assay to new sequences, and thus save time in delivery of
assay products to researchers.
[0413] Data Mining:
[0414] From failure analyses, it can be possible to recognize
oligonucleotide sequences that can be problematic so that
subsequently assays can be designed to be robust 5' nuclease
assays. Thus, a database containing failed assay designs can
provide a basis for improving the design process. For example,
extracting the oligonucleotide sequences from assays that failed in
the manufacturing process (e.g., quantitation, or analytical
quality control) allows comparison of problematic sequences to
identify commonalities. Certain types of sequences may tend to be
difficult to manufacture and such difficult to manufacture
sequences can be assessed a penalty for oligonucleotides containing
such problematic sequences. This in turn, decreases the failure
rate in subsequent manufacturing, and results in better functional
assays.
[0415] Evaluation of Designed Assays:
[0416] In a non-limiting example of an assay design process, over
16,000 RefSeq transcripts were run through the assay design
process. From these transcripts, 13,633 assays were sent to
manufacturing. There are .apprxeq.2000 transcripts for which no
order was to manufacturing, and these assays fall into the
following categories:
[0417] 1. No assay designed
[0418] 2. No designed assay passes the current penalty cut-off
[0419] a. intron size penalty (multi-exon genes only)
[0420] b. Transcript penalty
[0421] c. Genome penalty
[0422] Although many of the assays that do not pass the in silico
quality control standards may be suitable assays under certain
circumstances, especially rigorous standards can be used in certain
embodiments, to avoid manufacturing assays that have the potential
to produce difficult-to-interpret quantitative gene expression
results. There can be a variety of reasons why a designed assay may
not be a robust assay for quantitative determination of mRNA
transcript levels in a particular RNA sample. Thus, not all of
these in silico quality control steps may be important to all users
of an assay, but it can be, nevertheless desirable to provide the
most robust quantitative assays that will fit the requirements of
the entire spectrum of sample types and sample preparation
methodologies utilized by the broad range of users of a particular
assay.
[0423] Table 1 provides an example of how the process works,
showing all of the assays designed across the exon-exon boundaries
of the human plakophilin 4 (PKP4) mRNA (RefSeq ID
NM.sub.--003628).
6TABLE 1 Assay Final Design Intron Transcript Genomic RefSeq ID
AssayID Score Score Penalty Intron Size Penalty Penalty Status
NM_003628 Hs00269305_m1 High High 0 >10 Kb 0 0 Ordered
Hs00269306_m1 High High 0 >10 Kb 0 0 N.O. Hs00269307_m1 High
High 0 >10 Kb 0 0 N.O. Hs00269308_m1 mid High High <200 bp 0
0 N.O. Hs00269309_m1 High High 0 >3 Kb 0 0 N.O. Hs00269310_m1
High High 0 >3 Kb 0 0 N.O. Hs00269311_m1 Low High Low >1 Kb 0
High N.O. Hs00269312_m1 Low High 0 >10 Kb 0 High N.O.
Hs00269313_m1 Low High 0 >3 Kb 0 High N.O. Hs00269314_m1 Low
High Low >1 Kb High High N.O. Hs00269315_m1 Low High High
<200 bp 0 High N.O. Hs00269316_m1 Low High 0 >2 Kb 0 High
N.O. Hs00269317_m1 Low High 0 >3 Kb 0 High N.O. Hs00269318_m1
Low High High <200 bp 0 High N.O. Hs00269319_m1 High High 0
>2 Kb 0 0 N.O. Hs00269320_m1 High High Low >1 Kb 0 0 N.O.
Hs00269321_m1 Low High Low >1 Kb 0 High N.O.
[0424] As shown in the table, seventeen assays were designed for
this transcript. Of the 17 assays designed, only the top-scoring
assay that had no design penalties assigned was sent to
manufacturing. However, there are six other candidate assays that
met the manufacturing quality control cut-off for this particular
target that can be chosen if for some reason the top-scoring assay
fails along the downstream manufacturing and functional testing
processes. Of the assay designs that did not pass the in silico
quality control cut-off, one had a mid-level score because it was
designed over an intron shorter than 200 bp. The rationale for this
penalty score is that if the assay was being used to detect the
transcript in a total RNA sample contaminated with genomic DNA,
then the contaminating genomic DNA could be co-amplified with the
mRNA target, potentially leading to inaccurate quantitation of the
mRNA template. The likelihood of this occurring is low, since the
primers are at 900 nM each in the final reaction and the probe does
not detect genomic DNA, but these assays can be still penalized to
provide a robust assay to the customers. Co-amplifying targets that
do not bind to the probe will not interfere with quantitation when
present in small amounts. Such targets can be often spiked into a
reaction to serve as Internal Quantitation Controls (IQC) for
quantitation (Furtado et al., N. Engl. J. Med. 340:1614-1622, 1999;
Mulder et al., J. Clin. Microbiol. 32:292-300, 1994). Ten of the
assays designed to the PKP4 target received a low final score
because the primers/probe sequences for these assays exhibited high
homology to at least one other portion of the genome. This penalty
signals one of three possible situations: 1) that the domain which
these exons encode is conserved and is present in other genes, 2)
that there exists at least one pseudogene elsewhere in the genome,
or 3) that there is random sequence at another site in the genome
with very high homology to these particular exon sequences.
Regardless of the reason, the potential exists for these
low-scoring assays to generate less accurate quantitative results
in a total RNA sample contaminated with genomic DNA than in a
highly purified RNA sample. This points to the need for
high-quality RNA template preparation upstream of any RT-PCR
methodologies.
[0425] In some configurations, gene expression products ordered by
a requestor on demand can be available from the supplier with a FAM
label and the TaqMan.RTM. MGB probe technology, which utilizes a
nonfluorescent quencher for improved sensitivity and quantitation
precision. Addressing of the whole collection of human genes can be
facilitated by advantageously utilizing the design flexibility of
the shorter MGB probes. Also, in some configurations, TAMRA TaqMan
probes can be made available to requestors by the supplier of
customized products.
[0426] PCR efficiency of a given assay (or PCR reaction) can be
defined as follows. An assay that results in a doubling of the
amplicon with each PCR cycle has an efficiency of 100%. Efficiency
can be of interest when using the comparative Ct method of
quantification. One assumption in the equations used to calculate
fold-differences by the comparative Ct method is that the
assays/genes being compared must be of equivalent efficiency. A
test can be conducted in some configurations to find outliers,
i.e., assays of clearly poor efficiency, which may result from
design, as opposed to contamination. Subsets of genes designed and
tested for high efficiency can be offered in some
configurations.
[0427] Ordering Gene Expression Assays:
[0428] As discussed above, if the user desires at block 12 (see
FIG. 1) to obtain stock assays for gene expression experimentation,
the user can be directed through a series of inquiries at block 16
in which information regarding the nature of the gene expression
assays can be collected.
[0429] In some configurations, custom gene expression assays made
available for purchase may be selected by accession number (NCBI
RefSeq ID) gene name, gene family, and/or functional groups and
categories. For example, "Oncogene" is a category comprising three
groups. For each group, some configurations provide a list of
assays that a requestor can order as a set or individually. If a
requestor does not find their particular gene expression assay of
interest, the requestor can check back on a regular basis to
determine if a new assay has become available for the gene
expression of interest. Alternatively, a requestor may use the by
design service. In some configurations, stock assays and custom
assay designs can be made available for key splice variants. In
addition, other search options and information associated with
assays can be made available as desired.
[0430] A non-limiting example of a window pane which initiates the
collection of information for gene expression assays is shown in
FIG. 50. In this regard, the user can be provided with a
description of a stock assay service for gene expression as well as
the products which can be received upon submission of the
information necessary to obtain the stock assay for gene
expression.
[0431] Referring to FIG. 51, if, after viewing the overview of
stock assay systems at 220, the user desires to obtain ordering
information regarding stock assays for gene expression as indicated
by block 222, ordering information can be then provided to the user
at block 224. In this regard, the user can be provided with
information regarding the contents of the assay which will be
provided as well as technical information regarding the assay. In
addition, information regarding the volume and reactions to produce
can be provided as well as the necessary instrument platform. Part
number information can also be available for the assay, as well as
part numbers for related equipment. In one non-limiting example,
the user can be informed of the components of the gene expression
assays which will be received by the user. An exemplary window pane
in which this information is provided to the user is shown in FIG.
52.
[0432] The user may also be able to request documentation from the
system as indicated in FIG. 51 at decision block 226. If at block
226 the user requests documentation regarding gene expression
assays, the system delivers documentation regarding the stock assay
at block 228. This information may be brochures, product bulletins,
user bulletins as well as other type of instructional or other
information. This information may be delivered either via download,
fax, e-mail or hard copy. A representative window pane illustrating
the manner in which documents may be delivered to the user is shown
in FIG. 53. In some configurations, the user may be able to select
for delivery any number of the listed documents in any or all of
the available formats for delivery.
[0433] Further, the user may also be able to request reference
information at decision block 230. If the user requests reference
information at decision block 230, the user can be provided at
block 232 with reference information which may be links to publicly
available databases. For example, the user at block 232 may be
linked to the NCBI Reference Sequence Project (RefSeq) database. It
is to be understood, however, that other suitable database may be
referenced.
[0434] The user may also decide to search gene expression assays as
represented by block 230. If the user decides to search gene
expression assays at block 234, the user can be requested to accept
certain terms and conditions of use for the assay search at block
240 (see FIG. 54). In addition to providing terms and conditions of
use, the user can also be requested to provide information
concerning the user such as name, institution, e-mail, phone number
and/or address. In addition, the user can also be asked at block
240 whether the user would like information regarding products or
services. A representative window pane is shown in FIG. 55.
[0435] If the user accepts the terms and conditions of use, the
user can be directed at block 242 to a window pane which allows the
user to search for stock assays for gene expression products. An
exemplary window pane is shown in FIG. 56. The user can be then
given the opportunity to search for gene expression assays by
various techniques. For example, the user may at decision block 242
use keyword searching to find assays by searching for keywords such
as gene name, gene symbol or gene ontology classification. If the
user selects a keyword search at decision block 242, a keyword
search can be conducted at block 244 as more fully disclosed below.
The user may also decide to conduct a batch ID search at block 246
so as to find assays by searching for multiple accession numbers
from public or private sources such as, for example, from Celera,
Applied Biosystems or public databases. If the user selects to
perform a batch ID search at block 246, a batch ID search can be
performed at block 248 as will be more fully disclosed below.
Finally, the user may decide to perform a classification search at
decision block 250 to find assays by a suitable classification
system such as the Celera Panther protein classification
system.
[0436] If the user selects to perform a keyword search at block
242, the user may be able to perform either a basic or an advanced
keyword search. If a basic keyword is to be performed, the user is
able to select the search field in which the search is to be
conducted, as well as enter a specific search term. The specific
fields which can be searched include the non-limiting examples:
[0437] Gene Symbol
[0438] Gene Name
[0439] RefSeq Accession
[0440] Panther Function
[0441] Panther Process
[0442] GO Function
[0443] GO Process
[0444] GO ID
[0445] AB Assay ID
[0446] Celera gene (hCG)
[0447] Celera transcript (hCT)
[0448] Celera protein (hCP)
[0449] LocusLink ID
[0450] GenBank Nucleotide ID
[0451] GenBank Protein ID
[0452] Species
[0453] Chromosome
[0454] Cytoband
[0455] RefSeq GI
[0456] A non-limiting example of a window pane which permits the
entry of information for basic keyword searching is shown in FIG.
57.
[0457] If an advance keyword search is selected by the user, the
user can insert search criteria for all of the fields described
above. A non-limiting example of a window pane which permits entry
of information for advanced keyword searching is shown in FIG.
58.
[0458] If the user determines that it is desirable to conduct a
batch ID search at block 246, a batch ID search can be conducted at
block 248. The batch ID search finds assays by using a list
identification numbers. In this regard, the user is able to search
by identification numbers from a variety of sources such as:
[0459] RefSeq accession number
[0460] GenBank Protein (GenPept) accession number
[0461] GenBank GI number
[0462] LocusLink
[0463] LocusLink gene symbol
[0464] Celera Gene (hCG)
[0465] Celera Transcript (hCT)
[0466] Celera Protein (hCP)
[0467] AB Assay ID
[0468] The information can be entered in a number of formats such
as, for example, the identification numbers can be separated by
either a, tab, carriage return, line return, comma or space. In
addition, it is possible to upload a file containing the
identification numbers, or identification numbers, such as a file
which was previously exported following a gene expression search.
An exemplary window pane which allows the user to enter information
for a batch ID search is shown in FIG. 59.
[0469] Finally, the user may,also be able to decide at block 250
whether a classification search, such as using the Celera panther
classification system, is be conducted. The Celera Panther
classification system is a system for classifying and predicting
the functions of proteins in the context of sequence-relationships
(see for example, U.S. patent application Ser. No. 60/[serial
number not yet assigned] filed Dec. 14, 2002, Attorney Docket No.
9692-30USB, entitled "Methods for identifying, viewing, and
analyzing syntenic and orthologous genomic regions between two or
more species," which is hereby incorporated by reference in its
entirety). Assays can be assigned to a Panther category based upon
a match to equivalently assigned Celera gene data. The Panther
categories can be constructed up to three levels deep with assay
assignments at any one of the three levels.
[0470] If the user desires to perform a classification search at
block 250, a classification search can be conducted at block 252.
The user is then able to search by molecular function categories
involving a property of the protein or of a particular biochemical
reaction performed by a protein, such as receptor, kinase or
hydrolase. In addition, the user may also be able to search by
biological process categories involving the biochemical reactions
that work together towards a common biological objective. The
process can be at the cellular level, such as glycolysis and signal
transduction, or at the system level, such as immunity and defense,
in sensory perception.
[0471] An example of the manner in which a classification search at
block 252 can be conducted is shown in FIG. 60. In this regard, the
user initiates a classification search at block 256. After the user
initiates the classification search, the user decides whether the
classification is to be conducted with respect to molecular
function or biological process at block 258. An exemplary window
pane which allows the user to make this selection is shown in FIG.
61. If the user decides at block 258 to search by molecular
function, then the user may be able to review a hierarchy of
molecular functions until a set of assays can be presented to the
user for the desired molecular function. In this regard, the user
selects at block 260 a category of molecular functions. The
processing then proceeds to block 262 to allow the user to decide
whether the hierarchy search has been completed. This can occur if
there are no further subclassifications within the category
searched. For example, if the category of molecular function which
is selected is "receptor", there are seven categories associated
with this molecular function, including three subcategories (i.e.,
protein kinase receptor, cytokine receptor and ligand-gated ion
channel receptor). An exemplary window pane showing the categories
associated with the receptor molecular function is illustrated in
FIG. 62. If at block 262, the user has decided to search a
subcategory of molecular function, the user then selects another
specific molecular function at block 260. For example, if the user
selects the subcategory of "protein kinase receptor" as shown in
FIG. 63, an exemplary window pane as shown in FIG. 64 may be
displayed indicating the categories of protein kinase receptors.
When the user has completed the hierarchal search at block 262, the
user can then identify and order the assay at block 264.
[0472] Similarly, the user can select at block 258 to conduct a
search based on biological processes. If the user makes the
selection, the user selects one of a number of broad categories of
biological processes which the system provides to the user at block
266. An exemplary window pane showing the biological processes from
which the user may select is illustrated in FIG. 65.
[0473] After selecting one of the broad categories of biological
process at block 266, the user determines whether the search
hierarchy has been completed at block 268. If the user has not
completed the search hierarchy (i.e., the relevant biological
process displayed to the user contains subcategories), the user
then again selects one of the subcategories at block 266. If the
user has completed this search hierarchy at block 268, the user
then identifies and orders the assay at 270.
[0474] A non-limiting example of a classification search relating
to biological processes is shown in FIG. 66. In this example, if
the user selects the biological processes associated with apoptosis
at block 266, the user is presented with a window pane similar to
that shown in FIG. 66. The user then may select the category
associated with the particular field of interest and the assays
associated therewith by clicking on the number associated with the
number of assays column.
[0475] After the user inputs the search information, the results of
the search can be provided to the user. One non-limiting example of
a window pane providing results to the user is shown in FIG. 67. In
this regard, the user can be provided with the assay ID, the RefSeq
ID, the LocusLink gene name, function, process, Celera ID and
location for the assays that satisfy the search criteria. The user
may sort the results alphabetically by depressing any of the
captions associated with each column. The window pane also includes
check boxes allowing the user to select one or more particular
assays which can then be added to the users "Shopping Basket" after
login, for subsequent purchase. The user can also select one or
more assays to be exported for purposes of, in non-limiting
example, archiving or sequence comparison analyses conducted
"off-line." A link can also be present which allows information
regarding the associated gene to be obtained from third party or
public databases, such as NCBI LocusLink. In addition, the user can
obtain information concerning the molecular function and/or
biological processes associated with the gene detected by the
assay.
[0476] If the user selects a given assay, information concerning
this specific assay can be presented in a manner similar to that
shown in FIG. 68. In this regard, the information regarding the
specific gene identification and location can be given as well as
information regarding its biological significance. In particular,
the information provided concerns both the molecular function as
well as the biological processes which can be present.
[0477] In some configurations, endogenous controls can be available
for relative quantitation of gene expression. For easy
identification and ordering, the controls can be highlighted in the
ordering system in some configurations.
[0478] Stock Assays: SNP Genotyping
[0479] In some configurations, at least 40,000 stock SNP genotyping
products can be available. In some of these configurations, at
least 77,000 such products can be available. In some of these
configurations, at least 150,000 such products can be available,
and in some of these configurations, at least 200,000 stock SNP
genotyping products can be available.
[0480] In various configurations, SNP genotyping products can
include, for example, 2 primers and 2 probes, each probe having a
different label such as vic or fam, in a single tube, with or
without assay information which can be provided on CD or other
media. Various configurations can include some or all of the
above.
[0481] In various configurations, at least 40,000 assays can be
available using TaqMan.RTM. MGB probe technology under universal
assay conditions. In some of these configurations, at least 150,000
such assays can be available, and in some of these configurations
at least 200,000 assays can be available using TaqMan.RTM. MGB
probe technology under universal assay conditions.
[0482] SNP Genotyping Assay Preparation:
[0483] In some configurations, SNP detection products include
off-the-shelf assays. Various configurations use 5' nuclease
chemistry with TaqMan.RTM. MGB probes and/or operate with universal
formulation and thermal cycling parameters (for example, in some of
these configurations, 900 nM primers, 250 nM probe). Some
configurations provide assays designed utilizing a bioinformatics
pipeline that includes private and public data, such as a
combination of Celera data and public data, or either private data
or public data alone.
[0484] The design of SNP genotyping assays can be similar to the
design of gene expression assays in a number of aspects In some
configurations, each SNP assay can include two unlabeled
oligonucleotide primers and two TaqMan.RTM. probes, each probe
having a fluorophore, a fluorescence quencher, and a minor groove
binder. Assay design can include selection of SNPs for assay design
in a pre-processing selection process, design of the primers and
probes, and in silico quality control prior to manufacture of the
primers and probes.
[0485] Pre-Processing: In some configurations, certain sequence
regions within the transcript can be identified in the
pre-processing step for designing the oligonucleotide primers and
probes for a 5' nuclease assay as described above for gene
expression assay design. Repetitive and low complexity regions in
can be masked (i.e. nucleotides replaced by an N) along with any
SNP other than the SNP for which the assay is to be designed.
Non-limiting examples of repetitive sequences which can be masked
include simple repeats (di- and tri-nucleotide repeats), Alu
restriction site repeats, long interspersed nuclear elements
(LINEs), and short interspersed nuclear elements (SINEs).
[0486] SNPs can be identified in a gene region by performing a
BLAST analysis against genomic databases using methods known in the
art (see Altschul et al., J. Mol. Biol. 215:403-410, 1990), or can
be identified in a SNP database (for example, the dbSNP database
accessible at http://www.ncbi.nlm.nih.gov/SNP/). If discrepancies
are discovered, discrepancy masking steps can be used to help
ensure that no oligonucleotide primers or probes are designed over
ambiguous nucleotide(s).
[0487] Assay Design: The SNP assay design can be based upon
specifications such as optimal T.sub.m requirements, GC-content,
buffer/salt conditions, oligonucleotide concentrations, secondary
structure, optimal amplicon size, and reduction of primer-dimer
formation as described above for gene expression assays.
[0488] In silico Quality Control: In some configurations, after
design, primer and probe sets can be processed through a quality
control step. This process, although conceptually similar to that
described above for gene expression assays, involves quality
control steps applicable to SNP genotyping assays as described
below. The quality control step penalizes an assay at each phase of
testing to generate a penalty score specific to a given assay
design. A final penalty score for each assay design comprises the
sum of each of the individual penalty scores. The assay design with
the lowest cumulative penalty score for each SNP can be the assay
that is chosen for manufacturing.
[0489] In some configurations, the in silico quality control
process for SNP genotyping assays can involve genome BLAST scoring,
which involves determining the degree of homology, through BLAST,
between the assay and non-self regions of genomic DNA (e.g.
homologous genes and pseudogenes). A penalty can be assigned if an
assay hits a second (or greater number) physical location on the
genome in addition to the location of the gene-of-interest.
[0490] For all BLAST searches, a quality control query construct
can be made by generating an amplicon sequence that includes each
of the two primers and the intervening probes; the amplicon can be
created by padding the specific number of nucleotides between the
primers and the probes with N's. The quality control query
construct for each 5' nuclease assay can be BLASTed against a
genomic database to ensure that 1) each primer/probe set in the
quality control query sequence matches perfectly to the target SNP
sequence (except for the SNP alleles in the probes), and that 2)
each assay is specific for the SNP of interest and will not detect
SNPs from any other regions of the genome. Primers with homology to
other genes (with an intervening homologous probe) can produce an
unwanted fluorescent signal, and thus mask the analysis of a true
SNP. Primers to homologous genes (without an intervening homologous
probe) may amplify homologous genes in addition to the gene
comprising the target SNP and cause competition for reagents in the
PCR reaction, causing spurious results. If homology exists, an
assay can be assigned a penalty score based on the degree of
homology to other SNPs. Two sets of numbers can be reported in this
SNP BLAST step and are described below.
[0491] (a) BLAST hit to self.
[0492] The high scoring pair (HSP) from this BLAST can produce a
match of 100% homology with self. This HSP represents the alignment
of the quality control query construct to the target SNP in a SNP
database, and shows a "0 0 0" (representing 0 mismatches in the
forward primer sequence, 0 mismatches in the probe sequence (except
for the SNP allele), and 0 mismatches in the reverse primer
sequence) when BLASTed against the database from which the target
SNP was retrieved. If the quality control query construct has no
hits against any SNP in a SNP database, then the mismatch can be
reported as "50 50 50" (an artificially high mismatch value) and
the assay can be flagged as being problematic.
[0493] (b) Continuous BLAST hits to non-self SNPs.
[0494] In this set of BLAST results the top non-self HSPs can be
reported (i.e. BLAST results to homologous SNPs). The highest
penalty can be assigned to the HSP that is the closest homolog but
that is not a perfect match to the quality control query construct.
If two HSPs have the same homology score to the query construct,
then the one with the higher homology to the probe region can be
chosen as the top hit.
[0495] Two or more highly homologous genes may end up with an
identical assay design in regions where the genes have identical
sequence. If two or more highly homologous genes have identical
assays designed (for example, in a region where the two different
genes have identical sequence) then the assays can be assigned a
large penalty because it can be assumed that a second hit is to a
separate and distinct gene.
[0496] Linking Assays to SNPs:
[0497] A large number of BLAST searches against a variety of
databases can be performed during the assay design process, as
outlined above. In one non-limiting example, about 100 BLAST
results can be stored for each assay. The BLAST files that can be
loaded into a database such as TaqDB contain the mismatch
information resulting from the comparison of the primers and probes
to these various databases. When there is a BLAST file showing a
perfect match to a set of primers and SNP probes (this will, by
definition, occur for the SNP from which the assay was originally
designed) then a link can be created in the database between the
assay and the accession ID of that SNP. When there are additional
SNPs that perfectly match the primers and probe, they can also be
added to the database and can be "virtually" linked to that
particular assay. These links can be considered virtual because
they can be links to SNPs that the assay was not originally
designed to detect, but which it will detect. Cross referencing all
of the BLAST files with all of the assays in this manner allows
creation of many-to-many relationships between assays and
transcripts, thus defining which SNPs an assay may amplify. As a
result of this process, an assay can match multiple SNP accession
IDs, for example, multiple RefSeq entries. In addition, other BLAST
files that contain small mismatches can also be loaded into the
database and linked to the assay as BLAST quality control data.
[0498] The SNP to genome relationships can be displayed on the
online ordering system so that a researcher will have information
on the SNP prior to purchasing the assay (see, for example, FIG.
76).
[0499] Remapping:
[0500] In certain configurations, BLAST searching can be repeated
for SNP genotyping assays as updated SNP databases are released in
a manner similar to that described above for gene expression
assays. This process keeps the information current through the
identification of every known SNP that a particular assay can
amplify, and it also allows the removal any assay in the collection
that no longer maps to the up-to-date SNPs. In addition, it can
often be the case that a link from an existing assay can be found
to new sequences identified in an updated SNP database, thus saving
time in delivery of assay products to researchers.
[0501] Data Mining:
[0502] In certain configurations, as was described above for gene
expression assays, analysis of assay design failures can be
performed to provide information for improving the design process.
This decreases the failure rate in subsequent manufacturing, and
results in better functional assays.
[0503] Evaluation of Designed Assays:
[0504] In a non-limiting example of an assay design process,
several hundred thousand SNPs were run through the assay design
process. From these SNPs, over 100,000 assays were sent to
manufacturing. There can be many SNPs for which no order has been
sent to manufacturing, and these assays fall into the following
categories:
[0505] 1. No assay designed
[0506] 2. No designed assay passes the current penalty cut-off
[0507] Although many of the assays that do not pass the in silico
quality control standards may be suitable assays under certain
circumstances, especially rigorous standards can be used in certain
situations, to avoid manufacturing assays that have the potential
to produce difficult-to-interpret results. There can be a variety
of reasons why a designed assay may not be a robust assay for a
SNP. Thus, not all of these in silico quality control steps may be
important to all users of an assay, but it can be, nevertheless
desirable to provide the most robust quantitative assays that will
fit the requirements of the entire spectrum of sample types and
sample preparation methodologies utilized by the broad range of
users of a particular assay.
[0508] Ordering SNP Genotyping Assays:
[0509] If the user desires to obtain a stock assay for SNP
genotyping products, the user selects this feature at block 12, as
shown in FIG. 1. When a user selects a stock assay for SNP
genotyping, the user can be directed through a series of inquiries
at block 18 in which information regarding the nature of the SNP
assay can be collected. An exemplary window pane, which provides
the user with an overview of the Stock Assays for SNP genotyping
products is shown in FIG. 69.
[0510] After the user reviews an overview of the stock assay system
for SNP genotyping at block 272 (see FIG. 70), the user decides
whether it would be useful to review ordering information at block
274. If the user desires to review ordering information, the system
provides the user with ordering information at block 276. The
ordering information includes the part number of the SNP genotyping
product, as well as the contents of the assay. For example, the
ordering information may include the following:
[0511] Pre-formulated Assays (187.5 .mu.L, 20.times. mix)
[0512] 2 unlabeled primers
[0513] 1 FAM.TM. dye-labeled TaqMan.RTM. MGB probe
[0514] 1 VIC.RTM. dye-labeled TaqMan.RTM. MGB probe
[0515] Compact disk containing:
[0516] Protocol
[0517] Product insert hard copies of these documents can also be
provided.
[0518] Assay Information File containing: sales order number, well
location, assay ID, vial ID, Celera ID, gene name, gene symbol,
category, category ID, group name, group ID, chromosome,
cytogenetic band, NCBI gene reference, NCBI SNP reference, SNP
minor allele frequencies, SNP type, context sequence, reporter
dyes
[0519] With each order:
[0520] 2-D barcode laser-etched on the bottom of each assay
tube
[0521] 1-D barcode printed on each rack of tubes
7 Instrument platform: 7900 HT 7700, 7000 Reaction volume: 5 .mu.L
25 .mu.L Reactions/tube 750 150
[0522] The user may also be able to also order documentation
describing the SNP genotyping products. In this regard, the user
selects to order documentation at block 278. If the user selects to
order documentation at block 278, documentation relating to SNP
genotyping assays can be provided to the user at block 280. In
particular, the documentation can be provided by a window pane in a
manner similar to that associated with gene expression assays (see
FIG. 53).
[0523] In addition, the user may also be able to decide whether the
user would like to receive reference information at block 282. This
information may include the general steps for using SNP genotyping
products as well as for providing general information regarding
allele frequency. If the user decides to obtain reference
information at block 282, the user can be provided with this
information at block 284. In addition, the user may be able to
search for assays used for SNP genotyping at block 286. If the user
decides to search for assays at block 286, the user conducts a
search at block 288.
[0524] Referring to FIG. 77, after the user accepts the terms and
conditions of the search at block 292, the user can be then given
the opportunity to search for SNP genotyping assays by various
techniques. For example, the user may at decision block 294 use
keyword searching to find assays by searching for keywords, such as
gene name, gene symbol or gene ontology classification. If the user
selects a keyword search at decision block 294, a keyword search
can be conducted at block 296 as more fully disclosed below. The
user may also decide to conduct a location search at block 298 so
as to find assays. If the user selects to perform a location search
at block 298, a location search can be performed at block 300, as
will be more fully disclosed below. Finally, the user may decide to
perform a batch ID search at decision block 302 to find assays by
searching for multiple accession numbers from public or private
sources such as, for example, from Celera, Applied Biosystems or
public databases. If the user selects to perform a batch ID search
at decision block 302, then a batch ID search can be performed at
block 304. Finally, the user may decide to exit the system at block
306.
[0525] If the user decides to perform a keyword search at block 294
with respect to SNP genotyping, the user is able to search by
selective fields for select terms. The specific fields which may be
searched can be as follows:
[0526] dbSNP rs#ID
[0527] dbSNP ss#ID.
[0528] Gene Symbol
[0529] LocusLink Gene Name
[0530] RefSeq Accession
[0531] AB Assay ID
[0532] Celera SNP (hCV)
[0533] Celera gene (hCG)
[0534] Celera transcript (hCT)
[0535] Celera protein (hCP)
[0536] Chromosome
[0537] Cytoband
[0538] LocusLink ID
[0539] In addition, it is possible to filter the search by the
specific SNP type which include:
[0540] acceptor splice site
[0541] coding region
[0542] donor splice site
[0543] intergenic/unknown
[0544] intron
[0545] mis-sense mutation
[0546] nonsense mutation
[0547] putative utr (untranslated region) 3
[0548] putative utr 5
[0549] repeats
[0550] silent mutation
[0551] utr 3
[0552] utr 5
[0553] In addition, it is possible to search all these SNP types
together.
[0554] In addition, the system also permits the use of a filter to
exclude 10 kb flanking sequence. For a given gene, all the RefSeq
sequence data associated with the gene in LocusLink are mapped on
the genome. A gene may be defined as the furthest 5' and furthest
3' base of RefSeq sequence data associated with the gene. When
searching on gene-related fields, the user may choose whether to
include or exclude 10 Kb flanking sequence. Accordingly, when the
system searches it can include up to 10 Kb of upstream sequence and
downstream sequence in the query. This filter can be valid for the
following fields:
[0555] Gene Symbol
[0556] LocusLink Gene Name
[0557] RefSeq Accession
[0558] Celera Transcript (hCT)
[0559] Celera Protein (hCP)
[0560] Celera Gene (hCG)
[0561] LocusLink ID
[0562] In certain configurations, the system will ignore this
filter if the user searches on fields not listed above. If
searching for SNP assays by Celera Gene (hCG) ID, a user can select
a search within a gene by setting a search filter at 0 Kb or within
a gene region which includes 10 Kb of 5' and 3' flanking sequence.
An exemplary window pane permitting the user to perform a keyword
search with search filter is shown in FIG. 71.
[0563] Alternatively, it can also be possible to perform an advance
keyword search in which search terms can be placed in one or more
various field for SNP genotyping as described above. An exemplary
window pane allowing the user to perform an advanced keyword search
is shown in FIG. 72.
[0564] In addition, the system also allows users to select ranges
of Caucasian and African-American minor allele frequency. The
allele frequency indicates the number of occurrences of an allele
seen in the total number of chromosomes sequenced at the SNP site.
The allele frequency for stock assay SNP genotyping products may be
obtained from 90 individual human genomic DNA samples, 45
African-Americans and 45 Caucasian from the Coriell Human Variation
collection. The samples can be run in a validation laboratory in
order to ensure that every SNP provided in the stock assay SNP
genotyping product is polymorphic and that the allele frequency can
be adequate for association studies in a variety of populations.
The results obtained from such a validation step also allow
inference of haplotype blocks and the analysis of the extent of
linkage disequilibrium among these makers. A selection and
validation criteria for a set of SNP Genotyping Assays is described
in Francisco de la Vega, et al., "Selection of Single Nucleotide
Polymorphisms for a Whole Genome Linkage Disequilibrium Mapping
Set". To access the poster, go to www.allsnps.com.
[0565] When the user selects to search by location at a block 298,
the user initially selects the mapping type and relevant
identification information at block 300. In this regard, the user
can select the assay by SNP, gene or marker location within a given
range. Alternatively, the SNP assay may also be determined on the
position of the chromosome. This can be done by initially selecting
the available chromosome and then the position within the
chromosome, which may be reported in units of megabases.
Alternatively, the SNP assay may be determined by location using
ABI PRISM.RTM. Linkage Mapping Sets v2.5. ABI PRISM.RTM. Linkage
Mapping Sets v2.5 consist of 811 fluorescent-labeled PCR markers
selected to amplify high informative two base-pair repeat
microsatellite loci. These markers can be arranged in two sets to
provide coverage of the human genome at 5 C.sup.M and 10 C.sup.M
average resolution. The markers can be from the 1996 Genethon Human
genetic map and were selected based on chromosomal location and
heterozygosity. More information regarding ABI PRISM.RTM. Link
Mapping Sets v2.5 can be obtained from Applied Biosystems.
[0566] After the mapping type and identification information has
been entered, the user also has the opportunity to select flanking
region display results. A flanking region of 10 Kb can be selected,
or alternatively, the system can be configured so that the user can
select 0 Kb, 100 Kb, 500 Kb, and 100 Mb. Finally, the user may be
able to filter the results using Caucasian and African-American
minor allele frequency as well as SNP type. An exemplary window
pane allowing the user to search by location is shown at FIG.
73.
[0567] Finally, the user can also decide whether to search for SNP
genotyping assays using a batch ID search at decision block 302. In
this regard, the user enters a valid ID type into the system at
block 288. The valid ID types can be, for example, one or more of
the following.:
[0568] dbSNP reference cluster or assay ID
[0569] Celera hCV
[0570] AB Assay ID
[0571] LocusLink gene symbol
[0572] RefSeq accession number
[0573] Celera Gene (hCG)
[0574] Alternatively, the user can upload a file on the user's
computer from a previously exported results from a SNP genotyping
search. In this case, if the file contains a list of identification
numbers, each of the identification numbers can, in various
embodiments, be separated by a tab, a carriage return, a line
return, a comma or a space. If the user selects to use previously
exported assays results, then a tab delimited file resulting from
the stock assay export feature may be used. An exemplary window
pane allowing the user to conduct a batch ID search is shown in at
FIG. 74.
[0575] The results from a SNP genotyping assay search can be
provided to the user in a manner similar to that described above
for gene expression assays. One non-limiting example of a window
pane providing results to the user is shown in FIG. 75. In this
regard, the user can be provided with the dbSNP ID, the LocusLink
gene location by name and symbol, the absolute position, the
distance to the next SNP, the main minor allele frequency in
Caucasians and African-Americans as well as the Celera ID. The
window pane also includes check boxes which allow the user to
select one or more particular assays for order by added those
assays to the users "Shopping Basket". In addition, the user can
also select one or more assays and information related to the
assays for export and for further in silico work such as, in the
non-limiting examples, archiving or sequence comparison analyses or
for linkage to genomic databases such as NCBI LocusLink.
[0576] If the user selects a given assay, information concerning
this specific assay can be presented in a manner similar to that
shown in FIG. 76. In this regard, data can be provided such as the
specific gene associated with the assay, the gene's location, as
well as information pertaining to the gene's biochemical and
biological functions.
[0577] High Capacity Manufacturing
[0578] In various configurations, high capacity and high throughput
equipment can be used for oligonucleotide synthesis and validation.
Manufacturing activity can be process driven with well defined and
validated procedures for every step in the manufacturing
process.
[0579] DNA synthesizers are well know in the art. A DNA synthesizer
may be used to manufacture oligonucleotides beginning with a
primary residue which is the 3'-most nucleotide, anchored to a
solid support. Each additional nucleotide can then be added in the
desired order to assemble the nucleotide chain while proceeding in
the 3'-to-5' direction.
[0580] Phosphoramidite chemistry may be employed for the addition,
although alternative chemistries such as the H-phosphonate method
can be used (for review see Brown et al, "Modern machine-aided
methods of oligonucleotide synthesis", in Oligonucleotides and
Analogues a Practical Approach. Ed. F. Eckstien, IRL Press, Oxford
UK, 1995). Four steps are performed in the synthesis. The first
base is attached to a solid support which can be typically
controlled pore glass, via an ester linkage to the 3'-hydroxyl of
the base. The 5'-trityl blocking group of the base can be then
cleaved to initiate synthesis using brief treatment with an acid
such as, for example, dichloroacetic acid or trichloroacetic acid
in dichloromethane. The next monomer of the oligonucleotide being
synthesized is then added in the form of a DNA phosphoramidite in
tetrazole and coupled to the available 5'-hydroxyl group of the
first base. The resulting phosphite linkage is then oxidized to
phosphate by treatment with iodine in an aqueous solution
containing THF and pyridine to complete the first cycle of
oligonucleotide synthesis. This can be then repeated for each base
being added.
[0581] The DNA synthesizer used in some configurations of the
present invention can be capable of producing oligonucleotides in
amounts of about 40 nmol, about 0.2 .mu.mol or about 1 .mu.mol. In
various configurations, a DNA synthesizer can be used that can
produce at least about 100, at least about 200 or more primer
length oligos in 40 and 200 nmol amounts over a period of about 10
hours.
[0582] The DNA synthesizer used in some configurations of the
present invention can also be capable of attaching appropriate
fluorophores or quenchers to probes after synthesis.
[0583] For SNP assays based upon TaqMan.RTM. methods, probes and
primers can be synthesized for performing TaqMan.RTM. assays. In
certain embodiments, two TaqMan.RTM. MGB probes can be designed and
manufactured to distinguish between two SNP alleles. Each
TaqMan.RTM. MGB probes contains, in some configurations a reporter
dye at the 5' end of each probe. The reporter dyes can be any of a
number of suitable dyes, such as, for example, a VIC.TM. dye or a
b-FAM.TM. dye. Thus, for example a VIC.TM. dye can be linked to the
5' end of a first probe specific for one allele of a SNP and a
6-FAM.TM. dye can be linked to the 5' end of a second probe
specific for the second allele for use in a given assay. An MGB, as
described above, can also be included in each probe. This increases
the melting temperature (T.sub.m) without increasing probe length,
thereby permitting the design of shorter probes. The use of MGBs
results in greater differences in T.sub.m values between matched
and mismatched probes, which produces more accurate allelic
discrimination.
[0584] In certain other configurations, probes and primers of gene
expression assays can be synthesized. In some configurations a
reporter dye can be attached at the 5' end of each probe. The
reported dye can be any suitable dye, for example, a dye such as a
VIC.TM. dye or a 6-FAM.TM. dye. An MGB, as described above, can
also included in the probe. Thus, for example, one FAM.TM.
dye-labeled, TaqMan.RTM. MGB probe can be synthesized along with
two target-specific primers for use in a given assay.
[0585] In certain aspects, a quencher can also be attached to the
probes for both SNP and gene expression assays. The quencher, in
various configurations, can be an NFQ attached to the 3' end of
each probe.
[0586] In various configurations of the present invention, the
synthesized oligonucleotide can be subjected to purification
methods which may include, for example, polyacrylamide gel
electrophoresis (PAGE) for oligonucleotides of greater than 50
bases in length and high performance liquid chromatography (HPLC)
for oligonucleotides of less than 50 bases in length. A typical
anion-exchange HPLC profile of a 23-mer is shown in FIG. 78, which
shows that 90% of the output product can be the full-length
oligonucleotide.
[0587] The DNA synthesizer used in some configurations of the
present invention can be coupled to a computer which allows
conditions to be set for automatic performance the DNA
synthesis.
[0588] In some configurations of the present invention, the DNA
synthesizer used can be capable of synthesizing DNA
oligonucleotides with rapid cycle times, low reagent consumption
and reliability. One such high-capacity, high-throughput DNA
synthesizer suitable for use is the commercially available ABI 3900
DNA Synthesizer (Applied Biosystems, Foster City, Calif.).
[0589] In various configurations, a large number of at least 10, at
least 20, at least 50, at least 70 or more DNA synthesizers can be
employed in the manufacturing facility. Multiple manufacturing
facilities can also be used and the production of oligonucleotides
in the individual facilities can be coordinated if desired. The
multiple manufacturing facilities may be located in strategic
geographic sites so as to efficiently supply a world-wide
market.
[0590] Post-Manufacturing Validation and Quality Control
[0591] In various configurations of the present invention, selected
quality checks can be performed by the supplier. Quality checks may
include synthesis yield, analytical quality control (which may be
performed, for example, using mass spectrometry), functional
testing and validation testing. Validation testing can be performed
on the manufactured assay prior to delivering to the consumer to
verify that the assay meets the specified characteristics. If the
assays do not meet the quality check or checks, they may be
resynthesized before shipping or other appropriate corrective
action taken before the assays are shipped to the requester. The
testing may include confirming that a synthesized oligonucleotide
sequence is correct by testing primers and/or probes individually
by mass spectroscopy, and/or, for human SNP assays, functionally
testing using human genomic DNA to confirm that amplification
occurs and at least one allelic discrimination cluster
(heterozygous or homozygous, compared to no template controls).
[0592] Synthesis Yield Testing:
[0593] In various configurations, each component that makes up an
assay. i.e. probes and primers, can be tested for yield after
synthesis. Such testing can be done as part of the purification
process and any suitable method known in the art can be used
including PAGE and HPLC. Ion exchange HPLC can be, in various
configurations, used for oligonucleotides having a length of less
than about 40 to about 50 bases. Such anion exchange HPLC can be
performed as an integrated function of the ABI 3900 DNA
Synthesizers (see FIG. 78 for HPLC percent yield plot).
[0594] In various configurations, individual components of assays
must meet a minimum yield specification. Such minimum yield
specification may be, for example, at least about 60% (w/w), at
least about 80% (w/w), at least about 90% (w/w) or at least about
95% (w/w) or greater expressed as the weight of the desired
oligonucleotide to the total weight of the synthesis product
multiplied by 100. The particular percent yield set as the minimum
yield specification will depend upon the application, however,
typically at least about 90% yield is desirable. Low yield
synthesis reactions, i.e. reactions producing less than about 40%,
less than about 80%, less than about 90% or less than about 95% can
be rejected in some configurations of the present invention.
[0595] In certain aspects, the synthesis yield testing can be
performed for each of the probes and primers of every assay.
[0596] Analytical Quality Control:
[0597] In various configurations, each of the probes and primers
can be individually tested to ensure the accuracy of its sequence.
Any method known in the art can be used to validate the sequence
accuracy of the probes and primers. One such method used in some
configurations of the present invention and which is adaptable to
high-throughput manufacturing and validation is mass spectrometry.
Mass spectrometry is an analytical tool that detects ions and
measures their mass to charge ratio. Ionization techniques such as
matrix assisted laser desorption-ionization and electrospray
ionization allow the measurement of high molecular weight molecules
such as DNA. The matrix assisted laser desorption ionization
coupled with time of flight mass spectrometry (referred to as
MALDI-TOF) allows high-throughput analysis of DNA molecules. One
such mass spectrometer suitable for use in analytical quality
control is the commercially available ABI Voyager-DE.TM. STR
MALDI-TOF Mass Spectrometer (Applied Biosystems, Foster City,
Calif.)
[0598] In various configurations, the DNA sample can be mixed with
an organic matrix and co-crystallized on a sample plate. A fixed,
pulsed laser beam then irradiates the sample plate. The matrix
absorbs and transfers the laser energy to the DNA to produce an
ionized gaseous phase. An electric field then accelerates the
ionized DNA molecules according to their mass such that molecules
of smaller mass are accelerated faster than molecules of larger
mass. Thus, the mass of the DNA molecule can be determined.
[0599] The measured mass can be then compared to the calculated
mass of the probe or primer. The probe or primer must be of the
same mass as calculated or within acceptable deviation to pass
specification. Acceptable deviations in various configurations of
the present invention can be, for example, such that the actual
mass of the DNA molecule may be not more than about 1%, not more
than about 2%, not more than about 5%, not more than about 10% or
not more than about 20% greater or lesser than the calculated
mass.
[0600] In some configurations, this analytical quality control test
can be performed for every assay.
[0601] Functional Testing:
[0602] In various configurations of the present invention,
functional testing can be performed on the assays as well, however,
different functional tests can be performed on the SNP assays and
gene expressions assays in some configurations.
[0603] SNP Tests:
[0604] In various configurations, all human SNP assays can be
tested on samples from a panel of at least 10 to 20 human genomic
DNA samples. A sequence detection system capable of performing the
assays of the present invention can be used. In some
configurations, the sequence detection system can be capable of
performing fluorogenic 5' nuclease chemistry assays using
TaqMan.RTM. probes. One suitable sequence detection system is the
ABI Prism.RTM. 7900HT Sequence Detection System (Applied Biosystems
Foster City, Calif.).
[0605] Reference human genomic samples can be from a mixed ethnic
group or from a single ethnic group and samples can be obtained
from human cell repositories such as the Coriell Cell Repositories
(Coriell Institute for Medical Research, Camden, N.J.).
[0606] In some configurations, a universal master mix, including
test probes and primers, can be added directly to plates of dry or
fresh DNA samples using standard robotics. Plates can be sealed and
cycled using a standard thermal cycler such as, for example,
Applied Biosystems Dual 384-well GeneAmp.RTM. PCR System 9700
thermal cycler (Applied Biosystems, Foster City, Calif.). Following
cycling, plates can be automatically read on the 7900HT Sequence
Detector. The availability of thermal cyclers such as the 9700 with
automated lid handling can increase throughput by enabling robotics
integration for 24-hour unattended operation.
[0607] In a two-allele system, TaqMan.RTM. probes for each allele
can be multiplexed in a single tube, each probe having a different
5' fluorescent dye. End-point fluorescence can be measured by the
7900HT system and experimental results can be displayed on an
allelic discrimination viewer. The discrimination viewer displays
fluorescence values of one of the dyes which represents one allele
against fluorescence values of the other dye.
[0608] Typically four clusters of points, each from a different
sample, fall into separate quadrants of a rectangle (FIG. 79). One
cluster of points will fall in a quadrant showing high fluorescence
from one dye and little or none from the other indicating samples
can be homozygous for one allele. This is the case for the squares
and triangles in FIG. 79. Another cluster will show fluorescence
from both fluorescent dyes such as illustrated with the diamonds in
FIG. 79. The fourth cluster of points, represented by circles in
FIG. 79, results from the no template control (NTC) sample.
[0609] Pseudo-SNPs can be a common problem that arises from
misassemblies, paralogs, or repeat elements. Similar sequences from
different regions in the genome may erroneously align due to
matching at only a few bases. These differing bases may then
incorrectly assumed to be SNPs. If a pseudo-SNP is genotyped, every
sample will appear to be heterozygous since each sample contains
both the pseudo-alleles (see FIG. 80)
[0610] Another problem that can arise can be the unexpected
clustering of dye intensities as shown in FIG. 81, which can be
caused by, among other things, unknown SNPs residing within the
probe or primer sequences. This makes accurate genotype decisions
difficult. Thus, in some configurations, information about the
sequence surrounding the SNP can be obtained and consulted before
attempting to design a SNP assay.
[0611] Although, clustering can be normally in four quadrants as
shown in FIG. 79, other variations are possible. For example, two
clusters can be the result of all homozygous genotypes as shown in
FIG. 82. Three clusters can result from a SNP with no rare allele
homozygotes as shown in FIG. 83. Five clusters can be produced by
the presence of an unknown SNP (FIG. 81). FIG. 84 shows scattered
clusters.
[0612] Determination of genotype can be done by a trained observer
in some configurations or by an automated system in others (see for
example, Mein et al., Genome Research 10:330-343, 2000).
[0613] In various configurations, an assay can be considered to
meet specifications if it amplifies at least one cluster and it can
be distinguishable from the No Template Control (NTC). Excess
scattering of clusters such that genotype cannot be distinguished
results in the assay not being considered to meet specifications.
In some configurations, this test can be performed for both custom
assay products and stock assay products.
[0614] Gene Expression Tests:
[0615] In various configurations, gene expressions assays can be
tested against both a genomic DNA (gDNA) template and a no-template
control (NTC).
[0616] In some configurations, gene expression assays can be
performed in a two step RT-PCR reaction. In the reverse
transcription (RT) step, cDNA can be reverse transcribed from total
RNA samples using a reverse transcriptase. Commercially available
RT kits can be used such as the High-Capacity cDNA Archive Kit
(Applied Biosystems, Foster City, Calif.). The PCR step uses a DNA
polymerase. The process involves preparing the master mix from the
kit, preparing the cDNA archive reaction plate and performing the
reverse transcription. The RT reaction can be performed in any
suitable system such as, for example, the Applied Biosystems Dual
384-well GeneAmp.RTM. PCR System 9700 thermal cycler (Applied
Biosystems, Foster City, Calif.) or the ABI PRISM.TM. 6700
Automated Nucleic Acid Workstation, (Applied Biosystems, Foster
City, Calif.). Target amplification, using cDNA as the template,
can be the second step in the gene expression assays in various
configurations of the present invention. In this step, AmpliTaq
Gold DNA polymerase from the TaqMan.RTM. Universal PCR Master Mix
(Applied Biosystems, Foster City, Calif.) can be used. This
amplifies target cDNA synthesized from the RNA sample, using
sequence-specific primers and TaqMan.RTM. MGB probe from the Gene
Expression Assay Mix (Applied Biosystems, Foster City, Calif.). The
PCR step must be performed on an ABI PRIS.TM. Sequence Detection
System such as, for example the 7900HT Sequence Detection System.
Performing the PCR step for singleplex assays in 384-well format
may involve configuring the sequence detector plate document,
preparing the reaction plate and running the plate.
[0617] In various configurations, assays to multi-exon genes
(denoted with an "_m" in the Assay ID) must show no amplification
against gDNA, while assays to single-exon genes (denoted with an
"_s" in the Assay ID) will amplify the target in gDNA.
[0618] Validation Testing:
[0619] In various configurations of the present invention, SNP
assays and Gene Expression assays undergo validation testing.
[0620] SNP Tests:
[0621] In some configurations, for all human SNP assays, each
target can be run against a large number of human genomic DNA
samples to verify functionality, judge the "robustness" of the
assay and validate an allele frequency. One such group of 90 human
genomic samples has been obtained from both Caucasian and African
American populations. Genomic DNA samples of 45 African Americans
and 45 Caucasians can be obtained from the Coriell Human Variation
Collection (Coriell Cell Repositories, Coriell Institute for
Medical Research, Camden, N.J.).
[0622] In various configurations of the present invention, SNP
assays can be performed as described above. This validation process
provides allele frequency data and confirms assay performance. In
some configurations, to pass validation, SNPs must have a minimum
defined allele frequency to provide a meaningful assay. In various
configurations, the minimum allele frequency can be at least about
8%, at least about 10%, at least about 12%, at least about 15%, at
least about 18% or at least about 20% or more or at any desired
allele frequency. This test verifies that the SNP can be a true
SNP, that the allele frequency meets the minimum defined allele
frequency and that the system performs in a manner suitable for a
viable assay.
[0623] FIG. 85 shows an allele frequency distribution of validated
SNPs. As can be seen in the figure greater than about 93% of the
SNPs had an allele frequency of 10% or greater in either the
Caucasian or the African-American groups.
[0624] Thus, in various configurations, manufactured and validated
products can exhibit low background signal, adequate signal
generation, allele signal specificity and at least 2 allele
clusters.
[0625] In some configurations, only assays that yield a minimum
allele frequency and produce robust assay may be manufactured for
sale.
[0626] Gene Expression Tests:
[0627] In various configurations of the present invention, for gene
expression assays, each target can be run against one or more pools
of human cDNA produced from RNA to verify functionality. In certain
aspects, at least about 10 human cDNA samples comprise such
pools.
[0628] In various configurations, functional testing of custom
assays can be performed in accordance with the procedures described
above. For example, a primary template useful in some
configurations can be the Universal Human Reference RNA
(Stratagene, La Jolla, Calif.); while useful secondary templates
include Discovery Line.TM. pre-isolated human total RNA
(Invitrogen, Carlsbad, Calif.) from brain, heart, kidney, liver,
and lung, and a pool of the 5 tissues; and Raji-Control human Total
RNA (Applied Biosystems, Foster City, Calif.).
8TABLE 2A C.sub.T (PCR Thresold Cycle) Values Determined in Various
Tissues Using Assays-on-Demand .TM. products. Source Tissue for RNA
Universal human Raji- Reference Pooled Control Gene RNA Tissue
Total Symbol (Statagene) RNAs Brain Heart Kidney Liver Lung RNA
AARS 22.39 24.58 26.24 25.97 24.91 27.61 27.39 21.8 ALAD 23.26
22.22 26.27 24.94 24 23.18 24.51 24.37 WNT8B 40 40 40 38.93 40 40
40 40 ATP7B 24.43 27.75 29.61 27.81 25.99 25.9 27.3 28.54 GRIN2C 40
31.71 31.04 40 40 40 40 40 SERPING1 25.38 20.1 26.57 21.99 20.94
19.62 21.91 25.86 C3 21.81 19.88 27.91 24 27.01 19.87 23.19
22.07
[0629]
9TABLE 2B Summary of Gene Expression Across Tissues Using
Assays-on- Demand .TM. Products. Total Number of assays processed
2348 Total number expressed (Ct<35) in at least 1 tissue 2293
97.7% Total number not expressed (Ct>35) in any tissues 55
2.3%
[0630] As seen in the tables in this example, approximately 98% of
the manufactured assays gave positive results in a functional use
test in at least one tissue sample tested.
[0631] In some configurations, only assays that yield amplification
on the human cDNA pools within the specifications, i.e. showing
expression against sample tissue RNA references may be manufactured
for sale.
[0632] Overall manufacturing and validation systems for some
configurations of the present invention are illustrated for SNP and
Gene Expression assays in FIGS. 86 and 87, respectively.
[0633] As shown in FIG. 86, in some configurations, probes and
primers can be designed based upon bioinformatics and manufactured
using a DNA synthesizer such as the ABI 3900. Following synthesis
yield testing and analytical quality control testing (not shown)
functional and validation testing can be performed using a ABI
PRISM.RTM. 7900HT Sequence Detection System. Probes and primers
suitable for assays which can distinguish allele pairs can be
validated.
[0634] As shown in FIG. 87, in some configurations, probes and
primers can be designed based upon bioinformatics and manufactured
using a DNA synthesizer such as the ABI 3900. Following synthesis
yield testing and analytical quality control testing (not shown)
functional and validation testing can be performed using
GeneAmp.RTM. PCR System 9700 and ABI PRISM.RTM. 7900HT Sequence
Detection System. Probes and primers which may be able to detect
reference RNA samples can be suitable for assays and can be
considered validated.
[0635] Shipping:
[0636] In various configurations of the present invention,
customers can be informed of assays accepted for order, and of
final shipment of assays passing quality control (QC) functional
testing. Depending at least in part upon the capacity of the
supplier's manufacturing and testing facilities, delivery of assays
together with associated information and materials (the "assay kit"
308, a non-limiting example of which is illustrated in FIG. 88) may
be made, in some configurations, in about 14 days from the date the
order is accepted. Delivery may also take more or less time,
depending upon the number of assays ordered. For example, in some
configurations, turn around time can be 14 working days from when
an order is accepted for under 3,000 assays.
[0637] In some configurations, the assay probes include a
non-fluorescent dye that can be configured to reduce background
fluorescence and increase quenching efficiency. Thus, such assays
can be particularly suitable and provide a substantial benefit to
consumers using PCR sequence detection systems such as the Applied
Biosystems PRISM.RTM. 7900HT Sequence Detection System, enabling
high-throughput SNP genotyping in which approximately 250,000
genotypes per day can be analyzed, each needing only a small amount
of sample DNA. In some configurations, MGB technology can be
utilized with non-fluorescent quenchers. Shorter MGB probes
provided in these configurations provide more flexibility in assay
design, yielding more robust assays as well as a larger number of
assays for more targets. The non-fluorescent quencher eliminates
background fluorescence, and improves sensitivity.
[0638] In various configurations, components of SNP assays (human
or non-human) supplied by the supplier may include one or more of
the following:
[0639] One TaqMan.RTM. MGB 6-FAM.TM. dye-labeled probe;
[0640] One TaqMan.RTM. MGB VIC.TM. dye-labeled probe; and/or
[0641] Two target-specific primers configured to distinguish
between two alleles.
[0642] The two TaqMan.RTM. MGB probes can be configured to
distinguish between two alleles. Each TaqMan.RTM. MGB probe
contains, in some configurations:
[0643] a reporter dye at the 5' end of each probe, wherein a
VIC.TM. dye is linked to the 5' end of the allele 1 probe and a
6-FAM.TM. dye is linked to the 5' end of the allele 2 probe;
[0644] an MGB, which increases the melting temperature (T.sub.m)
without increasing probe length, thereby permitting the design of
shorter probes. The use of MGBs results in greater differences in
T.sub.m values between matched and mismatched probes, which
produces more accurate allelic discrimination; and
[0645] an NFQ at the 3' end of the probe. Because the quencher does
not fluoresce, various sequence detection systems, including those
of Applied Biosystems, can measure reporter dye contributions more
accurately.
[0646] During PCR, each TaqMan.RTM. MGB probe anneals specifically
to a complementary sequence between the forward and reverse primer
sites. When the probe is intact, the proximity of the reporter dye
to the quencher dye results in suppression of the reporter
fluorescence primarily by Forster-type energy suppression.
[0647] AmpliTaq Gold.RTM. DNA polymerase cleaves only probes that
can be hybridized to the target. (AmpliTaq Gold.RTM. DNA Polymerase
is a thermostable polymerase complexed with a non-thermostable
polymerase inhibitor, for example, an antibody directed against the
polymerase. The combination has its activity inhibited until it is
heated.)
[0648] Cleavage separates a reporter dye from the quencher dye,
which results in increased fluorescence by the reporter. The
increase in fluorescence signal occurs if the target sequence is
complementary to the probe and is amplified during PCR. Thus, the
fluorescence signal generated by PCR amplification indicates which
alleles are present in the sample.
[0649] A correlation exists between fluorescence signals and
sequences present in a sample, in various configurations of the
present invention. More particularly, in various configurations, a
VIC dye fluorescence without a 6-FAM dye fluorescence indicates a
homozygosity for allele 1. A 6-FAM dye fluorescence without a VIC
dye fluorescence indicates a homozygosity for allele 2.
Fluorescence of both dyes indicates an allele 1-allele 2
heterozygosity.
[0650] Also in various configurations, components of gene
expression assays supplied by the supplier include one or more of
the following:
[0651] One TaqMan MGB 6_FAM dye-labeled probe; and/or
[0652] Two target-specific primers.
[0653] In some configurations, custom assays combine two PCR
primers and one FAM.TM. dye-labeled, TaqMan.RTM. MGB probe in a
single-tube, ready-to-use, 20.times. mix (250 uL). Various
configurations can be designed and optimized for two-step RT-PCR
using TaqMan.RTM. Universal PCR Master Mix and complementary DNA
(cDNA). An AB High Capacity cDNA Archive Kit (P/N 4322171) for
converting RNA to cDNA, for example, can be used. Assays may also
be tested for use on the ABI PRISM.RTM. 7900HT, 7700, and 7000
Sequence Detection Systems. In various configurations, products can
be formulated at preselected universal concentration conditions
(for example, final reaction concentrations of 900 nM primer and
250 nM probe) and configured to run using preselected universal
thermal cycling parameters. As a result, in a variety of
configurations, multiple assays can be run on a single plate,
laboratory methods can easily be transferred to other researchers,
and gene expression results can be directly compared to those of
other researchers and other labs. In some configurations, assays
can be configured for running in singleplex format with external
endogenous controls run in separate wells on a plate.
[0654] Gene expression products ordered from stock may be used in
RT-PCR protocols in configurations in which assays can be optimized
for the two-step RT-PCR protocol. If, to use these products with
RNA, RNA must be converted to cDNA, an AB High Capacity cDNA
Archive Kit (P/N 4322171) or other suitable conversion product can
be used for this conversion. A one-step protocol may be used in
some configurations, such as by using the TaqMan.RTM. One-Step
RT-PCR Master Mix Reagents Kit Protocol (P/N 4310299).
[0655] Stock assays for gene expression provided by some
configurations of the present invention can be used for
multiplexing. To use in single-plex reactions, users choose an
appropriate endogenous control to be run in a separate well. A set
of external, endogenous controls can be provided that have the same
concentration and labeling (e.g., a TaqMan.RTM. MGB probe, labeled
with the FAM.TM. dye) as the gene expression products. For
multiplex reactions the endogenous control of choice can be run in
separate wells (single-plex) as it does not require time-consuming
validation experiments for the user to confirm that there is no PCR
competition. However, if users choose to try multiplex experiments,
the user can perform an experiment in which a multiplex versus
singleplex assay can be performed to confirm that the PCR reactions
and relative quantitation calculations can be unaffected by
multiplexing.
[0656] Stock assays may be delivered with certain sequence
information. For example, some sequence context information
(forward primer location in the RefSeq sequence) and denote which
exon-exon junction the assay covers so that users can get a sense
of where the assay can be positioned in the transcript. More
information can also be provided.
[0657] In some configurations, standardized assay designs can be
provided for custom assays and/or stock assays, including either
universal concentration or uniform thermal cycling parameters, or
both, allowing results to be more easily compared with and/or
transferred to other researchers and labs. Also, in some
configurations, assays can be formulated in a single-tube 20.times.
mix format that is convenient and easy to use, requiring no
preparation or clean-up and providing faster time to results.
[0658] In some configurations, the manufactured assays can be
shipped as homogenous assays in a single tube format. For example,
in at least some configurations, a single tube, ready to use format
can be provided that is suitable for immediate use on an ABI
PRISM.RTM. Sequence Detection System platforms for one or more
applications.
[0659] Referring to FIGS. 88 and 89, in addition to a
human-readable label 310 (for example, a label on which appears the
assay name) on each tube 312, in some configurations, a 2-D barcode
314 can be laser-etched on the bottom of each assay tube, and a 1-D
barcode (not shown) on each 96-tube rack 316 of assays, making the
assay tubes and racks machine-identifiable, so that the assays can
be compatible with automation for high throughput applications.
[0660] In various configurations, an E-datasheet, or Assay
Information File, can be provided with an assay. The E-datasheet or
Assay Information File can be, in some configurations, an
electronic file or data electronically stored on a data storage
medium 318. This file or data can contain, for example, information
on one or more assays, information on one or more polynucleotide
sequences, an alphanumeric sequence representing a polynucleotide
sequence, or the like. Alternatively, or in addition, a print copy
or a printout of the E-datasheet or E-datasheet information can be
provided.
[0661] In some configurations, a printed copy of a data sheet can
also be provided, containing information about each assay. This
information may include, among other things, the position of each
assay in the plate rack. Some configurations provide, either in
place of, or in addition to the printed copy of the data sheet, a
CD-ROM with one or more data files recorded thereon. The data files
may include, for example, any or all of the following files,: an
electronic assay workbook, including data sheet(s) and shipped
worksheet(s); an electronically readable and/or printable copy of
instructions for assay protocol; an electronically readable and/or
printable copy the order request as well as the submission request
protocol ; and/or an electronically readable copy of a product
insert.
[0662] In some configurations of the present invention, a data
sheet and/or an electronic assay workbook can be provided with
custom assays. In some configurations, an electronic assay workbook
can be included with each order of up to 92 assays. In various
configurations, the workbook file name includes the number on the
bar code on the plate for easy correlation. In some configurations,
the workbook contains two worksheets, namely, the "data sheet"
worksheet and the "shipped" worksheet. Also in some configurations,
the workbook can be a spreadsheet file, such as a Microsoft.RTM.
Excel.RTM. file, which may contain macros and/or be password
protected. Cells of the workbook can be copied and pasted into a
new worksheet and modified in the new worksheet. A printed copy of
the datasheet from the electronic file may be included with a
shipment of assays ordered by design. The datasheet includes a
correlation of the 2-D barcodes on the tubes to the corresponding
assay names and primer and probe specific information.
[0663] In some configurations, a datasheet included with an order
includes all of the following information: an identification of the
assay in each tube; assay names; which target site was used, if the
requestor submitted a sequence record that included more than one
target site; locations of each tube in the assay rack; sequences of
the primers and probes; and concentrations (.mu.M) of primers and
probes. Other configurations do not necessarily include all of this
information and may include either more or less information.
[0664] For example, in some configurations, data sheets have the
following columns:
[0665] Customer name (assigned by the supplier);
[0666] Order number (assigned by the supplier, in some
configurations, corresponds to a number on a 1-D bar code on the
plate);
[0667] Ship date (date shipped by the supplier)
[0668] Set ID (an assay name created from the record information in
the requestor's submission file, including the record name and the
target site name from the target site coordinate; if the sequence
record submitted contained multiple target sites, the value of the
Set ID can be used to determine which site was used to create the
assay);
[0669] Set No. (may be used for internal quality control by the
supplier)
[0670] Plate ID (assigned by the supplier, includes the order
number value, and appears on the plate rack as the 1-D bar
code);
[0671] Vial ID (a 2-D bar code number that appears on the bottom of
each tube; entry in the datasheet may have leading zeros dropped in
some configurations);
[0672] Well location (location of assay tube in the plate rack)
[0673] Line item (may be used for internal quality control by the
supplier)
[0674] VIC probe name (may be used for internal quality control by
the supplier);
[0675] VIC probe sequence (5' to 3' sequence of the probe labeled
with VIC dye; in some configurations, the 3' non-fluorescent
quencher-minor groove binder (NFQ-MGB) is not listed but is present
on the probe);
[0676] VIC (.mu.M) concentration (probe concentration)
[0677] Line item (may be used for internal quality control by the
supplier)
[0678] 6FAM probe name (may be used for internal quality control by
the supplier)
[0679] 6FAM probe sequence (5' to 3' sequence of the probe labeled
with 6-FAM dye; note that in some configurations, the 3' NFQ-MGB is
not listed but is present on the probe)
[0680] 6FAM (.mu.M) concentration (probe concentration)
[0681] Line item (may be used for internal quality control by the
supplier)
[0682] Forward primer name (may be used for internal quality
control by the supplier)
[0683] Forward primer sequence
[0684] Forward (.mu.M) primer concentration
[0685] Line item (may be used for internal quality control by the
supplier)
[0686] Reverse primer name (may be used for internal quality
control by the supplier)
[0687] Reverse primer sequence
[0688] Reverse (.mu.M) primer concentration
[0689] Part number (the part number ordered by the requester).
[0690] The shipped worksheet can be provided to enable a user of
the assays to determine that the tubes can be in the same positions
in the plate rack as when the assays were shipped. For example, in
some configurations, the following columns appear in the shipped
worksheet:
[0691] Position (position in the plate)
[0692] Vial ID (a 2-D bar code number on the bottom of the tube at
the indicated position; in some configurations, leading zeros can
be dropped).
[0693] Usage of Assays:
[0694] The 5' nuclease allelic discrimination method used in
TaqMan.RTM. platforms utilized by some configurations of the
present invention reduces human labor while in the laboratory.
Unlike other methods that may require hybridization to chips or
separate allele reactions, TaqMan.RTM. PCR preparation avoids
hybridization to chips or separate allele reactions by adding a
pre-made master mix containing buffer, deoxyribonucleotides, and
DNA polymerase to the sample template and SNP specific
oligonucleotides.
[0695] TaqMan.RTM. chemistry for SNP genotyping assays employs two
allele specific probes for each SNP in addition to the common PCR
primers. Each probe contains a 5' fluorescent dye, such as, for
example, VIC or FAM, to detect the presence of the specific allele,
and a 3' quencher to absorb fluorescence when the allele may not be
present. The result can be much like any microarray or molecular
beacon technology, one of the dyes will fluoresce for homozygous
alleles and both dyes will fluoresce for heterozygotes.
[0696] In some configurations, ABI Prism.RTM. 7700 and ABI
Prism.RTM. 7900HT Sequence Detection Systems available from Applied
Biosystems may be used for endpoint analysis of 96 and 384 well
plates, respectively, to record the fluorescence of the PCR product
of each well. The latter may be bundled with an 84 plate robot for
long term hands-free automation.
[0697] About 26 dual plate GeneAmp.RTM. PCR System 9700 thermal
cyclers can be used in some configurations to keep one 7900HT
supplied with an adequate number of PCR plates for continuous
operation. However, different quantities and/or types of thermal
cyclers may be used in some configurations, for example, if
continuous operation and/or greater or lesser capacity is desired.
Also in some configurations, barcoding can be used to record
information hardware used, plates, assay probes and primers,
technicians and times to evaluate performance.
[0698] In some configurations, assays themselves can be configured
to be stored at between -15 and -25.degree. C., but the number of
freeze-thaw cycles can be minimized by storing multiple aliquots of
the working stocks. In addition, the fluorescent probes can be
protected by avoiding direct exposure of the assays to light.
[0699] In some configurations, assays can be diluted and aliquoted
for routine use to minimize freeze-thaw cycles and to protect assay
mixes from exposure to light. To dilute assay mixes, 40.times. or
80.times. SNP assay mixes can be diluted to a 20.times. working
stock with 1.times. TE. The 1.times. TE can be 10 mM Tris-HCl, 1 mM
EDTA pH 8.0, and made using DNase-free, sterile-filtered water.
Multiple aliquots of the assay mixes may then be stored at -15 to
-25.degree. C.
[0700] A manual method may be used by a user of the assays to
validate each tube position in the rack plate. In these
configurations, the rack plate position and assay name on the tube
label can be compared with the values in the well location and set
ID columns in the data sheet worksheet. (This "validation" can be
different from the validation of assays, in that validation of each
tube position in a plate rack can be performed by the user, and
merely confirms that the tubes are in positions matching the
"shipped" worksheet. If the tubes are not in the correction
position, they may be rearranged to match the worksheet. The
operational quality of the assays contained within the tubes can be
validated at the supplier's factory.)
[0701] In some configurations, an automated method can be used by a
user of the assays to validate each tube position in the rack
plate. This method includes scanning the plate and tubes using a
2-D bar code reader, and executing a plate validation spreadsheet
macro (for example, a Microsoft.RTM. Excel.RTM. macro). In some
configurations, to scan the plate and tubes, the plate rack can be
placed on the 2-D bar code reader in a standard orientation. For
example, tube position "A1" can be placed in the top left corner of
the reader. The 1-D bar code on the plate rack can be then scanned.
The bar code reader can be then configured, if necessary, to read
positions in one column and to read bar codes in a column next to
the positions column. Next, the plate rack can be scanned and the
results can be saved to a directory that can be accessed from the
computer containing the electronic file. In some configurations,
the scanning results can be saved as a tab-delimited file.
[0702] To validate, the "shipped" worksheet can be opened in the
spreadsheet, macros can be enabled, and the validation macro can be
run. In some configurations utilizing software that can generate a
text file, the validation can be performed by opening the
electronic workbook, clicking a mouse on a "shipped" tab to view
the worksheet containing the validation macro, clicking on the
"validate" button to start the plate validation macro, and, when an
"import plate scan" dialog box is presented, selecting "browse" to
locate the file from the 2-D bar code scan. After "browse" is
selected, the file that resulted from the 2-D bar code scan can be
selected and imported into a new worksheet, which, in some
configurations, can be called "received". The macro then compares
each bar code and its position in the plate rack with the
corresponding bar code in the "shipped" worksheet (i.e., the value
in the "Vial ID" column). The macro then enters the result in a
"validation" column in the "shipped" worksheet. The results for
each entry may either be "OK" (or any entry understood as
indicating a match) or "ERROR" (or any other entry understood as
indicating a non-match). Next, a "shipment validation" dialog box
alerts that the validation is complete, and the user clicks "OK" to
dismiss the dialog box.
[0703] Plate validation errors indicate that the tubes may not in
the same position as they were shipped by the supplier to the
requestor. The user can resolve plate validation errors by
rearranging the tubes to match the "shipped" worksheet; The user
can then rescan the plate and execute the validation macro again to
validate the plate.
[0704] Laboratory Information Management System
[0705] In various configurations of the present invention, oligo
sets may be supplied in one tube, or in 96 well microtiter plates
that can be already barcoded, as described above, to facilitate use
of a laboratory information management system employed by the user
of the oligo sets. In various configurations, supplied oligos can
be scanned into the database, inventory can be tracked, and a
nightly report can be generated to notify lab managers of sets
ready to be run the following day.
[0706] In some configurations of the present invention, the samples
supplied to the requestor can be arrayed in 96 or 384 well plates
and a map of the plate entered into the database. To conserve
clinical DNA, various configurations of the present invention
supply only SNPs that pass validation and meet the required
population frequencies on the clinical samples.
[0707] In various configurations of the present invention, an assay
can be prepared for a given run using the probe and primer set and
a TaqMan.RTM. Universal PCR Master Mix. A robot, such as a
Protedyne robot prepares daughter sample plate by adding the assay
mixture to the plate wells. The plate can be thermal cycled using,
for example, a GeneAmp.RTM. 9700. Each step in the assay
performance can be logged in the LIMS to allow software to
automatically trigger and create a sequence detection system (SDS)
binary file that can be used by the 7900HT. This procedure allows
laboratory staff to simply place the plate into a stacker of one of
the 7900HTs and select a pre-created file in the robot program. In
various configurations, an SDS file need not be manually created
using SDS software.
[0708] In some configurations, the scanned data file from the
7900HT can be recognized by software that passes it to
multicomponent analysis software. This analysis software creates a
multicomponent file containing the dye intensities of each well and
subsequently passes the file to an autocaller program. As
discussed, in more detail below, the autocaller program identifies
the genotype clusters and assigns appropriate calls to the wells.
In some configurations, the putative genotypes can be loaded into
the database for either manual review or immediate release,
depending on the confidence of the autocaller.
[0709] In various configurations, the 7900HT and multicomponent
analysis software can be controlled by a combination of automated
software and triggers which allow the anticipation and detection of
the steps in the laboratory performance of assays, thereby allowing
continuous scanning by the 7900HT without having to manually
create, identify, locate, analyze, call genotypes, or export data
files.
[0710] In some configurations of the present invention, a
laboratory information management system can also be used in the
post-manufacturing validation process. Thus, an automated computer
system can be provided to support high throughput SNP genotyping
that satisfies the increasing demand that disease association
studies are placing on current genotyping facilities. This system
provides target SNP selection, automated oligo design, in silico
assay quality validation, laboratory management of samples,
reagents and plates, automated allele calling, optional manual
review of autocalls, regular status reports, and linkage
disequilibrium analysis. In some configurations, it has been found
practical to generate over 2.5 million genotypes from more than
10,000 SNPs, with a target capacity of at least 10,000 genotypes
per machine per hour utilizing only limited human intervention and
laboratory hardware.
[0711] In various configurations, information gathered throughout
the genotyping process can be stored in a central database, which
can be divided into project management and laboratory schemas.
[0712] The project schema facilitates management of abstract
entities such as SNP, sample donor, or genotype. For example,
projects can be created by indicating an intended customer and
loading desired SNP information. The requestor determines what SNP
is ordered, scanned, considered validated, possibly discarded or
re-designed, and delivered to the requester. In various
configurations, reports can be generated regarding the current
progress of a SNP, failure rate of samples, or allele frequencies
per population.
[0713] The project management component permits fast data analysis,
by allowing efficient phenotype relations to both donors and SNPs.
In various configurations, the project schema also has the ability
to store haplotypes constructed from specific SNP alleles after
analysis. The schema may also track literature references for
individual SNPs and donors.
[0714] In various configurations, a the laboratory component
provides tracking details of the process taken by the actual
physical aspects of the laboratory performance and this can be
mirrored in the project management component. Samples can be
received, barcoded, and placed into plates and freezers. Oligos can
be received, diluted, assigned into sets, and also placed into
freezers. Plates can be arrayed with particular samples and oligos
for specific projects. Each well can be scanned (and, in some
configurations, re-scanned many times) to provide high accuracy.
However, in various configurations, only a `final` genotype is
copied to the project management component where it may eventually
be delivered to the customer.
[0715] An advantage of having common but separated partitions of
the project management and laboratory components is that the
laboratory space provides a tracking environment in which
experiments can be re-arrayed, rerun, and reviewed multiple times,
whereas the project management component remains uncluttered with
details as analysis requires a compact schema designed for speed
and clarity. This integration of LIMS and data analysis provides
for segregated storage to satisfy each schema's different
requirements, while keeping the data in one repository for the
ability to track an individual genotype's entire history.
[0716] The database schema also supports large scale resequencing
laboratories by adding relatively few tables, thereby combining SNP
discovery, validation, and genotyping into one central
repository.
[0717] As various changes could be made in the above methods and
compositions without departing from the scope of the inventions, it
is intended that all matter contained in the above description be
interpreted as illustrative and not in a limiting sense. Where
examples are recited herein, such examples are intended to be
non-limiting. Also as used herein, unless otherwise explicitly
stated, the terms "a," "an," "the," "said," and "at least one" are
not intended to be limited in number to "one," but rather are
intended to be read as encompassing "more than one" (i.e., a
plurality) as well.
[0718] The description of the invention is merely exemplary in
nature and, thus, variations that do not depart from the gist of
the invention are intended to be within the scope of the invention.
Such variations are not to be regarded as a departure from the
spirit and scope of the invention.
[0719] All references cited herein are hereby incorporated by
reference in their entireties U.S. application, Attorney Docket No.
4797 (5010-022-12) entitled "Methods of Validating SNPs and
Compiling Libraries of Assays", inventors De La Vega, Francisco et
al., filed Jan. 2, 2003 and U.S. application, Attorney Docket No.
4797 (5010-002-13) entitled "Single-tibe, Ready to Use Assay Kits,
and Methods Using Same", inventors De La Vega, Francisco et al.,
filed Jan. 2, 2003 are both hereby incorporated by reference in
their entireties.
* * * * *
References