U.S. patent application number 14/512369 was filed with the patent office on 2015-07-23 for system and methods for detecting genetic variation.
The applicant listed for this patent is Counsyl, Inc.. Invention is credited to Clement CHU, Eric EVANS, A. Scott PATTERSON, Hunter RICHARDS, Abhik SHAH, Balaji SRINIVASAN, Subramaniam SRINIVASAN.
Application Number | 20150205914 14/512369 |
Document ID | / |
Family ID | 50547815 |
Filed Date | 2015-07-23 |
United States Patent
Application |
20150205914 |
Kind Code |
A1 |
RICHARDS; Hunter ; et
al. |
July 23, 2015 |
System and Methods for Detecting Genetic Variation
Abstract
The invention provides methods, apparatuses, and compositions
for high-throughput amplification sequencing of specific target
sequences in one or more samples. In some aspects, barcode-tagged
polynucleotides are sequenced simultaneously and sample sources are
identified on the basis of barcode sequences. In some aspects,
sequencing data are used to determine one or more genotypes at one
or more loci comprising a causal genetic variant. In some aspects,
systems and methods of detecting genetic variation are
provided.
Inventors: |
RICHARDS; Hunter; (San
Francisco, CA) ; EVANS; Eric; (San Bruno, CA)
; SRINIVASAN; Balaji; (South San Francisco, CA) ;
SRINIVASAN; Subramaniam; (Plainview, NY) ; SHAH;
Abhik; (San Francisco, CA) ; PATTERSON; A. Scott;
(San Francisco, CA) ; CHU; Clement; (San
Francisco, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Counsyl, Inc. |
South San Francisco |
CA |
US |
|
|
Family ID: |
50547815 |
Appl. No.: |
14/512369 |
Filed: |
October 10, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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13665671 |
Oct 31, 2012 |
|
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14512369 |
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Current U.S.
Class: |
506/2 ;
702/19 |
Current CPC
Class: |
C40B 30/00 20130101;
G16B 20/00 20190201; G16B 30/00 20190201; C12Q 1/6874 20130101 |
International
Class: |
G06F 19/18 20060101
G06F019/18; G06F 19/22 20060101 G06F019/22; C12Q 1/68 20060101
C12Q001/68 |
Claims
1-60. (canceled)
61. A method of detecting genetic variation in a subject's genome
comprising: (a) providing a plurality of clusters of
polynucleotides, wherein (i) each cluster comprises multiple copies
of a nucleic acid duplex attached to a support; (ii) each duplex in
a cluster comprises a first molecule comprising sequences
A-B-G'-D'-C' from 5' to 3' and a second molecule comprising
sequences C-D-G-B'-A' from 5' to 3'; (iii) sequence A' is
complementary to sequence A, sequence B' is complementary to
sequence B, sequence C' is complementary to sequence C, sequence D'
is complementary to sequence D, and sequence G' is complementary to
sequence G; (iv) sequence G is a portion of a target polynucleotide
sequence from a subject and is different for each of a plurality of
clusters; (v) sequence B' is located 5' with respect to sequence G
in the corresponding target polynucleotide sequence; and (vi) each
first molecule comprises a barcode sequence; (b) sequencing
sequence G' by extension of a first primer comprising sequence D to
produce an R1 sequence for each cluster; (c) sequencing sequence B'
by extension of a second primer comprising sequence A to produce R2
sequence for each cluster; (d) hybridizing a third primer to
sequence C' and sequencing the barcode sequence by extension of the
third primer to produce a barcode sequence for each cluster; (e)
performing a first alignment using a first algorithm to align all
R1 sequences to a first reference sequence; (f) performing a second
alignment using a second algorithm to locally align R1 sequences
identified in said first alignment as likely to contain an
insertion or deletion with respect to the first reference sequence,
to produce a single consensus alignment for each insertion or
deletion; (g) performing an R2 alignment by aligning all R2
sequences to a second reference sequence; and (h) determining the
presence or absence of a sequence variation identified by steps (e)
to (g).
62. The method of claim 61, further comprising transmitting a
report with the sequence variation determined in step (h) to a
receiver.
63. The method of claim 61, wherein the first reference sequence
comprises a reference genome.
64. The method of claim 61, wherein the second reference sequence
consists of every sequence B for every different target
polynucleotide.
65. The method of claim 61, wherein R2 sequences are aligned
independently of R1 sequences.
66. The method of claim 61, further comprising discarding an R1
sequence that aligns to a first position in the first reference
sequence that is more than 10,000 base pairs away from a second
position in the first reference sequence to which the R2 sequence
for the same cluster aligns.
67. The method of claim 61, further comprising deleting a portion
of an R1 sequence for a cluster when the portion of R1 sequence to
be deleted is identical to at least a portion of sequence B' for
that cluster and sequence G is shorter than the R1 sequence for
that cluster.
68. The method of claim 61, further comprising deleting a portion
of an R1 sequence for a cluster when the portion of R1 sequence to
be deleted is identical to at least a portion of any sequence B',
the portion includes either the 5' or 3' nucleotide of R1, and
either (i) no R2 sequence was produced for the cluster or (ii) R2
sequence produced is not identical to any sequence B.
69. The method of claim 61, wherein performing the first alignment
with a system using the first algorithm takes less time to align
all R1 reads than would be taken if the system used the second
algorithm to perform the first alignment.
70. The method of claim 61, wherein performing the first alignment
with a system using the first algorithm uses less system memory to
align all R1 reads than would be used if the system used the second
algorithm to perform the first alignment.
71. The method of claim 61, wherein said first algorithm is based
on Burrows-Wheeler transform.
72. The method of claim 61, wherein said second algorithm is based
on Smith-Waterman algorithm or a hash function.
73. The method of claim 61, wherein R1 and R2 sequences are
generated for at least 100 different target polynucleotides.
74. The method of claim 61, wherein each barcode differs from every
other barcode in a plurality of different barcodes analyzed in
parallel. reaction.
75. The method of claim 61, wherein the barcode sequence is located
5' from sequence D'.
76. The method of claim 61, further comprising grouping sequences
from the clusters based on the barcode sequences.
77. The method of claim 75, further comprising discarding all but
one of a plurality of R1 sequences having the same sequence and
alignment within a barcode sequence grouping.
78. The method of claim 61, wherein sequences A, B, C, and D are at
least 5 nucleotides in length.
79. The method of claim 61, wherein sequence G of every cluster is
1 to 1000 nucleotides in length.
80. The method of claim 61, wherein each probe sequence B of a
plurality of clusters is complementary to a sequence comprising a
causal genetic variant or a sequence within 200 nucleotides of a
causal genetic variant.
81. The method of claim 61, wherein an R1 sequence is produced for
at least about 10.sup.8 clusters in a single reaction.
82. The method of claim 61, wherein presence, absence, or allele
ratio of one or more causal genetic variants is determined with an
accuracy of at least about 90%.
83. The method of claim 61, wherein the consensus sequence
identifies an insertion, a deletion, or an insertion and a deletion
in a target polynucleotide with an accuracy of at least about
90%.
84. The method of claim 61, wherein each probe sequence B of a
plurality of clusters is complementary to a sequence comprising a
non-subject sequence or a sequence within 200 nucleotides of a
non-subject sequence.
85. The method of claim 61, wherein the presence or absence of one
or more non-subject sequences is determined with an accuracy of at
least about 90%.
86. The method of claim 61, further comprising calculating a
plurality of probabilities based on the R1 sequences for the
subject and including the probabilities in the report, wherein each
probability is a probability of the subject or a subject's
offspring having or developing a disease or trait.
87. A method of detecting genetic variation in a subject's genome
comprising: (a) providing a plurality of clusters of
polynucleotides, wherein (i) each cluster comprises multiple copies
of a nucleic acid duplex attached to a support; (ii) each duplex in
a cluster comprises a first molecule comprising sequences
A-B-G'-D'-C' from 5' to 3' and a second molecule comprising
sequences C-D-G-B'-A' from 5' to 3', (iii) sequence A' is
complementary to sequence A, sequence B' is complementary to
sequence B, sequence C' is complementary to sequence C, sequence D'
is complementary to sequence D, and sequence G' is complementary to
sequence G; (iv) sequence G is a portion of a target polynucleotide
sequence from a subject and is different for each of a plurality of
clusters; (v) sequence B' is located 5' with respect to sequence G
in the corresponding target polynucleotide sequence; and (vi) each
first molecule comprises a barcode sequence; (b) sequencing
sequence G' by extension of a first primer comprising sequence D to
produce an R1 sequence for each cluster; (c) sequencing sequence B'
by extension of a second primer comprising sequence A to produce R2
sequence for each cluster; (d) further comprising hybridizing a
third primer to sequence C' and sequencing the barcode sequence by
extension of the third primer to produce a barcode sequence for
each cluster (e) performing a first alignment using a first
algorithm to align all R1 sequences to a first reference sequence;
(f) performing a second alignment using a second algorithm to
locally align R1 sequences identified in said first alignment as
likely to contain an insertion or deletion with respect to the
first reference sequence, to produce a single consensus alignment
for each insertion or deletion; (g) performing an R2 alignment by
aligning all R2 sequences to a second reference sequence; and (h)
calculating a plurality of probabilities based on the R1 sequences
for the subject and including the probabilities in a report
identifying sequence variation identified by steps (e) to (g),
wherein each probability is a probability of the subject or a
subject's offspring having or developing a disease or trait.
88. The method of claim 87, further comprising transmitting a
report with the sequence variation determined in step (h) to a
receiver.
89. The method of claim 87, wherein the first reference sequence
comprises a reference genome.
90. The method of claim 87, wherein the second reference sequence
consists of every sequence B for every different target
polynucleotide.
91. The method of claim 87, wherein R2 sequences are aligned
independently of R1 sequences.
92. The method of claim 87, further comprising discarding an R1
sequence that aligns to a first position in the first reference
sequence that is more than 10,000 base pairs away from a second
position in the first reference sequence to which the R2 sequence
for the same cluster aligns.
93. The method of claim 87, further comprising deleting a portion
of an R1 sequence for a cluster when the portion of R1 sequence to
be deleted is identical to at least a portion of sequence B' for
that cluster and sequence G is shorter than the R1 sequence for
that cluster.
94. The method of claim 87, further comprising deleting a portion
of an R1 sequence for a cluster when the portion of R1 sequence to
be deleted is identical to at least a portion of any sequence B',
the portion includes either the 5' or 3' nucleotide of R1, and
either (i) no R2 sequence was produced for the cluster or (ii) R2
sequence produced is not identical to any sequence B.
95. The method of claim 87, wherein performing the first alignment
with a system using the first algorithm takes less time to align
all R1 reads than would be taken if the system used the second
algorithm to perform the first alignment.
96. The method of claim 87, wherein performing the first alignment
with a system using the first algorithm uses less system memory to
align all R1 reads than would be used if the system used the second
algorithm to perform the first alignment.
97. The method of claim 87, wherein said first algorithm is based
on Burrows-Wheeler transform.
98. The method of claim 87, wherein said second algorithm is based
on Smith-Waterman algorithm or a hash function.
99. The method of claim 87, wherein R1 and R2 sequences are
generated for at least 100 different target polynucleotides.
100. The method of claim 87, wherein each barcode differs from
every other barcode in a plurality of different barcodes analyzed
in parallel.
101. The method of claim 87, wherein the barcode sequence is
associated with a single sample in a pool of samples sequenced in a
single reaction.
102. The method of claim 87, wherein each of a plurality of barcode
sequences is uniquely associated with a single sample in a pool of
samples sequenced in a single reaction.
103. The method of claim 87, wherein the barcode sequence is
located 5' from sequence D'.
104. A method of detecting genetic variation in a subject's genome
comprising: (a) providing a plurality of clusters of
polynucleotides, wherein (i) each cluster comprises multiple copies
of a nucleic acid duplex attached to a support; (ii) each duplex in
a cluster comprises a first molecule comprising sequences
A-B-G'-D'-C' from 5' to 3' and a second molecule comprising
sequences C-D-G-B'-A' from 5' to 3; (iii) sequence A' is
complementary to sequence A, sequence B' is complementary to
sequence B, sequence C' is complementary to sequence C, sequence D'
is complementary to sequence D, and sequence G' is complementary to
sequence G; (iv) sequence G is a portion of a target polynucleotide
sequence from a subject and is different for each of a plurality of
clusters; (v) sequence B' is located 5' with respect to sequence G
in the corresponding target polynucleotide sequence; and (vi) each
first molecule comprises a barcode sequence; (b) sequencing
sequence G' by extension of a first primer comprising sequence D to
produce an R1 sequence for each cluster; (c) sequencing sequence B'
by extension of a second primer comprising sequence A to produce R2
sequence for each cluster; (d) hybridizing a third primer to
sequence C' and sequencing the barcode sequence by extension of the
third primer to produce a barcode sequence for each cluster; (e)
further comprising grouping sequences from the clusters based on
the barcode sequences; (f) performing a first alignment using a
first algorithm to align all R1 sequences to a first reference
sequence; (g) performing a second alignment using a second
algorithm to locally align R1 sequences identified in said first
alignment as likely to contain an insertion or deletion with
respect to the first reference sequence, to produce a single
consensus alignment for each insertion or deletion; (h) performing
an R2 alignment by aligning all R2 sequences to a second reference
sequence; and (i) calculating a plurality of probabilities based on
the R1 sequences for the subject and including the probabilities in
a report identifying sequence variation identified by steps (f) to
(h), wherein each probability is a probability of the subject or a
subject's offspring having or developing a disease or trait.
105. A method of detecting genetic variation in a subject's genome
comprising: (a) providing a plurality of clusters of
polynucleotides, wherein (i) each cluster comprises multiple copies
of a nucleic acid duplex attached to a support; (ii) each duplex in
a cluster comprises a first molecule comprising sequences
A-B-G'-D'-C' from 5' to 3' and a second molecule comprising
sequences C-D-G-B'-A' from 5' to 3'; (iii) sequence A' is
complementary to sequence A, sequence B' is complementary to
sequence B, sequence C' is complementary to sequence C, sequence D'
is complementary to sequence D, and sequence G' is complementary to
sequence G; (iv) sequence G is a portion of a target polynucleotide
sequence from a subject and is different for each of a plurality of
clusters; (v) sequence B' is located 5' with respect to sequence G
in the corresponding target polynucleotide sequence; and (vi) each
first molecule comprises a barcode sequence; (b) sequencing
sequence G' by extension of a first primer comprising sequence D to
produce an R1 sequence for each cluster; (c) sequencing sequence B'
by extension of a second primer comprising sequence A to produce R2
sequence for each cluster; (d) hybridizing a third primer to
sequence C' and sequencing the barcode sequence by extension of the
third primer to produce a barcode sequence for each cluster (e)
grouping sequences from the clusters based on the barcode
sequences; and (f) further comprising discarding all but one of a
plurality of R1 sequences having the same sequence and alignment
within a barcode sequence grouping; (g) performing a first
alignment using a first algorithm to align all R1 sequences to a
first reference sequence; (h) performing a second alignment using a
second algorithm to locally align R1 sequences identified in said
first alignment as likely to contain an insertion or deletion with
respect to the first reference sequence, to produce a single
consensus alignment for each insertion or deletion; (i) performing
an R2 alignment by aligning all R2 sequences to a second reference
sequence; and (j) calculating a plurality of probabilities based on
the R1 sequences for the subject and including the probabilities in
a report identifying sequence variation identified by steps (d) to
(f), wherein each probability is a probability of the subject or a
subject's offspring having or developing a disease or trait.
106. The method of claim 87, wherein sequences A, B, C, and D are
at least 5 nucleotides in length.
107. The method of claim 87, wherein sequence G of every cluster is
1 to 1000 nucleotides in length.
108. The method of claim 87, wherein each probe sequence B of a
plurality of clusters is complementary to a sequence comprising a
causal genetic variant or a sequence within 200 nucleotides of a
causal genetic variant.
109. The method of claim 87, wherein sequence B of one or more of
the clusters comprises a sequence selected from the group
consisting of SEQ ID NOs:22-121.
110. The method of claim 87, wherein an R1 sequence is produced for
at least about 10.sup.8 clusters in a single reaction.
111. The method of claim 87, wherein presence, absence, or allele
ratio of one or more causal genetic variants is determined with an
accuracy of at least about 90%.
112. The method of claim 87, wherein the consensus sequence
identifies an insertion, a deletion, or an insertion and a deletion
in a target polynucleotide with an accuracy of at least about
90%.
113. The method of claim 87, wherein each probe sequence B of a
plurality of clusters is complementary to a sequence comprising a
nonsubject sequence or a sequence within 200 nucleotides of a
non-subject sequence.
114. The method of claim 87, wherein the presence or absence of one
or more non-subject sequences is determined with an accuracy of at
least about 90%.
115. The method of claim 104 further comprising transmitting the
report of step (i) to a receiver.
116. The method of claim 105 further comprising transmitting the
report of step (j) to a receiver.
117. A method of detecting genetic variation in a subject's genome
comprising: a. Providing a plurality of fragmented polynucleotides
from the subject; b. Ligating a first partially single-stranded
adapter to the polynucleotides of step (a), wherein the partially
single-stranded adapter has a double-stranded region at one end
(sequence U hybridized to complementary sequence U') and the
single-stranded sequence Y that does not hybridize to the target
polynucleotide under the hybridization and extension conditions
used, and further wherein ligation adds sequence Y to both 5' ends
of the target polynucleotides; c. Hybridizing a plurality of a
plurality of different oligonucleotide primers, each having a
different target-specific sequence W at the 3' end and extending
the primers to produce an extended oligonucleotide with sequence Y'
(complement of Y) at the 3' end; d. Optionally, amplifying the
extended oligonucleotides with a pair of amplification primers
comprising: i. A first amplification primer comprising sequence X
and sequence Y, with sequence Y at the 3' end for hybridization to
sequence Y'; ii. A second amplification primer comprising sequences
V and Z, with Z at the 3' end for hybridization to sequence Z' of
an extended X-Y primer; Wherein amplification produces a plurality
of extended X-Y oligonucleotides comprising sequences X, Y, W', and
Z' (5' to 3'; where W' is the complement of W, and Z' is the
complement of Z) from the first amplification primer, and a
plurality of sequences comprising V, Z, Y', and X' (5' to 3'; where
X' is the complement of X) from the second amplification primer; e.
Sequencing a plurality of different target polynucleotides, each
contained in a polynucleotide comprising one strand comprising
sequences V, Z, W, Y', and X' (from 5' to 3'), and another strand
comprising sequences X, Y, W', Z', and V' (from 5' to 3'), with
target polynucleotide sequence located between Z/Y' and between
Z'/Y; f. Determining if the subject has a genetic variation based
on the sequencing of step (e).
118. The method of claim 117, wherein each oligonucleotide primer
of step (c) further comprises a binding partner at the 5' end.
119. The method of claim 117, wherein the extended oligonucleotides
are amplified.
120. The method of claim 119, wherein the extended oligonucleotides
are exponentially amplified.
121. The method of claim 117, wherein sequence Z is common among
all oligonucleotide primers.
122. The method of claim 117, wherein sequence W is different for
each different oligonucleotide primer, is positioned at the 3' end
of each oligonucleotide primer, and is complementary to a sequence
comprising a causal genetic variant or a sequence within 200
nucleotides of a causal genetic variant.
123. The method of claim 117, wherein one or more of sequences V,
W, X, Y, and Z are different sequences.
124. The method of claim 117, wherein one or more of sequences V,
W, X, Y, and Z comprise 5 or more nucleotides each.
125. The method of claim 117, wherein sequence W of one or more of
the plurality of oligonucleotide primers comprises a sequence
selected from the group consisting of SEQ ID NOs 22-121.
126. The method of claim 117, wherein the fragmented
polynucleotides have a median length between about 200 and about
1000 base pairs.
127. The method of claim 117, wherein sequence Y is positioned at
the 3' end of the adapter.
128. The method of claim 117, wherein the fragmented
polynucleotides are treated to produce blunt ends or to have a
defined overhang prior to step (a).
129. The method of claim 128, wherein the overhang consists of an
adenine.
130. The method of claim 117, further comprising transmitting a
report identifying the sequence variation determined in step (f) to
a receiver.
Description
RELATED APPLICATIONS
[0001] This application is a Continuation of U.S. application Ser.
No. 13/665,671 filed 31 Oct. 2012, now U.S. Pat. No. ______. The
disclosures of the foregoing applications are herein incorporated
by reference in their entireties.
BACKGROUND OF THE INVENTION
[0002] Next-generation sequencing (NGS) allows small-scale,
inexpensive genome sequencing with a turnaround time measured in
days. However, as NGS is generally performed and understood, all
regions of the genome are sequenced with roughly equal probability,
meaning that a large amount of genomic sequence is collected and
discarded to collect sequence information from the relatively low
percentage of areas where function is understood well enough to
interpret potential mutations. Generally, purifying from a
full-genome sample only those regions one is interested in is
conducted as a separate step from sequencing. It is usually a
days-long, low efficiency process in the current state of the
art.
[0003] Direct Targeted Sequencing (DTS) is a modification to the
standard sequencing protocol employed by Illumina, Inc. that allows
the sequencing substrate (i.e. the flow cell) to become a genomic
sequence capture substrate as well. Without adding another
instrument to the normal flow of a typical next generation
sequencing protocol, the DTS protocol modifies the sequencing
surface to capture gDNA from a specially prepared library. The
captured library is then sequenced as a normal gDNA library would
be. However, modification of the sequencing substrate and
accompanying library preparation according to previous suggestions
result in inefficiencies, reduced reliability and reproducibility,
and waste valuable sample. Improvements to the DTS process are
therefore desirable.
SUMMARY OF THE INVENTION
[0004] In one aspect, the invention provides an apparatus and a
method of producing an apparatus for sequencing a plurality of
target polynucleotides. In one embodiment, the method comprises (a)
providing a solid support having a reactive surface; and (b)
attaching to the solid support a plurality of oligonucleotides. In
some embodiments, the plurality of oligonucleotides comprises (i) a
plurality of different first oligonucleotides comprising sequence A
and sequence B, wherein sequence A is common among all first
oligonucleotides; and further wherein sequence B is different for
each different first oligonucleotide, is at the 3' end of each
first oligonucleotide, and is complementary to a sequence
comprising a causal genetic variant or a sequence within 200
nucleotides of a causal genetic variant; (ii) a plurality of second
oligonucleotides comprising sequence A at each 3' end; and (iii) a
plurality of third oligonucleotides comprising sequence C at each
3' end, wherein sequence C is the same as a sequence shared by a
plurality of different target polynucleotides. In some embodiments,
A, B, and C are different sequences and comprise 5 or more
nucleotides each.
[0005] In some embodiments, sequences A, B, and C have less than
90% sequence identity with one another. In some embodiments, the
plurality of oligonucleotides comprise a reactive moiety, such that
a reaction between the reactive surface and the reactive moiety
attaches the plurality of oligonucleotides to the solid support. In
some embodiments, the plurality of first oligonucleotides comprises
at least about 100 different first oligonucleotides each comprising
a different sequence B. In some embodiments, sequence B of one or
more of the plurality of first oligonucleotides comprises a
sequence selected from the group consisting of SEQ ID NOs 22-121,
shown in FIG. 4. In some embodiments, the solid support is a
channel of a flow cell. In some embodiments, the reactive surface
comprises functionalized polyacrylamide, which may be produced from
a polymerization mixture comprising acrylamide,
N-(5-bromoacetamidylpentyl) acrylamide, tetramethylethylenediamine,
and potassium persulfate. In some embodiments, the amount of the
plurality of second oligonucleotides is at least about 1000-fold or
10000-fold higher than the amount of the plurality of first
oligonucleotides; and the amount of the plurality of second
oligonucleotides and the amount of the plurality of third
oligonucleotides are in a ratio of about 1 to 1. In some
embodiments, each of the first oligonucleotides is added to the
solid support at a concentration of about 50 pM. In some
embodiments, the concentration of the plurality of second
oligonucleotides and of the plurality of third oligonucleotides is
about 500 nM. In some embodiments, the invention provides a method
of sequencing a plurality of target polynucleotides, the method
comprising exposing an apparatus produced according to a method of
the invention to a sample comprising target polynucleotides and
non-target polynucleotides, wherein sequencing data is enriched for
target genomic sequences relative to non-target genomic sequences.
In some embodiments, the plurality of different first
oligonucleotides further comprises additional first
oligonucleotides comprising sequence A and sequence B, wherein
sequence B is different for each different additional first
oligonucleotide, is at the 3' end of each additional first
oligonucleotide, and is complementary to a sequence comprising a
non-subject sequence or a sequence within 200 nucleotides of a
non-subject sequence.
[0006] In one aspect, the invention provides a method for
sequencing a plurality of target polynucleotides in a sample. In
one embodiment, the method comprises: (a) fragmenting target
polynucleotides to produce fragmented polynucleotides; (b) joining
adapter oligonucleotides to the fragmented polynucleotides, each of
the adapter oligonucleotides comprising sequence D, to produce
adapted polynucleotides comprising sequence D hybridized to
complementary sequence D' at both ends of the adapted
polynucleotides, optionally wherein sequence D' is produced by
extension of a target polynucleotide 3' end; (c) amplifying the
adapted polynucleotides using amplification primers comprising
sequence C, sequence D, and a barcode associated with the sample,
wherein sequence D is positioned at the 3' end of the amplification
primers; (d) hybridizing amplified target polynucleotides to a
plurality of different first oligonucleotides that are attached to
a solid surface; (e) performing bridge amplification on a solid
surface; and (f) sequencing a plurality of polynucleotides from
step (e). The solid surface may comprise a plurality of
oligonucleotides as described herein, including an apparatus as
described herein and optionally produced according to the methods
described herein. In some embodiments, the solid surface comprises
(i) a plurality of different first oligonucleotides comprising
sequence A and sequence B, wherein sequence A is common among all
first oligonucleotides; and further wherein sequence B is different
for each different first oligonucleotide, is at the 3' end of each
first oligonucleotide, and is complementary to a sequence
comprising a causal genetic variant or a sequence within 200
nucleotides of a causal genetic variant; (ii) a plurality of second
oligonucleotides comprising sequence A at each 3' end; and (iii) a
plurality of third oligonucleotides comprising sequence C at each
3' end. In some embodiments, sequences A, B, and C are different
sequences and comprise 5 or more nucleotides each.
[0007] In some embodiments, the method further comprises a second
amplification step before step (d), wherein amplified
polynucleotides are amplified using a second amplification primer
having a 3' end comprising sequence complementary to at least a
portion of one or more sequences added to the target
polynucleotides in step (c). In some embodiments, sequences A, B,
and C have less than 90% sequence identity with one another. In
some embodiments, the plurality of first oligonucleotides comprises
at least about 100 different first oligonucleotides each comprising
a different sequence B. In some embodiments, sequence B of one or
more of the plurality of first oligonucleotides comprises a
sequence selected from the group consisting of SEQ ID NOs 22-121,
shown in FIG. 4. In some embodiments, each barcode differs from
every other barcode in a pool of two or more samples at at least
three nucleotide positions. In some embodiments, samples are pooled
such that all four nucleotide bases A, G, C, and T are
approximately evenly represented at every position along each
barcode in the pool. In some embodiments, one or more barcodes are
selected from the group consisting of: AGGTCA, CAGCAG, ACTGCT,
TAACGG, GGATTA, AACCTG, GCCGTT, CGTTGA, GTAACC, CTTAAC, TGCTAA,
GATCCG, CCAGGT, TTCAGC, ATGATC, and TCGGAT. In some embodiments,
the barcode is located between sequence C and sequence D. In some
embodiments, the method further comprises the step of identifying
the sample from which a target polynucleotide is derived based on
the barcode sequence. In some embodiments, the fragmented
polynucleotides have a median length between about 200 and about
1000 base pairs. In some embodiments, step (f) comprises (i)
sequencing by extension of a first sequencing primer that
hybridizes to a position located 3' from the barcode; and then (ii)
sequencing by extension of a second sequencing primer that
hybridizes to a position located 5' from the barcode. In some
embodiments, the solid support is a channel of a flow cell. In some
embodiments, steps (b) and (c) are performed by an automated
system, such as a liquid handler (e.g. a Biomek FXP). In some
embodiments, step (d) is performed by an automated system, such as
a system comprising a cBot machine. In some embodiments, the
automated system that performs step (d) also performs step (e). In
some embodiments, sequencing data are generated for at least about
100 different target polynucleotides. In some embodiments, step (d)
utilizes at least about 10 .mu.g of DNA in a single flow cell. In
some embodiments, the method is performed on a plurality of samples
in parallel. In some embodiments, step (c) is performed in
quadruplicate for each of a plurality of samples. In some
embodiments, the amount of DNA is measured at the completion of one
or more of steps (a), (b), and (c). In some embodiments, one or
more of steps (a), (b), and (c) has a minimum threshold for the
amount of DNA remaining at the end of that step to be used in the
next step, such as 1 .mu.g, 0.8 .mu.g, 13 .mu.g, respectively. In
some embodiments, sequencing data are generated for at least about
10.sup.8 target sequences in a single reaction. In some
embodiments, sequencing data are generated for less than about
10.sup.7 target sequences per sample in a single reaction. In some
embodiments, presence or absence of one or more causal genetic
variants is determined with an accuracy of at least about 90%. In
some embodiments, the plurality of different first oligonucleotides
further comprises additional first oligonucleotides comprising
sequence A and sequence B, wherein sequence B is different for each
different additional first oligonucleotide, is at the 3' end of
each additional first oligonucleotide, and is complementary to a
sequence comprising a non-subject sequence or a sequence within 200
nucleotides of a non-subject sequence.
[0008] In one aspect, the invention provides a method of enriching
a plurality of different target polynucleotides in a sample. In
some embodiments, the method comprises: (a) joining an adapter
oligonucleotide to each of the target polynucleotides, wherein the
adapter oligonucleotide comprises sequence Y; (b) hybridizing a
plurality of different oligonucleotide primers to the adapted
target polynucleotides, wherein each oligonucleotide primer
comprises sequence Z and sequence W; wherein sequence Z is common
among all oligonucleotide primers; and further wherein sequence W
is different for each different oligonucleotide primer, is
positioned at the 3' end of each oligonucleotide primer, and is
complementary to a sequence comprising a causal genetic variant or
a sequence within 200 nucleotides of a causal genetic variant; (c)
in an extension reaction, extending the oligonucleotide primers
along the adapted target polynucleotides to produce extended
primers comprising sequence Z and sequence Y', wherein sequence Y'
is complementary to sequence Y; and (d) exponentially amplifying
the purified extension products using a pair of amplification
primers comprising (i) a first amplification primer comprising
sequence V and sequence Z, wherein sequence Z is positioned at the
3' end of the first amplification primer; and (ii) a second
amplification primer comprising sequence X and sequence Y, wherein
sequence Y is positioned at the 3' end of the second amplification
primer. In some embodiments, sequences W, Y, and Z are different
sequences and comprise 5 or more nucleotides each. Each
oligonucleotide primer may or may not comprise a first binding
partner. In some embodiments, the method further comprises, before
step (d), exposing the extended primers to a solid surface
comprising a second binding partner that binds to the first binding
partner, thereby purifying the extended primers away from one or
more components of the extension reaction. In some embodiments, the
method does not comprise a purification step.
[0009] In some embodiments, the plurality of oligonucleotide
primers comprises at least about 100 different oligonucleotide
primers each comprising a different sequence W. In some
embodiments, sequence W of one or more of the plurality of
oligonucleotide primers comprises a sequence selected from the
group consisting of SEQ ID NOs 22-121, shown in FIG. 4. In some
embodiments, the target polynucleotides comprise fragmented
polynucleotides. In some embodiments, the fragmented
polynucleotides have a median length between about 200 and about
1000 base pairs. In some embodiments, the fragmented
polynucleotides are treated to produce blunt ends or to have a
defined overhang prior to step (a), such as an overhang consisting
of an adenine. In some embodiments, the first binding partner and
the second binding partner are members of a binding pair, such as
streptavidin and biotin. In some embodiments, the solid surface is
a bead, such as a bead that is responsive to a magnetic field. In
some embodiments, the purifying step comprises application of a
magnetic field to purify the beads. In some embodiments, the
extended primers are purified away from the target polynucleotides.
In some embodiments, the method further comprises sequencing the
products of step (d). In some embodiments, sequencing comprises
amplifying the products of step (d) by bridge amplification with
bound oligonucleotides attached to a solid support to produce
double-stranded bridge polynucleotides; cleaving one strand of a
bridge polynucleotide at a cleavage site in a bound
oligonucleotide; denaturing the cleaved bridge polynucleotide to
produce a free single-stranded polynucleotide comprising a target
sequence attached to the solid support; and sequencing the target
sequence by extending a sequencing primer hybridized to at least a
portion of one or more sequences added during one or more of steps
(a), (c), or (d). In some embodiments, sequencing comprises
amplifying the products of step (d) by extension of a bound primer
on a solid support to produce bound templates, hybridizing a
sequencing primer to a bound template, extending the sequencing
primer, and identifying nucleotides added by extension of the
sequencing primer. In some embodiments, the plurality of different
oligonucleotide primers further comprises additional
oligonucleotide primers comprising sequence Z and sequence W,
wherein sequence W is different for each different additional
oligonucleotide primer, is at the 3' end of each additional
oligonucleotide primer, and is complementary to a sequence
comprising a non-subject sequence or a sequence within 200
nucleotides of a non-subject sequence.
[0010] In one aspect, the invention provides a method of enriching
a plurality of different target polynucleotides in a sample. In
some embodiments, the method comprises: (a) hybridizing a plurality
of different oligonucleotide primers to the target polynucleotides,
wherein each oligonucleotide primer comprises sequence Z and
sequence W; wherein sequence Z is common among all oligonucleotide
primers; and further wherein sequence W is different for each
different oligonucleotide primer, is positioned at the 3' end of
each oligonucleotide primer, and is complementary to a sequence
comprising a causal genetic variant or a sequence within 200
nucleotides of a causal genetic variant; (b) in an extension
reaction, extending the oligonucleotide primers along the target
polynucleotides to produce extended primers; (c) joining an adapter
oligonucleotide to each extended primer, wherein the adapter
oligonucleotide comprises sequence Y', and further wherein sequence
Y' is the complement of a sequence Y; and (d) exponentially
amplifying the purified extension products using a pair of
amplification primers comprising (i) a first amplification primer
comprising sequence V and sequence Z, wherein sequence Z is
positioned at the 3' end of the first amplification primer; and
(ii) a second amplification primer comprising sequence X and
sequence Y, wherein sequence Y is positioned at the 3' end of the
second amplification primer. In some embodiments, sequences W, Y,
and Z are different sequences and comprise 5 or more nucleotides
each. Each oligonucleotide primer may or may not comprise a first
binding partner. In some embodiments, the method further comprises,
before step (d), exposing the extended primers to a solid surface
comprising a second binding partner that binds to the first binding
partner, thereby purifying the extended primers away from one or
more components of the extension reaction. In some embodiments, the
method does not comprise a purification step.
[0011] In some embodiments, the plurality of oligonucleotide
primers comprises at least about 100 different oligonucleotide
primers each comprising a different sequence W. In some
embodiments, sequence W of one or more of the plurality of
oligonucleotide primers comprises a sequence selected from the
group consisting of SEQ ID NOs 22-121, shown in FIG. 4. In some
embodiments, the target polynucleotides comprise fragmented
polynucleotides. In some embodiments, the fragmented
polynucleotides have a median length between about 200 and about
1000 base pairs. In some embodiments, step (b) further comprises
treating the extended primers and the target polynucleotides to
which they are hybridized to produce blunt ends or to have a
defined overhang prior to step (c), such as an overhang consisting
of an adenine. In some embodiments, the first binding partner and
the second binding partner are members of a binding pair, such as
streptavidin and biotin. In some embodiments, the solid surface is
a bead, such as a bead that is responsive to a magnetic field. In
some embodiments, the purifying step comprises application of a
magnetic field to purify the beads. In some embodiments, the
extended primers are purified away from the target polynucleotides.
In some embodiments, the method further comprises sequencing the
products of step (d). In some embodiments, sequencing comprises
amplifying the products of step (d) by bridge amplification with
bound oligonucleotides attached to a solid support to produce
double-stranded bridge polynucleotides, cleaving one strand of a
bridge polynucleotide at a cleavage site in a bound
oligonucleotide, denaturing the cleaved bridge polynucleotide to
produce a free single-stranded polynucleotide comprising a target
sequence attached to the solid support, and sequencing the target
sequence by extending a sequencing primer hybridized to at least a
portion of one or more sequences added during one or more of steps
(b), (c), or (d). In some embodiments, sequencing comprises
amplifying the products of step (d) by extension of a bound primer
on a solid support to produce bound templates, hybridizing a
sequencing primer to a bound template, extending the sequencing
primer, and identifying nucleotides added by extension of the
sequencing primer. In some embodiments, the plurality of different
oligonucleotide primers further comprises additional
oligonucleotide primers comprising sequence Z and sequence W,
wherein sequence W is different for each different additional
oligonucleotide primer, is at the 3' end of each additional
oligonucleotide primer, and is complementary to a sequence
comprising a non-subject sequence or a sequence within 200
nucleotides of a non-subject sequence.
[0012] In one aspect, the invention provides a method of detecting
genetic variation in a subject's genome. In some embodiments, the
method comprises: (a) providing a plurality of clusters of
polynucleotides, wherein (i) each cluster comprises multiple copies
of a nucleic acid duplex attached to a support; (ii) each duplex in
a cluster comprises a first molecule comprising sequences
A-B-G'-D'-C' from 5' to 3' and a second molecule comprising
sequences C-D-G-B'-A' from 5' to 3'; (iii) sequence A' is
complementary to sequence A, sequence B' is complementary to
sequence B, sequence C' is complementary to sequence C, sequence D'
is complementary to sequence D, and sequence G' is complementary to
sequence G; (iv) sequence G is a portion of a target polynucleotide
sequence from a subject and is different for each of a plurality of
clusters; and (v) sequence B' is located 5' with respect to
sequence G in the corresponding target polynucleotide sequence; (b)
sequencing sequence G' by extension of a first primer comprising
sequence D to produce an R1 sequence for each cluster; (c)
sequencing sequence B' by extension of a second primer comprising
sequence A to produce R2 sequence for each cluster; (d) performing
a first alignment using a first algorithm to align all R1 sequences
to a first reference sequence; (e) performing a second alignment
using a second algorithm to locally align R1 sequences identified
in said first alignment as likely to contain an insertion or
deletion with respect to the first reference sequence, to produce a
single consensus alignment for each insertion or deletion; (f)
performing an R2 alignment by aligning all R2 sequences to a second
reference sequence; and (g) transmitting a report identifying
sequence variation identified by steps (d) to (f) to a
receiver.
[0013] In some embodiments, the first reference sequence comprises
a reference genome. In some embodiments, the second reference
sequence consists of every sequence B for every different target
polynucleotide. In some embodiments, R2 sequences are aligned
independently of R1 sequences. In some embodiments, the method
further comprises discarding an R1 sequence that aligns to a first
position in the first reference sequence that is more than 10,000
base pairs away from a second position in the first reference
sequence to which the R2 sequence for the same cluster aligns. In
some embodiments, the method further comprises deleting a portion
of an R1 sequence for a cluster when the portion of R1 sequence to
be deleted is identical to at least a portion of sequence B' for
that cluster and sequence G is shorter than the R1 sequence for
that cluster. In some embodiments, the method further comprises
deleting a portion of an R1 sequence for a cluster when the portion
of R1 sequence to be deleted is identical to at least a portion of
any sequence B', the portion includes either the 5' or 3'
nucleotide of R1, and either (i) no R2 sequence was produced for
the cluster or (ii) R2 sequence produced is not identical to any
sequence B. In some embodiments, performing the first alignment
with a system using the first algorithm takes less time and/or uses
less system memory to align all R1 reads than would be taken and/or
used if the system used the second algorithm to perform the first
alignment. In some embodiments, the first algorithm is based on the
Burrows-Wheeler transform. In some embodiments, the second
algorithm is based on the Smith-Waterman algorithm or a hash
function. In some embodiments, R1 and R2 sequences are generated
for at least 100 different target polynucleotides. In some
embodiments, sequences A, B, C, and D are at least 5 nucleotides in
length. In some embodiments, sequence G of every cluster is 1 to
1000 nucleotides in length. In some embodiments, each probe
sequence B of a plurality of clusters is complementary to a
sequence comprising a causal genetic variant or a sequence within
200 nucleotides of a causal genetic variant. In some embodiments,
sequence B of one or more of the clusters comprises a sequence
selected from the group consisting of SEQ ID NOs: 22-121. In some
embodiments, an R1 sequence is produced for at least about 10.sup.8
clusters in a single reaction. In some embodiments, presence,
absence, or allele ratio of one or more causal genetic variants is
determined with an accuracy of at least about 90%. In some
embodiments, the consensus sequence identifies an insertion, a
deletion, or an insertion and a deletion in a target polynucleotide
with an accuracy of at least about 90%. In some embodiments each
probe sequence B of a plurality of clusters is complementary to a
sequence comprising a non-subject sequence or a sequence within 200
nucleotides of a non-subject sequence. In some embodiments, the
presence or absence of one or more non-subject sequences is
determined with an accuracy of at least about 90%. In some
embodiments, the method further comprises calculating a plurality
of probabilities based on the R1 sequences for the subject and
including the probabilities in the report, wherein each probability
is a probability of the subject or a subject's offspring having or
developing a disease or trait.
[0014] In some embodiments, each first molecule comprises a barcode
sequence. In some embodiments, each barcode differs from every
other barcode in a plurality of different barcodes analyzed in
parallel. In some embodiments, the barcode sequence is associated
with a single sample in a pool of samples sequenced in a single
reaction. In some embodiments, each of a plurality of barcode
sequences is uniquely associated with a single sample in a pool of
samples sequenced in a single reaction. In some embodiments, the
barcode sequence is located 5' from sequence D'. In some
embodiments, the method further comprises hybridizing a third
primer to sequence C' and sequencing the barcode sequence by
extension of the third primer to produce a barcode sequence for
each cluster. In some embodiments, the method further comprises
grouping sequences from the clusters based on the barcode
sequences. In some embodiments, the method further comprises
discarding all but one of a plurality of R1 sequences having the
same sequence and alignment within a barcode sequence grouping.
[0015] In one aspect, the invention provides a method of detecting
genetic variation in a subject's genome. In some embodiments, the
method comprises: (a) providing sequencing data for a plurality of
clusters of polynucleotides, wherein (i) each cluster comprised
multiple copies of a nucleic acid duplex attached to a support;
(ii) each duplex in a cluster comprised a first molecule comprising
sequences A-B-G'-D'-C' from 5' to 3' and a second molecule
comprising sequences C-D-G-B'-A' from 5' to 3'; (iii) sequence A'
is complementary to sequence A, sequence B' is complementary to
sequence B, sequence C' is complementary to sequence C, sequence D'
is complementary to sequence D, and sequence G' is complementary to
sequence G; (iv) sequence G is a portion of a target polynucleotide
sequence from a subject and is different for each of a plurality of
clusters; (v) sequence B' is located 5' with respect to sequence G
in the corresponding target polynucleotide sequence; (viii) the
sequencing data comprises R1 sequences generated by extension of a
first primer comprising sequence D; and (vi) the sequencing data
comprises R2 sequences generated by extension of a second primer
comprising sequence A; (b) performing a first alignment using a
first algorithm to align all R1 sequences to a first reference
sequence; (c) performing a second alignment using a second
algorithm to locally align R1 sequences identified in said first
alignment as likely to contain an insertion or deletion with
respect to the first reference sequence, to produce a single
consensus alignment for each insertion or deletion; (d) performing
an R2 alignment by aligning all R2 sequences to a second reference
sequence; and (e) transmitting a report identifying sequence
variation identified by steps (b) to (d) to a receiver.
[0016] In some embodiments, the first reference sequence comprises
a reference genome. In some embodiments, the second reference
sequence consists of every sequence B for every different target
polynucleotide. In some embodiments, R2 sequences are aligned
independently of R1 sequences. In some embodiments, the method
further comprises discarding an R1 sequence that aligns to a first
position in the first reference sequence that is more than 10,000
base pairs away from a second position in the first reference
sequence to which the R2 sequence for the same cluster aligns. In
some embodiments, the method further comprises deleting a portion
of an R1 sequence for a cluster when the portion of R1 sequence to
be deleted is identical to at least a portion of sequence B' for
that cluster and sequence G is shorter than the R1 sequence for
that cluster. In some embodiments, the method further comprises
deleting a portion of an R1 sequence for a cluster when the portion
of R1 sequence to be deleted is identical to at least a portion of
any sequence B', the portion includes either the 5' or 3'
nucleotide of R1, and either (i) no R2 sequence was produced for
the cluster or (ii) R2 sequence produced is not identical to any
sequence B. In some embodiments, performing the first alignment
with a system using the first algorithm takes less time and/or uses
less system memory to align all R1 reads than would be taken and/or
used if the system used the second algorithm to perform the first
alignment. In some embodiments, the first algorithm is based on the
Burrows-Wheeler transform. In some embodiments, the second
algorithm is based on the Smith-Waterman algorithm or a hash
function. In some embodiments, the sequencing data comprises R1 and
R2 sequences for at least 100 different target polynucleotides. In
some embodiments, sequences A, B, C, and D are at least 5
nucleotides in length. In some embodiments, sequence G of every
cluster is 1 to 1000 nucleotides in length. In some embodiments,
each probe sequence B of a plurality of clusters is complementary
to a sequence comprising a causal genetic variant or a sequence
within 200 nucleotides of a causal genetic variant. In some
embodiments, sequence B of one or more of the clusters comprises a
sequence selected from the group consisting of SEQ ID NOs: 22-121.
In some embodiments, sequencing data comprises at least about
10.sup.8 R1 sequences from a single reaction. In some embodiments,
presence, absence, or allele ratio of one or more causal genetic
variants is determined with an accuracy of at least about 90%. In
some embodiments, the consensus sequence identifies an insertion, a
deletion, or an insertion and a deletion in a target polynucleotide
with an accuracy of at least about 90%. In some embodiments each
probe sequence B of a plurality of clusters is complementary to a
sequence comprising a non-subject sequence or a sequence within 200
nucleotides of a non-subject sequence. In some embodiments, the
presence or absence of one or more non-subject sequences is
determined with an accuracy of at least about 90%. In some
embodiments, the method further comprises calculating a plurality
of probabilities based on the R1 sequences for the subject and
including the probabilities in the report, wherein each probability
is a probability of the subject or a subject's offspring having or
developing a disease or trait.
[0017] In some embodiments, each first molecule comprises a barcode
sequence. In some embodiments, each barcode differs from every
other barcode in a plurality of different barcodes analyzed in
parallel. In some embodiments, the barcode sequence is associated
with a single sample in a pool of samples sequenced in a single
reaction and represented in the sequencing data. In some
embodiments, each of a plurality of barcode sequences is uniquely
associated with a single sample in a pool of samples sequenced in a
single reaction. In some embodiments, the barcode sequence is
located 5' from sequence D'. In some embodiments, the sequencing
data further comprises a barcode sequence for each cluster
generated by extension of a third primer comprising sequence C. In
some embodiments, the method further comprises grouping sequences
from the clusters based on the barcode sequences. In some
embodiments, the method further comprises discarding all but one of
a plurality of R1 sequences having the same sequence and alignment
within a barcode sequence grouping.
INCORPORATION BY REFERENCE
[0018] All publications, patents, and patent applications mentioned
in this specification are herein incorporated by reference to the
same extent as if each individual publication, patent, or patent
application was specifically and individually indicated to be
incorporated by reference.
BRIEF DESCRIPTION OF THE DRAWINGS
[0019] The novel features of the invention are set forth with
particularity in the appended claims. A better understanding of the
features and advantages of the present invention will be obtained
by reference to the following detailed description that sets forth
illustrative embodiments, in which the principles of the invention
are utilized, and the accompanying drawings of which:
[0020] FIG. 1 illustrates a portion of an example solid support
comprising attached oligonucleotides, and the first steps in an
example bridge amplification process to amplify a target
polynucleotide.
[0021] FIG. 2 illustrates an example capture and amplification
process in accordance with an embodiment of the invention.
[0022] FIG. 3 provides a table of example causal genetic
variants.
[0023] FIG. 4 provides a table of example sequences that are
complementary to example specific target sequences.
[0024] FIG. 5 illustrates an example amplification process in
accordance with an embodiment of the invention.
[0025] FIG. 6 illustrates an example process of target
amplification, bridge amplification, and sequencing.
[0026] FIG. 7 illustrates an example amplification process in
accordance with an embodiment of the invention.
[0027] FIG. 8 illustrates a non-limiting example of a computer
system useful in the methods of the invention.
[0028] FIG. 9A-M provides a number of AIMs that distinguish
different populations. The entries refer to items in the dbSNP
database, a database of genetic variants maintained by the US
government: www.ncbi.nlm.nih.gov/projects/SNP/. Curated records in
dbSNP contain information that describes the sequence and location
of genetic variants, and where available the frequency of alleles
of those variants in different populations. rs numbers (for
example, rs332, rs25, etc.) are the ID numbers used to index the
portion of the dbSNP database.
[0029] FIG. 10 illustrates an example data-handling process for
aligning sequencing data.
[0030] FIG. 11 illustrates an example process for generating an
alignment using sequencing data.
[0031] FIGS. 12A and 12B illustrate an alignment before and after a
fix_align step in an example alignment process.
[0032] FIGS. 13A and 13B illustrate an alignment before and after
an example local alignment step.
[0033] FIGS. 14-17 demonstrate exemplary processes of delivering a
probability that a user is a carrier of rare genetic disease.
[0034] FIG. 18 illustrates exemplary the input and output steps for
report generation for two hypothetical parents: Mama Hen (Jane Doe)
and Papa Hen (John Doe).
[0035] FIG. 19 illustrates the positional relationship of sequence
regions considered in a step of a sample probe design process.
[0036] The patent or application file contains at least one drawing
executed in color. Copies of this patent or patent application
publication with color drawing(s) will be provided by the Office
upon request and payment of the necessary fee.
DETAILED DESCRIPTION OF THE INVENTION
[0037] The terms "polynucleotide", "nucleotide", "nucleotide
sequence", "nucleic acid" and "oligonucleotide" are used
interchangeably. They refer to a polymeric form of nucleotides of
any length, either deoxyribonucleotides or ribonucleotides, or
analogs thereof. Polynucleotides may have any three dimensional
structure, and may perform any function, known or unknown. The
following are non limiting examples of polynucleotides: coding or
non-coding regions of a gene or gene fragment, intergenic DNA, loci
(locus) defined from linkage analysis, exons, introns, messenger
RNA (mRNA), transfer RNA, ribosomal RNA, short interfering RNA
(siRNA), short-hairpin RNA (shRNA), micro-RNA (miRNA), small
nucleolar RNA, ribozymes, cDNA, recombinant polynucleotides,
branched polynucleotides, plasmids, vectors, isolated DNA of any
sequence, isolated RNA of any sequence, nucleic acid probes,
adapters, and primers. A polynucleotide may comprise modified
nucleotides, such as methylated nucleotides and nucleotide analogs.
If present, modifications to the nucleotide structure may be
imparted before or after assembly of the polymer. The sequence of
nucleotides may be interrupted by non nucleotide components. A
polynucleotide may be further modified after polymerization, such
as by conjugation with a labeling component, tag, reactive moiety,
or binding partner. Polynucleotide sequences, when provided, are
listed in the 5' to 3' direction, unless stated otherwise.
[0038] As used herein, the term "target polynucleotide" refers to a
nucleic acid molecule or polynucleotide in a population of nucleic
acid molecules having a target sequence to which one or more
oligonucleotides of the invention are designed to hybridize. In
some embodiments, a target sequence uniquely identifies a sequence
derived from a sample, such as a particular genomic, mitochondrial,
bacterial, viral, or RNA (e.g. mRNA, miRNA, primary miRNA, or
pre-miRNA) sequence. In some embodiments, a target sequence is a
common sequence shared by multiple different target
polynucleotides, such as a common adapter sequence joined to
different target polynucleotides. "Target polynucleotide" may be
used to refer to a double-stranded nucleic acid molecule comprising
a target sequence on one or both strands, or a single-stranded
nucleic acid molecule comprising a target sequence, and may be
derived from any source of or process for isolating or generating
nucleic acid molecules. A target polynucleotide may comprise one or
more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) target
sequences, which may be the same or different. In general,
different target polynucleotides comprise different sequences, such
as one or more different nucleotides or one or more different
target sequences.
[0039] "Hybridization" and "annealing" refer to a reaction in which
one or more polynucleotides react to form a complex that is
stabilized via hydrogen bonding between the bases of the nucleotide
residues. The hydrogen bonding may occur by Watson Crick base
pairing, Hoogstein binding, or in any other sequence specific
manner. The complex may comprise two strands forming a duplex
structure, three or more strands forming a multi stranded complex,
a single self hybridizing strand, or any combination of these. A
hybridization reaction may constitute a step in a more extensive
process, such as the initiation of a PCR, or the enzymatic cleavage
of a polynucleotide by a ribozyme. A first sequence that can be
stabilized via hydrogen bonding with the bases of the nucleotide
residues of a second sequence is said to be "hybridizable" to the
second sequence. In such a case, the second sequence can also be
said to be hybridizable to the first sequence.
[0040] In general, a "complement" of a given sequence is a sequence
that is fully complementary to and hybridizable to the given
sequence. In general, a first sequence that is hybridizable to a
second sequence or set of second sequences is specifically or
selectively hybridizable to the second sequence or set of second
sequences, such that hybridization to the second sequence or set of
second sequences is preferred (e.g. thermodynamically more stable
under a given set of conditions, such as stringent conditions
commonly used in the art) to hybridization with non-target
sequences during a hybridization reaction. Typically, hybridizable
sequences share a degree of sequence complementarity over all or a
portion of their respective lengths, such as between 25%-100%
complementarity, including at least about 25%, 30%, 35%, 40%, 45%,
50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99%, and 100% sequence complementarity.
[0041] The term "hybridized" as applied to a polynucleotide refers
to a polynucleotide in a complex that is stabilized via hydrogen
bonding between the bases of the nucleotide residues. The hydrogen
bonding may occur by Watson Crick base pairing, Hoogstein binding,
or in any other sequence specific manner. The complex may comprise
two strands forming a duplex structure, three or more strands
forming a multi-stranded complex, a single self hybridizing strand,
or any combination of these. The hybridization reaction may
constitute a step in a more extensive process, such as the
initiation of a PCR reaction, ligation reaction, sequencing
reaction, or cleavage reaction.
[0042] The practice of the present invention employs, unless
otherwise indicated, conventional techniques of immunology,
biochemistry, chemistry, molecular biology, microbiology, cell
biology, genomics and recombinant DNA, which are within the skill
of the art. See e.g. Sambrook, Fritsch and Maniatis, MOLECULAR
CLONING: A LABORATORY MANUAL, 2nd edition (1989); CURRENT PROTOCOLS
IN MOLECULAR BIOLOGY (F. M. Ausubel, et al. eds., (1987)); the
series METHODS IN ENZYMOLOGY (Academic Press, Inc.): PCR 2: A
PRACTICAL APPROACH (M. J. MacPherson, B. D. Hames and G. R. Taylor
eds. (1995)), Harlow and Lane, eds. (1988) ANTIBODIES, A LABORATORY
MANUAL, and ANIMAL CELL CULTURE (R. I. Freshney, ed. (1987)).
[0043] In one aspect, the invention provides a method of producing
an apparatus for sequencing a plurality of target polynucleotides.
In one embodiment, the method comprises (a) providing a solid
support having a reactive surface; and (b) attaching to the solid
support a plurality of oligonucleotides. In some embodiments, the
plurality of oligonucleotides comprises (i) a plurality of
different first oligonucleotides comprising sequence A and sequence
B, wherein sequence A is common among all first oligonucleotides;
and further wherein sequence B is different for each different
first oligonucleotide, is at the 3' end of each first
oligonucleotide, and is complementary to a sequence comprising a
causal genetic variant or a sequence within 200 nucleotides of a
causal genetic variant; (ii) a plurality of second oligonucleotides
comprising sequence A at each 3' end; and (iii) a plurality of
third oligonucleotides comprising sequence C at each 3' end,
wherein sequence C is the same as a sequence shared by a plurality
of different target polynucleotides. In some embodiments, one or
more of sequences A, B, and C are different sequences. In some
embodiments, one or more of sequences A, B, and C are about, less
than about, or more than about 5%, 10%, 15%, 20%, 25%, 30%, 40%,
50%, 60%, 70%, 80%, 90%, or more different from one or more of the
other of sequences A, B, and C (e.g. have less than about 10%, 20%,
30%, 40%, 50%, 60%, 70%, 80%, 90%, or more sequence identity). In
some embodiments, one or more of sequences A, B, and C comprise
about, less than about, or more than about 1, 2, 3, 4, 5, 6, 7, 8,
9, 10, 15, 20, or more nucleotides each.
[0044] A variety of suitable solid support materials are known in
the art. Non-limiting examples of solid support materials include
silica-based substrates, such as glass, fused silica and other
silica-containing materials; silicone hydrides or plastic
materials, such as polyethylene, polystyrene, poly(vinyl chloride),
polypropylene, nylons, polyesters, polycarbonates, poly(methyl
methacrylate), and cyclic olefin polymer substrates; and other
solid support materials, such as gold, titanium dioxide, or silicon
supports. The solid support materials may be provided in any
suitable form, including but not limited to beads, nanoparticles,
nanocrystals, fibers, microfibers, nanofibers, nanowires,
nanotubes, mats, planar sheets, planar wafers or slides, multiwell
plates, optical slides, flow cells, and channels. A solid support
may further include one or more additional structures, such as
channels, microfluidic channels, capillaries, and wells. In some
embodiments, the solid support is a channel of a flow cell.
[0045] When referring to immobilization or attachment of molecules
(e.g. nucleic acids) to a solid support, the terms "immobilized"
and "attached" are used interchangeably herein and both terms, are
intended to encompass direct or indirect, covalent or non-covalent
attachment, unless indicated otherwise. In some embodiments of the
invention, covalent attachment may be preferred, but generally all
that is required is that the molecules (e.g. nucleic acids) remain
immobilized or attached to the support under the conditions in
which it is intended to use the support, for example in nucleic
acid amplification and/or sequencing applications.
[0046] In some embodiments, a solid support material comprises a
material that is reactive, such that under specified conditions, a
molecule (such as an oligonucleotide or modified oligonucleotide)
can be attached directly to the surface of the solid support. In
some embodiments, a solid support material comprises an inert
substrate or matrix (e.g. glass slides, polymer beads, or other
solid support material) that has been "functionalized", for example
by application of a layer or coating of an intermediate material
comprising reactive groups which permit attachment (e.g. covalent
attachment) to biomolecules, such as polynucleotides. Examples of
such supports include, but are not limited to, polyacrylamide
hydrogels supported on an inert substrate such as glass. In such
embodiments, the biomolecules (e.g. oligonucleotide) may be
directly covalently attached to the intermediate material (e.g. the
hydrogel) but the intermediate material may itself be
non-covalently attached to the substrate or matrix (e.g. the glass
substrate).
[0047] A non-limiting example of a reactive surface includes the
use of biotinylated albumins (BSA) to form a stable attachment of
biotin groups by physisorption of the protein onto surfaces.
Covalent modification can be performed using silanes, which have
been used to attach molecules to a solid support, usually a glass
slide. By way of example, a mixture of tetraethoxysilane and
triethoxy-bromoacetamidopropyl-silane (e.g. in a ratio of 1:100)
can be used to prepare functionalized glass slides which permit
attachment of nucleic acids including a thiophosphate or
phosphorothioate functionality. Biotin molecules can be attached to
surfaces using appropriately reactive species such as
biotin-PEG-succinimidyl ester which reacts with an amino
surface.
[0048] In some embodiments, oligonucleotides to be attached to the
solid support comprise a reactive moiety. In general, a reactive
moiety includes any moiety that facilitates attachment to the solid
support by reacting with the reactive surface. In some embodiments,
functionalized polyacrylamide hydrogels are used to attach a
plurality of oligonucleotides comprising a reactive moiety, wherein
the reactive moiety is a sulfur-containing nucleophilic group.
Examples of appropriate sulfur nucleophile-containing
polynucleotides are disclosed in Zhao et al (Nucleic Acids
Research, 2001, 29(4), 955-959) and Pirrung et al (Langmuir, 2000,
16, 2185-2191) and include, for example, simple thiols,
thiophosphates, and thiophosphoramidates. Preferred hydrogels are
those formed from a mixture of (i) a first co-monomer which is
acrylamide, methacrylamide, hydroxyethyl methacrylate, or N-vinyl
pyrrolidinone; and (ii) a second co-monomer which is a
functionalized acrylamide or acrylate, such as
N-(5-bromoacetamidylpentyl) acrylamide, tetramethylethylenediamine.
In some embodiments, a reactive surface comprising a functionalized
polyacrylamide is produced from a polymerization mixture comprising
acrylamide, N-(5-bromoacetamidylpentyl) acrylamide,
tetramethylethylenediamine, and potassium persulfate. Further
non-limiting examples of support materials and reactive surfaces
are provided by US20120053074 and WO2005065814, which are hereby
incorporated by reference in their entireties.
[0049] Oligonucleotides to which the solid support is exposed for
attachment may be of any suitable length, and may comprise one or
more sequence elements. Examples of sequence elements include, but
are not limited to, one or more amplification primer annealing
sequences or complements thereof, one or more sequencing primer
annealing sequences or complements thereof, one or more common
sequences shared among multiple different oligonucleotides or
subsets of different oligonucleotides, one or more restriction
enzyme recognition sites, one or more target recognition sequences
complementary to one or more target polynucleotide sequences, one
or more random or near-random sequences (e.g. one or more
nucleotides selected at random from a set of two or more different
nucleotides at one or more positions, with each of the different
nucleotides selected at one or more positions represented in a pool
of oligonucleotides comprising the random sequence), one or more
spacers, and combinations thereof. Two or more sequence elements
can be non-adjacent to one another (e.g. separated by one or more
nucleotides), adjacent to one another, partially overlapping, or
completely overlapping. For example, an amplification primer
annealing sequence can also serve as a sequencing primer annealing
sequence. Sequence elements can be located at or near the 3' end,
at or near the 5' end, or in the interior of the oligonucleotide.
In general, as used herein, a sequence element located "at the 3'
end" includes the 3'-most nucleotide of the oligonucleotide, and a
sequence element located "at the 5' end" includes the 5'-most
nucleotide of the oligonucleotide. In some embodiments, a sequence
element is about, less than about, or more than about 1, 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30,
35, 40, 50, or more nucleotides in length. In some embodiments, an
oligonucleotide is about, less than about, or more than about 5,
10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, or more
nucleotides in length.
[0050] A spacer may consist of a repeated single nucleotide (e.g.
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more of the same nucleotide in a
row), or a sequence of 2, 3, 4, 5, 6, 7, 8, 9, 10, or more
nucleotides repeated 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more times.
A spacer may comprise or consist of a specific sequence, such as a
sequence that does not hybridize to any target sequence in a
sample. A spacer may comprise or consist of a sequence of randomly
selected nucleotides.
[0051] In some embodiments, a plurality of different first
oligonucleotides are attached to the solid support, each comprising
a sequence A that is common among all first oligonucleotides and a
sequence B that is different for each different first
oligonucleotide. In some embodiments, sequence B of each first
oligonucleotide is complementary to a different target sequence. In
some embodiments, the plurality of first oligonucleotides comprises
about, less than about, or more than about 5, 10, 25, 50, 75, 100,
125, 150, 175, 200, 300, 400, 500, 750, 1000, 2500, 5000, 7500,
10000, 20000, 50000, or more different first oligonucleotides, each
comprising a different sequence B. In some embodiments, sequence B
of one or more of the plurality of first oligonucleotides comprises
a sequence selected from the group consisting of SEQ ID NOs 22-121,
shown in FIG. 4 (e.g. 1, 5, 10, 25, 50, 75, or 100 different
oligonucleotides each with a different sequence from FIG. 4). In
some embodiments, sequence B or the target sequence to which it
specifically hybridizes comprises a causal genetic variant. In some
embodiments, sequence B or the target sequence to which it
specifically hybridizes is within about, less than about, or more
than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40,
45, 50, 60, 70, 80, 90, 100, 200, 500 or more nucleotides of a
causal genetic variant. Causal genetic variants are typically
located downstream of a first oligonucleotide, such that at least a
portion of the causal genetic variant serves as template for
extension of a first oligonucleotide. In general, causal genetic
variants are genetic variants for which there is statistical,
biological, and/or functional evidence of association with a
disease or trait. A single causal genetic variant can be associated
with more than one disease or trait. In some embodiments, a causal
genetic variant can be associated with a Mendelian trait, a
non-Mendelian trait, or both. Causal genetic variants can manifest
as variations in a polynucleotide, such 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 20, 50, or more sequence differences (such as between a
polynucleotide comprising the causal genetic variant and a
polynucleotide lacking the causal genetic variant at the same
relative genomic position). Non-limiting examples of types of
causal genetic variants include single nucleotide polymorphisms
(SNP), deletion/insertion polymorphisms (DIP), copy number variants
(CNV), short tandem repeats (STR), restriction fragment length
polymorphisms (RFLP), simple sequence repeats (SSR), variable
number of tandem repeats (VNTR), randomly amplified polymorphic DNA
(RAPD), amplified fragment length polymorphisms (AFLP),
inter-retrotransposon amplified polymorphisms (IRAP), long and
short interspersed elements (LINE/SINE), long tandem repeats (LTR),
mobile elements, retrotransposon microsatellite amplified
polymorphisms, retrotransposon-based insertion polymorphisms,
sequence specific amplified polymorphism, and heritable epigenetic
modification (for example, DNA methylation). A causal genetic
variant may also be a set of closely related causal genetic
variants. Some causal genetic variants may exert influence as
sequence variations in RNA polynucleotides. At this level, some
causal genetic variants are also indicated by the presence or
absence of a species of RNA polynucleotides. Also, some causal
genetic variants result in sequence variations in protein
polypeptides. A number of causal genetic variants are known in the
art. An example of a causal genetic variant that is a SNP is the Hb
S variant of hemoglobin that causes sickle cell anemia. An example
of a causal genetic variant that is a DIP is the delta508 mutation
of the CFTR gene which causes cystic fibrosis. An example of a
causal genetic variant that is a CNV is trisomy 21, which causes
Down's syndrome. An example of a causal genetic variant that is an
STR is tandem repeat that causes Huntington's disease. FIG. 3
provides a table of non-limiting examples of causal genetic
variants, and associated diseases. Non-limiting examples of causal
genetic variants are also described in US20100022406, which is
hereby incorporated by reference in its entirety.
[0052] Causal genetic variants can be originally discovered by
statistical and molecular genetic analyses of the genotypes and
phenotypes of individuals, families, and populations. The causal
genetic variants for Mendelian traits are typically identified in a
two-stage process. In the first stage, families in which multiple
individuals who possess the trait are examined for genotype and
phenotype. Genotype and phenotype data from these families is used
to establish the statistical association between the presence of
the Mendelian trait and the presence of a number of genetic
markers. This association establishes a candidate region in which
the causal genetic variant is likely to map. In a second stage, the
causal genetic variant itself is identified. The second step
typically entails sequencing the candidate region. More
sophisticated, one-stage processes are possible with more advanced
technologies which permit the direct identification of a causal
genetic variant or the identification of smaller candidate regions.
After one causal genetic variant for a trait is discovered,
additional variants for the same trait can be discovered by simple
methods. For example, the gene associated with the trait can be
sequenced in individuals who possess the trait or their relatives.
The invention of new methods for discovering causal genetic
variants is an active area of research. The application of existing
methods and the incorporation of new methods is expected to
continue to result in the discovery of additional causal genetic
variants which can be used or tested for by the devices, systems,
and methods herein. Many causal genetic variants are cataloged in
databases including the Online Mendelian Inheritance in Man (OMIM)
and the Human Gene Mutation Database (HGMD). Causal genetic
variants are also reported in the scholarly literature, at
conferences, and in personal communications between scholars.
[0053] A causal genetic variant may exist at any frequency within a
specified populations. In some embodiments, at least one of the
causal genetic variants causes a trait having an incidence of no
more than 1% a reference population. In another embodiment at least
one of the causal genetic variants causes a trait having an
incidence of no more than 1/10,000 in a reference population. In
some embodiments, a causal genetic variant is associated with a
disease or trait. In some embodiments, a causal genetic variant is
a genetic variant the presence of which increases the risk of
having or developing a disease or trait by about, less than about,
or more than about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%,
70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more. In some
embodiments, a causal genetic variant is a genetic variant the
presence of which increases the risk of having or developing a
disease or trait by about, less than about, or more than about
1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold,
9-fold, 10-fold, 25-fold, 50-fold, 100-fold, 500-fold, 1000-fold,
10000-fold, or more. In some embodiments, a causal genetic variant
is a genetic variant the presence of which increases the risk of
having or developing a disease or trait by any statistically
significant amount, such as an increase having a p-value of about
or less than about 0.1, 0.05, 10.sup.-3, 10.sup.-4, 10.sup.-5,
10.sup.-6, 10.sup.-7, 10.sup.-8, 10.sup.-9, 10.sup.-10, 10.sup.-11,
10.sup.-12, 10.sup.-13, 10.sup.-14, 10.sup.-15, or smaller.
[0054] In some embodiments, a causal genetic variant has a
different degree of association with a disease or trait between two
or more different populations of individuals, such as between two
or more human populations. In some embodiments, a causal genetic
variant has a statistically significant association with a disease
or trait only within one or more populations, such as one or more
human populations. A human population can be a group of people
sharing a common genetic inheritance, such as an ethnic group (for
example, Caucasian). A human population can be a haplotype
population or group of haplotype populations (for example,
haplotype H1, M52). A human population can be a national group (for
example, Americans, English, Irish). A human population can be a
demographic population such as those delineated by age, sex, and
socioeconomic factors. Human populations can be historical
populations. A population can consist of individuals distributed
over a large geographic area such that individuals at extremes of
the distribution may never meet one another. The individuals of a
population can be geographically dispersed into discontinuous
areas. Populations can be informative about biogeographical
ancestry. Populations can also be defined by ancestry. Genetic
studies can define populations. In some embodiments, a population
may be based on ancestry and genetics, with major human populations
corresponding to continental scale groupings, which include Western
Eurasian, sub-Saharan African, East Asian, and Native American.
Most humans can be assigned to at least one of these populations on
the basis of ancestry. A number of smaller populations are also
distinguished as continental groups, including Indigenous
Australian, Oceanian, and Bushmen.
[0055] Very often, populations can be further decomposed into
sub-populations. The relationship between populations and
subpopulations can be hierarchical. For example, the Oceanian
population can be further sub-divided into sub-populations
including Polynesians, Melanesians and Micronesians. The Western
Eurasian population can be further sub-divided into sub-populations
including European, Western/Central Asian, South Asian, and North
African. The European population can be further sub-divided into
sub-populations including North-Western European, Southern
European, and Ashkenazi Jewish populations. The North-Western
European population can be further sub-divided into national
populations including English, Irish, German, Finnish, and the
like. The East Asian population can be further sub-divided into
Chinese, Japanese, and Korean subpopulations. The South Asian
population can be further sub-divided into Indian and Pakistani
populations. The Indian population can be further sub-divided into
Dravidian people, Brahui people, Kannadigas, Malayalis, Tamils,
Telugus, Tuluvas, and Gonds. A sub-population may serve as a
population for the purpose of identifying a causal genetic
variant.
[0056] In some embodiments, a causal genetic variant is associated
with a disease, such as a rare genetic disease. Examples of
diseases with which a causal genetic variant may be associated
include, but are not limited to: 21-Hydroxylase Deficiency,
ABCC8-Related Hyperinsulinism, ARSACS, Achondroplasia,
Achromatopsia, Adenosine Monophosphate Deaminase 1, Agenesis of
Corpus Callosum with Neuronopathy, Alkaptonuria,
Alpha-1-Antitrypsin Deficiency, Alpha-Mannosidosis,
Alpha-Sarcoglycanopathy, Alpha-Thalassemia, Alzheimers, Angiotensin
II Receptor, Type I, Apolipoprotein E Genotyping,
Argininosuccinicaciduria, Aspartylglycosaminuria, Ataxia with
Vitamin E Deficiency, Ataxia-Telangiectasia, Autoimmune
Polyendocrinopathy Syndrome Type 1, BRCA1 Hereditary Breast/Ovarian
Cancer, BRCA2 Hereditary Breast/Ovarian Cancer, one or more other
types of cancer, Bardet-Biedl Syndrome, Best Vitelliform Macular
Dystrophy, Beta-Sarcoglycanopathy, Beta-Thalassemia, Biotinidase
Deficiency, Blau Syndrome, Bloom Syndrome, CFTR-Related Disorders,
CLN3-Related Neuronal Ceroid-Lipofuscinosis, CLN5-Related Neuronal
Ceroid-Lipofuscinosis, CLN8-Related Neuronal Ceroid-Lipofuscinosis,
Canavan Disease, Carnitine Palmitoyltransferase IA Deficiency,
Carnitine Palmitoyltransferase II Deficiency, Cartilage-Hair
Hypoplasia, Cerebral Cavernous Malformation, Choroideremia, Cohen
Syndrome, Congenital Cataracts, Facial Dysmorphism, and Neuropathy,
Congenital Disorder of Glycosylationla, Congenital Disorder of
Glycosylation Ib, Congenital Finnish Nephrosis, Crohn Disease,
Cystinosis, DFNA 9 (COCH), Diabetes and Hearing Loss, Early-Onset
Primary Dystonia (DYTI), Epidermolysis Bullosa Junctional,
Herlitz-Pearson Type, FANCC-Related Fanconi Anemia, FGFR1-Related
Craniosynostosis, FGFR2-Related Craniosynostosis, FGFR3-Related
Craniosynostosis, Factor V Leiden Thrombophilia, Factor V R2
Mutation Thrombophilia, Factor XI Deficiency, Factor XIII
Deficiency, Familial Adenomatous Polyposis, Familial Dysautonomia,
Familial Hypercholesterolemia Type B, Familial Mediterranean Fever,
Free Sialic Acid Storage Disorders, Frontotemporal Dementia with
Parkinsonism-17, Fumarase deficiency, GJB2-Related DFNA 3
Nonsyndromic Hearing Loss and Deafness, GJB2-Related DFNB 1
Nonsyndromic Hearing Loss and Deafness, GNE-Related Myopathies,
Galactosemia, Gaucher Disease, Glucose-6-Phosphate Dehydrogenase
Deficiency, Glutaricacidemia Type 1, Glycogen Storage Disease Type
1a, Glycogen Storage Disease Type Ib, Glycogen Storage Disease Type
II, Glycogen Storage Disease Type III, Glycogen Storage Disease
Type V, Gracile Syndrome, HFE-Associated Hereditary
Hemochromatosis, Halder AIMs, Hemoglobin S Beta-Thalassemia,
Hereditary Fructose Intolerance, Hereditary Pancreatitis,
Hereditary Thymine-Uraciluria, Hexosaminidase A Deficiency,
Hidrotic Ectodermal Dysplasia 2, Homocystinuria Caused by
Cystathionine Beta-Synthase Deficiency, Hyperkalemic Periodic
Paralysis Type 1,
Hyperornithinemia-Hyperammonemia-Homocitrullinuria Syndrome,
Hyperoxaluria, Primary, Type 1, Hyperoxaluria, Primary, Type 2,
Hypochondroplasia, Hypokalemic Periodic Paralysis Type 1,
Hypokalemic Periodic Paralysis Type 2, Hypophosphatasia, Infantile
Myopathy and Lactic Acidosis (Fatal and Non-Fatal Forms),
Isovaleric Acidemias, Krabbe Disease, LGMD2I, Leber Hereditary
Optic Neuropathy, Leigh Syndrome, French-Canadian Type, Long Chain
3-Hydroxyacyl-CoA Dehydrogenase Deficiency, MELAS, MERRF, MTHFR
Deficiency, MTHFR Thermolabile Variant, MTRNR1-Related Hearing Loss
and Deafness, MTTS1-Related Hearing Loss and Deafness,
MYH-Associated Polyposis, Maple Syrup Urine Disease Type 1A, Maple
Syrup Urine Disease Type 1B, McCune-Albright Syndrome, Medium Chain
Acyl-Coenzyme A Dehydrogenase Deficiency, Megalencephalic
Leukoencephalopathy with Subcortical Cysts, Metachromatic
Leukodystrophy, Mitochondrial Cardiomyopathy, Mitochondrial
DNA-Associated Leigh Syndrome and NARP, Mucolipidosis IV,
Mucopolysaccharidosis Type I, Mucopolysaccharidosis Type IIIA,
Mucopolysaccharidosis Type VII, Multiple Endocrine Neoplasia Type
2, Muscle-Eye-Brain Disease, Nemaline Myopathy, Neurological
phenotype, Niemann-Pick Disease Due to Sphingomyelinase Deficiency,
Niemann-Pick Disease Type Cl, Nijmegen Breakage Syndrome,
PPT1-Related Neuronal Ceroid-Lipofuscinosis, PROP1-related
pituitary hormome deficiency, Pallister-Hall Syndrome, Paramyotonia
Congenita, Pendred Syndrome, Peroxisomal Bifunctional Enzyme
Deficiency, Pervasive Developmental Disorders, Phenylalanine
Hydroxylase Deficiency, Plasminogen Activator Inhibitor I,
Polycystic Kidney Disease, Autosomal Recessive, Prothrombin G20210A
Thrombophilia, Pseudovitamin D Deficiency Rickets, Pycnodysostosis,
Retinitis Pigmentosa, Autosomal Recessive, Bothnia Type, Rett
Syndrome, Rhizomelic Chondrodysplasia Punctata Type 1, Short Chain
Acyl-CoA Dehydrogenase Deficiency, Shwachman-Diamond Syndrome,
Sjogren-Larsson Syndrome, Smith-Lemli-Opitz Syndrome, Spastic
Paraplegia 13, Sulfate Transporter-Related Osteochondrodysplasia,
TFR2-Related Hereditary Hemochromatosis, TPP1-Related Neuronal
Ceroid-Lipofuscinosis, Thanatophoric Dysplasia, Transthyretin
Amyloidosis, Trifunctional Protein Deficiency, Tyrosine
Hydroxylase-Deficient DRD, Tyrosinemia Type I, Wilson Disease,
X-Linked Juvenile Retinoschisis, and Zellweger Syndrome
Spectrum.
[0057] In some embodiments, sequence B of one or more of the
plurality of first oligonucleotides or the target sequence to which
it specifically hybridizes comprises a non-subject sequence. In
some embodiments, sequence B or the target sequence to which it
specifically hybridizes is within about, less than about, or more
than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40,
45, 50, 60, 70, 80, 90, 100, 200, 500 or more nucleotides of a
non-subject sequence. In general, a non-subject sequence
corresponds to a polynucleotide derived from an organism other than
the individual being tested, such as DNA or RNA from bacteria,
archaea, viruses, protists, fungi, or other organism. A non-subject
sequence may be indicative of the identity of an organism or class
of organisms, and may further be indicative of a disease state,
such as infection. An example of non-subject sequences useful in
identifying an organism include, without limitation, rRNA
sequences, such as 16s rRNA sequences (see e.g. WO2010151842). In
some embodiments, non-subject sequences are analyzed instead of, or
separately from causal genetic variants. In some embodiments,
causal genetic variants and non-subject sequences are analyzed in
parallel, such as in the same sample (e.g. using a mixture of first
oligonucleotides, some with a sequence B that specifically
hybridizes to a sequence comprising or near a causal genetic
variant, and some with a sequence B that specifically hybridizes to
a sequence comprising or near a non-subject sequence) and/or in the
same report.
[0058] In some embodiments, sequence B of one or more of the
plurality of first oligonucleotides or the target sequence to which
it specifically hybridizes comprises an ancestry informative marker
(AIM). In some embodiments, sequence B or the target sequence to
which it specifically hybridizes is within about, less than about,
or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30,
35, 40, 45, 50, 60, 70, 80, 90, 100, 200, 500 or more nucleotides
of an AIM. In general, an AIM is a genetic variant that differs in
frequency between two or more populations of individuals, such as
two or more human populations, and may be used to infer the
ancestry of a subject, either alone or in combination with one or
more other AIMs. An AIM may be used to classify a person as
belonging to or not belonging to one or more populations, such as a
population that is at increased risk for one of the causal genetic
variants. For example, an AIM can be diagnostic for a population in
which a trait is at increased prevalence. In certain instances the
AIM may distinguish between populations with finer granularity, for
example, between sub-continental groups or related ethnic groups.
In some embodiments, AIMs are analyzed instead of, or separately
from causal genetic variants and/or non-subject sequences. In some
embodiments, AIMs, causal genetic variants, and/or non-subject
sequences are analyzed in parallel, such as in the same sample
(e.g. using a mixture of first oligonucleotides, some with a
sequence B that specifically hybridizes to a sequence comprising or
near a causal genetic variant, and some with a sequence B that
specifically hybridizes to a sequence comprising or near an AIM)
and/or in the same report. Non-limiting examples of types of AIMs
include single nucleotide polymorphisms (SNP), deletion/insertion
polymorphisms (DIP), copy number variants (CNV), short tandem
repeats (STR), restriction fragment length polymorphisms (RFLP),
simple sequence repeats (SSR), variable number of tandem repeats
(VNTR), randomly amplified polymorphic DNA (RAPD), amplified
fragment length polymorphisms (AFLP), inter-retrotransposon
amplified polymorphisms (IRAP), long and short interspersed
elements (LINE/SINE), long tandem repeats (LTR), mobile elements,
retrotransposon microsatellite amplified polymorphisms,
retrotransposon-based insertion polymorphisms, sequence specific
amplified polymorphism, and heritable epigenetic modification (for
example, DNA methylation). AIMs can also be sequence variations in
RNA polynucleotides. Some AIMs can also be indicated by the
presence or the concentration of a species of RNA polynucleotides.
Some AIMs can also be sequence variations in protein polypeptides.
Some AIMs can also be indicated by the presence or absence of a
species of protein polypeptides. A number of ancestry informative
markers are identified in FIG. 9. Other AIMs are described in US
2007/0037182. An AIM may or may not also be a causal genetic
variant. For example, the Duffy Null (FY*0) genetic variant causes
an absence of a blood antigen. This variant is at nearly 100%
frequency in sub-Saharan African populations and at nearly 0%
frequency in populations outside of sub-Saharan Africa. Many causal
genetic variants associated with pigmentation are also AIMs. AIMs
that are not causal genetic variants can be indirectly associated
with traits caused by other AIMs.
[0059] AIMs can be discovered by determining the frequency of
genetic variants in a plurality of populations. This may be
achieved by determining the frequency of already known variants in
individuals from various populations. It may also be achieved
intrinsically during the process of variant discovery. Both tasks
were undertaken by the International HapMap project, which
catalogued SNP polymorphisms. Ancestry informative markers can be
ranked by a variety of measurements which judge their predictive
power. One measurement is Wright's F-statistic, called Fst or FST.
This variable is known by other names, including Fixation index.
Another metric for ranking AIMs is informativeness. Another method
of ranking AIMs is the PCA-correlated SNPs method of Paschou et al.
(Paschou et al. PCA-correlated SNPs for structure identification in
worldwide human populations. PLoS Genet (2007) vol. 3 (9) pp.
1672-86).
[0060] To achieve a pre-selected degree of confidence (e.g. at
least about 80%, 85%, 90%, 95%, 97.5%, 99%, or more) in ancestry
inference on the basis of ancestry informative markers, and to
achieve ancestry inference for a plurality of populations, it may
be necessary to examine more than one ancestry informative marker.
A sufficiently large panel of randomly selected genetic variants
can be used to infer ancestry (e.g. about or more than about 5, 10,
15, 25, 50, 100, 250, 500, 1000, 2500, 5000, or more AIMs). A
targeted set of especially appropriate AIMs can be constructed.
Many researchers have published lists of suggested ancestry
informative markers (for example: Seldin et al. Application of
ancestry informative markers to association studies in European
Americans. PLoS Genet (2008) vol. 4 (1) pp. e5; Halder et al. A
panel of ancestry informative markers for estimating individual
biogeographical ancestry and admixture from four continents:
utility and applications. Hum Mutat (2008) vol. 29 (5) pp. 648-58;
Tian et al. Analysis and application of European genetic
substructure using 300 K SNP information. PLoS Genet (2008) vol. 4
(1) pp. e4; Price et al. Discerning the ancestry of European
Americans in genetic association studies. PLoS Genet (2008) vol. 4
(1) pp. e236; Paschou et al. PCA-correlated SNPs for structure
identification in worldwide human populations. PLoS Genet (2007)
vol. 3 (9) pp. 1672-86; and Bauchet et al. Measuring European
population stratification with microarray genotype data. Am J Hum
Genet (2007) vol. 80 (5) pp. 948-56). These and similar lists can
be used to build a panel of AIMs for which a device or method
herein can be configured to test for.
[0061] In some embodiments, a plurality of second nucleotides and a
plurality of third nucleotides are attached to the solid support in
addition to the plurality of first nucleotides. In some
embodiments, the second nucleotides all comprise sequence A at the
3' end, where sequence A in the plurality of second
oligonucleotides is the same as sequence A in all of the first
oligonucleotides. In some embodiments, the third oligonucleotides
comprise sequence C at the 3' end, where sequence C is
complementary to a sequence shared by a plurality of different
target polynucleotides. In some embodiments, extension of a first
oligonucleotide along a target polynucleotide serving as a template
generates an extension product comprising sequence C', which is
complementary and specifically hybridizable to sequence C. In some
embodiments, the amount of the plurality of second oligonucleotides
exposed to the solid support is about, less than about, or more
than about 10-fold, 50-fold, 100-fold, 1000-fold, 5000-fold,
7500-fold, 10000-fold, 12500-fold, 15000-fold, 20000-fold,
50000-fold, 100000-fold, or more higher than the amount of the
plurality of first oligonucleotides exposed to the solid support,
such as in a reaction for attached the plurality of
oligonucleotides to the solid support. In some embodiments, the
ratio (or the inverse ratio) of the amount of the plurality of
second oligonucleotides to the amount of third oligonucleotides
exposed to the solid support is about, less than about, or more
than about 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, or
more. In some embodiments, the plurality of first oligonucleotides
is added to the solid support at a concentration of about, less
than about, or more than about 0.5 pM, 1 pM, 5 pM, 10 pM, 25 pM, 50
pM, 75 pM, 100 pM, 200 pM, 500 pM, 1 nM, 10 nM, 100 nM, 500 nM, or
higher. In some embodiments, the concentration of the plurality of
second oligonucleotides and/or the third oligonucleotides is about,
less than about, or more than about 0.5 nM, 1 nM, 5 nM, 10 nM, 25
nM, 50 nM, 75 nM, 100 nM, 200 nM, 500 nM, 5 .mu.M, 10 .mu.M, 25
.mu.M, 50 .mu.M, 100 .mu.M, 500 .mu.M, or higher.
[0062] In some embodiments, one or more the plurality of
oligonucleotides comprise one or more blocking groups. In general,
a blocking group is any modification that prevents extension of a
3' end of an oligonucleotide, such as by a polymerase, a ligase,
and/or other enzymes. A blocking group may be added before or after
an oligonucleotide is attached to the solid support. In some
embodiments, a blocking group is added during an amplification or
sequencing process. Examples of blocking groups include, but are
not limited to, alkyl groups, non-nucleotide linkers,
phosphorothioate, alkane-diol residues, peptide nucleic acid, and
nucleotide derivatives lacking a 3'-OH, including, for example,
cordycepin.
[0063] In some embodiments, one or more of the oligonucleotides
attached to the substrate comprise a cleavage site, such that
cleavage at that site releases all or a portion of the cleaved
polynucleotide from attachment to the solid support. In some
embodiments, cleavage produces a 3' end that may be extended along
a polynucleotide template. In some embodiments, only a portion of
the plurality of first, second, and/or third oligonucleotides
comprise a cleavage site (e.g. about, less than about, or more than
about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or more). The
cleavage site may be cleavable by any suitable means, including but
not limited to chemical, enzymatic, and photochemical cleavage. The
cleavage groups may be positioned between the first nucleotide and
the solid support, or at or after any number of nucleotides in the
oligonucleotide, such as about, less than about, or more than about
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more
nucleotides from the point of attachment to the solid support.
[0064] Processes for chemical, enzymatic, and photochemical
cleavage, and cleavage sites cleaved by such processes are known in
the art. Examples of cleavage means include, but are not limited
to, restriction enzyme digestion, in which case the cleavage site
is an appropriate restriction site for the enzyme which directs
cleavage of one or both strands of a duplex template; RNase
digestion or chemical cleavage of a bond between a
deoxyribonucleotide and a ribonucleotide, in which case the
cleavage site may include one or more ribonucleotides; chemical
reduction of a disulphide linkage with a reducing agent (e.g.
TCEP), in which case the cleavage site should include an
appropriate disulphide linkage; chemical cleavage of a diol linkage
with periodate, in which case the cleavage site should include a
diol linkage; generation of an abasic site and subsequent
hydrolysis. Cleavage may be followed by blocking to produce a 3'
end that cannot be extended, such as by a polymerase, a ligase,
and/or other enzymes. An example of a blocking agents include, but
are not limited to amines (e.g. ethanolamine), which may be added
before, during, or after the addition of a cleaving agent.
Additional non-limiting examples of cleavage processes and cleavage
sites are described in US20120053074, which is incorporated by
reference in its entirety.
[0065] In some embodiments, a plurality of target polynucleotides
are amplified according to a method that comprises exposing a
sample comprising a plurality of target polynucleotides to an
apparatus of the invention. In some embodiments, the amplification
process comprises bridge amplification. General methods for
conducting standard bridge amplification are known in the art. By
way of example, WO/1998/044151 and WO/2000/018957 both describe
methods of nucleic acid amplification which allow amplification
products to be immobilized on a solid support in order to form
arrays comprised of clusters or "colonies" formed from a plurality
of identical immobilized polynucleotide strands and a plurality of
identical immobilized complementary strands. In some embodiments, a
plurality of polynucleotides are sequenced according to a method
that comprises exposing a sample comprising a plurality of target
polynucleotides to an apparatus of the invention. General methods
for conducting sequencing using a plurality of oligonucleotides
attached to a solid support are known in the art, such as methods
disclosed in US20120053074 and US20110223601, which are hereby
incorporated by reference in their entirety. Non-limiting,
exemplary methods for amplifying and/or sequencing target
polynucleotides in accordance with the methods and apparatuses of
the invention are provided herein. In general, amplification of
specific target polynucleotides permits the generation of
sequencing data that is enriched for target polynucleotides, such
as target genomic sequences, relative to non-target
polynucleotides. In some embodiments, the enrichment of sequencing
data for target polynucleotides (especially sequencing data for
causal genetic variants) relative to non-target polynucleotides is
about or at least about 10-fold, 100-fold, 500-fold, 1000-fold,
5000-fold, 10000-fold, 50000-fold, 100000-fold, 1000000-fold, or
more.
[0066] Non-limiting examples of substrates comprising
oligonucleotides, methods for their production, and systems and
methods for their operation are provided in WO/2008/002502, which
in hereby incorporated by reference in its entirety.
[0067] In one aspect, the invention provides a method for
sequencing a plurality of target polynucleotides in a sample. In
one embodiment, the method comprises: (a) fragmenting target
polynucleotides to produce fragmented polynucleotides; (b) joining
adapter oligonucleotides to the fragmented polynucleotides, each of
the adapter oligonucleotides comprising sequence D, to produce
adapted polynucleotides comprising sequence D hybridized to
complementary sequence D' at both ends of the adapted
polynucleotides, optionally wherein sequence D' is produced by
extension of a target polynucleotide 3' end; (c) amplifying the
adapted polynucleotides using amplification primers comprising
sequence C, sequence D, and a barcode associated with the sample,
wherein sequence D is positioned at the 3' end of the amplification
primers; (d) hybridizing amplified target polynucleotides to a
plurality of different first oligonucleotides that are attached to
a solid surface; (e) performing bridge amplification on a solid
surface; and (f) sequencing a plurality of polynucleotides from
step (e). The solid surface may comprise a plurality of
oligonucleotides as described herein, including an apparatus as
described herein and optionally produced according to the methods
described herein. In some embodiments, the solid surface comprises
(i) a plurality of different first oligonucleotides comprising
sequence A and sequence B, wherein sequence A is common among all
first oligonucleotides; and further wherein sequence B is different
for each different first oligonucleotide, is at the 3' end of each
first oligonucleotide, and is complementary to a sequence
comprising a causal genetic variant or a sequence within 200
nucleotides of a causal genetic variant; (ii) a plurality of second
oligonucleotides comprising sequence A at each 3' end; and (iii) a
plurality of third oligonucleotides comprising sequence C at each
3' end. In some embodiments, one or more of sequences A, B, C, and
D are different sequences. In some embodiments, one or more of
sequences A, B, C, and D are about, less than about, or more than
about 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or
more different from one or more of the other of sequences A, B, C,
and D (e.g. have less than about 10%, 20%, 30%, 40%, 50%, 60%, 70%,
80%, 90%, or more sequence identity). In some embodiments, one or
more of sequences A, B, C, and D comprise about, less than about,
or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or more
nucleotides each.
[0068] Samples from which the target polynucleotides are derived
can comprise multiple samples from the same individual, samples
from different individuals, or combinations thereof. In some
embodiments, a sample comprises a plurality of polynucleotides from
a single individual. In some embodiments, a sample comprises a
plurality of polynucleotides from two or more individuals. An
individual is any organism or portion thereof from which target
polynucleotides can be derived, non-limiting examples of which
include plants, animals, fungi, protists, monerans, viruses,
mitochondria, and chloroplasts. Sample polynucleotides can be
isolated from a subject, such as a cell sample, tissue sample,
fluid sample, or organ sample derived therefrom (or cell cultures
derived from any of these), including, for example, cultured cell
lines, biopsy, blood sample, cheek swab, or fluid sample containing
a cell (e.g. saliva). The subject may be an animal, including but
not limited to, a cow, a pig, a mouse, a rat, a chicken, a cat, a
dog, etc., and is usually a mammal, such as a human. Samples can
also be artificially derived, such as by chemical synthesis. In
some embodiments, samples comprise DNA. In some embodiments,
samples comprise genomic DNA. In some embodiments, samples comprise
mitochondrial DNA, chloroplast DNA, plasmid DNA, bacterial
artificial chromosomes, yeast artificial chromosomes,
oligonucleotide tags, polynucleotides from an organism (e.g.
bacteria, virus, or fungus) other than the subject from whom the
sample is taken, or combinations thereof. In some embodiments, the
samples comprise DNA generated by amplification, such as by primer
extension reactions using any suitable combination of primers and a
DNA polymerase, including but not limited to polymerase chain
reaction (PCR), reverse transcription, and combinations thereof.
Where the template for the primer extension reaction is RNA, the
product of reverse transcription is referred to as complementary
DNA (cDNA). Primers useful in primer extension reactions can
comprise sequences specific to one or more targets, random
sequences, partially random sequences, and combinations thereof.
Reaction conditions suitable for primer extension reactions are
known in the art. In general, sample polynucleotides comprise any
polynucleotide present in a sample, which may or may not include
target polynucleotides. In some embodiments, a sample from a single
individual is divided into multiple separate samples (e.g. 2, 3, 4,
5, 6, 7, 8, 9, 10, or more separate samples) that are subjected to
the methods of the invention independently, such as analysis in
duplicate, triplicate, quadruplicate, or more.
[0069] Methods for the extraction and purification of nucleic acids
are well known in the art. For example, nucleic acids can be
purified by organic extraction with phenol,
phenol/chloroform/isoamyl alcohol, or similar formulations,
including TRIzol and TriReagent. Other non-limiting examples of
extraction techniques include: (1) organic extraction followed by
ethanol precipitation, e.g., using a phenol/chloroform organic
reagent (Ausubel et al., 1993), with or without the use of an
automated nucleic acid extractor, e.g., the Model 341 DNA Extractor
available from Applied Biosystems (Foster City, Calif.); (2)
stationary phase adsorption methods (U.S. Pat. No. 5,234,809; Walsh
et al., 1991); and (3) salt-induced nucleic acid precipitation
methods (Miller et al., (1988), such precipitation methods being
typically referred to as "salting-out" methods. Another example of
nucleic acid isolation and/or purification includes the use of
magnetic particles to which nucleic acids can specifically or
non-specifically bind, followed by isolation of the beads using a
magnet, and washing and eluting the nucleic acids from the beads
(see e.g. U.S. Pat. No. 5,705,628). In some embodiments, the above
isolation methods may be preceded by an enzyme digestion step to
help eliminate unwanted protein from the sample, e.g., digestion
with proteinase K, or other like proteases. See, e.g., U.S. Pat.
No. 7,001,724. If desired, RNase inhibitors may be added to the
lysis buffer. For certain cell or sample types, it may be desirable
to add a protein denaturation/digestion step to the protocol.
Purification methods may be directed to isolate DNA, RNA, or both.
When both DNA and RNA are isolated together during or subsequent to
an extraction procedure, further steps may be employed to purify
one or both separately from the other. Sub-fractions of extracted
nucleic acids can also be generated, for example, purification by
size, sequence, or other physical or chemical characteristic. In
addition to an initial nucleic acid isolation step, purification of
nucleic acids can be performed after any step in the methods of the
invention, such as to remove excess or unwanted reagents,
reactants, or products. Methods for determining the amount and/or
purity of nucleic acids in a sample are known in the art, and
include absorbance (e.g. absorbance of light at 260 nm, 280 nm, and
a ratio of these) and detection of a label (e.g. fluorescent dyes
and intercalating agents, such as SYBR green, SYBR blue, DAPI,
propidium iodine, Hoechst stain, SYBR gold, ethidium bromide).
[0070] In some embodiments, target polynucleotides are fragmented
into a population of fragmented polynucleotides of one or more
specific size range(s). In some embodiments, the amount of sample
polynucleotides subjected to fragmentation is about, less than
about, or more than about 50 ng, 100 ng, 200 ng, 300 ng, 400 ng,
500 ng, 600 ng, 700 ng, 800 ng, 900 ng, 1000 ng, 1500 ng, 2000 ng,
2500 ng, 5000 ng, 10 .mu.g, or more. In some embodiments, fragments
are generated from about, less than about, or more than about 1,
10, 100, 1000, 10000, 100000, 300000, 500000, or more
genome-equivalents of starting DNA. Fragmentation may be
accomplished by methods known in the art, including chemical,
enzymatic, and mechanical fragmentation. In some embodiments, the
fragments have an average or median length from about 10 to about
10,000 nucleotides. In some embodiments, the fragments have an
average or median length from about 50 to about 2,000 nucleotides.
In some embodiments, the fragments have an average or median length
of about, less than about, more than about, or between about
100-2500, 200-1000, 10-800, 10-500, 50-500, 50-250, or 50-150
nucleotides. In some embodiments, the fragments have an average or
median length of about, less than about, or more than about 200,
300, 500, 600, 800, 1000, 1500 or more nucleotides. In some
embodiments, the fragmentation is accomplished mechanically
comprising subjecting sample polynucleotides to acoustic
sonication. In some embodiments, the fragmentation comprises
treating the sample polynucleotides with one or more enzymes under
conditions suitable for the one or more enzymes to generate
double-stranded nucleic acid breaks. Examples of enzymes useful in
the generation of polynucleotide fragments include sequence
specific and non-sequence specific nucleases. Non-limiting examples
of nucleases include DNase I, Fragmentase, restriction
endonucleases, variants thereof, and combinations thereof. For
example, digestion with DNase I can induce random double-stranded
breaks in DNA in the absence of Mg++ and in the presence of Mn++.
In some embodiments, fragmentation comprises treating the sample
polynucleotides with one or more restriction endonucleases.
Fragmentation can produce fragments having 5' overhangs, 3'
overhangs, blunt ends, or a combination thereof. In some
embodiments, such as when fragmentation comprises the use of one or
more restriction endonucleases, cleavage of sample polynucleotides
leaves overhangs having a predictable sequence. In some
embodiments, the method includes the step of size selecting the
fragments via standard methods such as column purification or
isolation from an agarose gel. In some embodiments, the method
comprises determining the average and/or median fragment length
after fragmentation. In some embodiments, samples having an average
and/or median fragment length above a desired threshold are again
subjected to fragmentation. In some embodiments, samples having an
average and/or median fragment length below a desired threshold are
discarded.
[0071] In some embodiments, the 5' and/or 3' end nucleotide
sequences of fragmented polynucleotides are not modified prior to
ligation with one or more adapter oligonucleotides (also referred
to as "adapters"). For example, fragmentation by a restriction
endonuclease can be used to leave a predictable overhang, followed
by ligation with one or more adapter oligonucleotides comprising an
overhang complementary to the predictable overhang on a
polynucleotide fragment. In another example, cleavage by an enzyme
that leaves a predictable blunt end can be followed by ligation of
blunt-ended polynucleotide fragments to adapter oligonucleotides
comprising a blunt end. In some embodiments, the fragmented
polynucleotides are blunt-end polished (or "end repaired") to
produce polynucleotide fragments having blunt ends, prior to being
joined to adapters. The blunt-end polishing step may be
accomplished by incubation with a suitable enzyme, such as a DNA
polymerase that has both 3' to 5' exonuclease activity and 5' to 3'
polymerase activity, for example T4 polymerase. In some
embodiments, end repair is followed by or concludes with addition
of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20 or more nucleotides, such as one or more adenine ("A
tailing"), one or more thymine, one or more guanine, or one or more
cytosine, to produce an overhang. Polynucleotide fragments having
an overhang can be joined to one or more adapter oligonucleotides
having a complementary overhang, such as in a ligation reaction.
For example, a single adenine can be added to the 3' ends of end
repaired polynucleotide fragments using a template independent
polymerase, followed by ligation to one or more adapters each
having an overhanging thymine at a 3' end. In some embodiments,
adapter oligonucleotides can be joined to blunt end double-stranded
DNA fragment molecules which have been modified by extension of the
3' end with one or more nucleotides followed by 5' phosphorylation.
In some cases, extension of the 3' end may be performed with a
polymerase such as for example Klenow polymerase or any other
suitable polymerases known in the art, or by use of a terminal
deoxynucleotide transferase, in the presence of one or more dNTPs
in a suitable buffer containing magnesium. In some embodiments,
target polynucleotides having blunt ends are joined to one or more
adapters comprising a blunt end. Phosphorylation of 5' ends of
fragmented polynucleotides may be performed for example with T4
polynucleotide kinase in a suitable buffer containing ATP and
magnesium. The fragmented polynucleotides may optionally be treated
to dephosphorylate 5' ends or 3' ends, for example, by using
enzymes known in the art, such as phosphatases.
[0072] In some embodiments, fragmentation is followed by ligation
of adapter oligonucleotides to the fragmented polynucleotides. An
adapter oligonucleotide includes any oligonucleotide having a
sequence, at least a portion of which is known, that can be joined
to a target polynucleotide. Adapter oligonucleotides can comprise
DNA, RNA, nucleotide analogues, non-canonical nucleotides, labeled
nucleotides, modified nucleotides, or combinations thereof. Adapter
oligonucleotides can be single-stranded, double-stranded, or
partial duplex. In general, a partial-duplex adapter comprises one
or more single-stranded regions and one or more double-stranded
regions. Double-stranded adapters can comprise two separate
oligonucleotides hybridized to one another (also referred to as an
"oligonucleotide duplex"), and hybridization may leave one or more
blunt ends, one or more 3' overhangs, one or more 5' overhangs, one
or more bulges resulting from mismatched and/or unpaired
nucleotides, or any combination of these. In some embodiments, a
single-stranded adapter comprises two or more sequences that are
able to hybridize with one another. When two such hybridizable
sequences are contained in a single-stranded adapter, hybridization
yields a hairpin structure (hairpin adapter). When two hybridized
regions of an adapter are separated from one another by a
non-hybridized region, a "bubble" structure results. Adapters
comprising a bubble structure can consist of a single adapter
oligonucleotide comprising internal hybridizations, or may comprise
two or more adapter oligonucleotides hybridized to one another.
Internal sequence hybridization, such as between two hybridizable
sequences in an adapter, can produce a double-stranded structure in
a single-stranded adapter oligonucleotide. Adapters of different
kinds can be used in combination, such as a hairpin adapter and a
double-stranded adapter, or adapters of different sequences.
Different adapters can be joined to target polynucleotides in
sequential reactions or simultaneously. In some embodiments,
identical adapters are added to both ends of a target
polynucleotide. For example, first and second adapters can be added
to the same reaction. Adapters can be manipulated prior to
combining with target polynucleotides. For example, terminal
phosphates can be added or removed.
[0073] In some embodiments, an adapter is a mismatched adapter
formed by annealing two partially complementary polynucleotide
strands so as to provide, when the two strands are annealed, at
least one double-stranded region and at least one unmatched region.
The "double-stranded region" of the adapter is a short
double-stranded region, typically comprising 5 or more consecutive
base pairs, formed by annealing of the two partially complementary
polynucleotide strands. This term simply refers to a
double-stranded region of nucleic acid in which the two strands are
annealed and does not imply any particular structural conformation.
In some embodiments, the double-stranded region is about, less than
about, or more than about 5, 10, 15, 20, 25, 30, or more
nucleotides in length. Generally it is advantageous for the
double-stranded region of a mismatched adapter to be as short as
possible without loss of function. By "function" in this context is
meant that the double-stranded region form a stable duplex under
standard reaction conditions for an enzyme-catalyzed nucleic acid
ligation reaction, which conditions are known to those skilled in
the art (e.g. incubation at a temperature in the range of from
4.degree. C. to 25.degree. C. in a ligation buffer appropriate for
the enzyme), such that the two strands forming the adapter remain
partially annealed during ligation of the adapter to a target
molecule. It is not absolutely necessary for the double-stranded
region to be stable under the conditions typically used in the
annealing steps of primer extension or PCR reactions. Typically,
the double-stranded region is adjacent to the "ligatable" end of
the adapter, i.e. the end that is joined to a target polynucleotide
in a ligation reaction. The ligatable end of the adapter may be
blunt or, in other embodiments, short 5' or 3' overhangs of one or
more nucleotides may be present to facilitate/promote ligation. The
5' terminal nucleotide at the ligatable end of the adapter is
typically phosphorylated to enable phosphodiester linkage to a 3'
hydroxyl group on a sample polynucleotide. The term "unmatched
region" refers to a region of the adapter wherein the sequences of
the two polynucleotide strands forming the adapter exhibit a degree
of non-complementarity such that the two strands are not capable of
annealing to each other under standard annealing conditions for a
primer extension or PCR reaction. The two strands in the unmatched
region may exhibit some degree of annealing under standard reaction
conditions for an enzyme-catalyzed ligation reaction, provided that
the two strands revert to single stranded form under annealing
conditions.
[0074] Adapter oligonucleotides can contain one or more of a
variety of sequence elements, including but not limited to, one or
more amplification primer annealing sequences or complements
thereof, one or more sequencing primer annealing sequences or
complements thereof, one or more barcode sequences, one or more
common sequences shared among multiple different adapters or
subsets of different adapters, one or more restriction enzyme
recognition sites, one or more overhangs complementary to one or
more target polynucleotide overhangs, one or more probe binding
sites (e.g. for attachment to a sequencing platform, such as a flow
cell for massive parallel sequencing, such as an apparatus as
described herein, or flow cells as developed by Illumina, Inc.),
one or more random or near-random sequences (e.g. one or more
nucleotides selected at random from a set of two or more different
nucleotides at one or more positions, with each of the different
nucleotides selected at one or more positions represented in a pool
of adapters comprising the random sequence), and combinations
thereof. Two or more sequence elements can be non-adjacent to one
another (e.g. separated by one or more nucleotides), adjacent to
one another, partially overlapping, or completely overlapping. For
example, an amplification primer annealing sequence can also serve
as a sequencing primer annealing sequence. Sequence elements can be
located at or near the 3' end, at or near the 5' end, or in the
interior of the adapter oligonucleotide. When an adapter
oligonucleotide is capable of forming secondary structure, such as
a hairpin, sequence elements can be located partially or completely
outside the secondary structure, partially or completely inside the
secondary structure, or in between sequences participating in the
secondary structure. A sequence element may be of any suitable
length, such as about, less than about, or more than about 3, 4, 5,
6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more nucleotides
in length. Adapter oligonucleotides can have any suitable length,
at least sufficient to accommodate the one or more sequence
elements of which they are comprised. In some embodiments, adapters
are about, less than about, or more than about 10, 15, 20, 25, 30,
35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, 200, or more
nucleotides in length
[0075] In some embodiments, the adapter oligonucleotides joined to
fragmented polynucleotides from one sample comprise one or more
sequences common to all adapter oligonucleotides and a barcode that
is unique to the adapters joined to polynucleotides of that
particular sample, such that the barcode sequence can be used to
distinguish polynucleotides originating from one sample or adapter
joining reaction from polynucleotides originating from another
sample or adapter joining reaction. In some embodiments, an adapter
oligonucleotide comprises a 5' overhang, a 3' overhang, or both
that is complementary to one or more target polynucleotide
overhangs. Complementary overhangs can be one or more nucleotides
in length, including but not limited to 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, or more nucleotides in length.
Complementary overhangs may comprise a fixed sequence.
Complementary overhangs of an adapter oligonucleotide may comprise
a random sequence of one or more nucleotides, such that one or more
nucleotides are selected at random from a set of two or more
different nucleotides at one or more positions, with each of the
different nucleotides selected at one or more positions represented
in a pool of adapters with complementary overhangs comprising the
random sequence. In some embodiments, an adapter overhang is
complementary to a target polynucleotide overhang produced by
restriction endonuclease digestion. In some embodiments, an adapter
overhang consists of an adenine or a thymine.
[0076] In some embodiments, adapter oligonucleotides comprise one
strand comprising the sequence element sequence D. In some
embodiments, adapter oligonucleotides comprise sequence D
hybridized to complementary sequence D', where sequence D' is on
the same or different strand as sequence D. In some embodiments,
the 3' end of a target polynucleotide is extended along an adapter
oligonucleotide to generate complementary sequence D'. In a
preferred embodiment, fragmented polynucleotides and adapter
oligonucleotides are combined and treated (e.g. by ligation and
optionally by fragment extension) to produce double-stranded,
adapted polynucleotides comprising fragmented polynucleotide
sequence joined to adapter oligonucleotide sequences at both ends,
where both ends of the adapted polynucleotides comprise sequence D
hybridized to sequence D'. In some embodiments, the amount of
fragmented polynucleotides subjected to adapter joining is about,
less than about, or more than about 50 ng, 100 ng, 200 ng, 300 ng,
400 ng, 500 ng, 600 ng, 700 ng, 800 ng, 900 ng, 1000 ng, 1500 ng,
2000 ng, 2500 ng, 5000 ng, 10 .mu.g, or more (e.g. a threshold
amount). In some embodiments, the amount of fragmented
polynucleotides is determined before proceeding with adapter
joining, where adapter joining is not performed if the amount is
below a threshold amount.
[0077] The terms "joining" and "ligation" as used herein, with
respect to two polynucleotides, such as an adapter oligonucleotide
and a sample polynucleotide, refers to the covalent attachment of
two separate polynucleotides to produce a single larger
polynucleotide with a contiguous backbone. Methods for joining two
polynucleotides are known in the art, and include without
limitation, enzymatic and non-enzymatic (e.g. chemical) methods.
Examples of ligation reactions that are non-enzymatic include the
non-enzymatic ligation techniques described in U.S. Pat. Nos.
5,780,613 and 5,476,930, which are herein incorporated by
reference. In some embodiments, an adapter oligonucleotide is
joined to a fragmented polynucleotide by a ligase, for example a
DNA ligase or RNA ligase. Multiple ligases, each having
characterized reaction conditions, are known in the art, and
include, without limitation NAD.sup.+-dependent ligases including
tRNA ligase, Taq DNA ligase, Thermus filiformis DNA ligase,
Escherichia coli DNA ligase, Tth DNA ligase, Thermus scotoductus
DNA ligase (I and II), thermostable ligase, Ampligase thermostable
DNA ligase, VanC-type ligase, 9.degree. N DNA Ligase, Tsp DNA
ligase, and novel ligases discovered by bioprospecting;
ATP-dependent ligases including T4 RNA ligase, T4 DNA ligase, T3
DNA ligase, T7 DNA ligase, Pfu DNA ligase, DNA ligase 1, DNA ligase
III, DNA ligase IV, and novel ligases discovered by bioprospecting;
and wild-type, mutant isoforms, and genetically engineered variants
thereof. Ligation can be between polynucleotides having
hybridizable sequences, such as complementary overhangs. Ligation
can also be between two blunt ends. Generally, a 5' phosphate is
utilized in a ligation reaction. The 5' phosphate can be provided
by the fragmented polynucleotide, the adapter oligonucleotide, or
both. 5' phosphates can be added to or removed from polynucleotides
to be joined, as needed. Methods for the addition or removal of 5'
phosphates are known in the art, and include without limitation
enzymatic and chemical processes. Enzymes useful in the addition
and/or removal of 5' phosphates include kinases, phosphatases, and
polymerases. In some embodiments, both of the two ends joined in a
ligation reaction (e.g. an adapter end and a fragmented
polynucleotide end) provide a 5' phosphate, such that two covalent
linkages are made in joining the two ends, at one or both ends of a
fragmented polynucleotide. In some embodiments, 3' phosphates are
removed prior to ligation. In some embodiments, an adapter
oligonucleotide is added to both ends of a fragmented
polynucleotide, wherein one or both strands at each end are joined
to one or more adapter oligonucleotides. In some embodiments,
separate ligation reactions are carried out for different samples
using a different adapter oligonucleotide comprising at least one
different barcode sequence for each sample, such that no barcode
sequence is joined to the target polynucleotides of more than one
sample to be analyzed in parallel.
[0078] Non-limiting examples of adapter oligonucleotides include
the double-stranded adapter formed by hybridizing
CACTCAGCAGCACGACGATCACAGATGTGTATAAGAGACAGT (SEQ ID NO: 17) to
GTGAGTCGTCGTGCTGCTAGTGTCTACACATATTCTCTGTC (SEQ ID NO: 18).
Additional non-limiting examples of adapter oligonucleotides are
described in US20110319290 and US20070128624, which are
incorporated herein by reference.
[0079] In some embodiments, adapted polynucleotides are subjected
to an amplification reaction that amplifies target polynucleotides
in the sample. In some embodiments, amplification uses primers
comprising sequence C, sequence D, and a barcode associated with
the sample, wherein sequence D is positioned at the 3' end of the
amplification primers. Amplification primers may be of any suitable
length, such as about, less than about, or more than about 5, 10,
15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, or
more nucleotides, any portion or all of which may be complementary
to the corresponding target sequence to which the primer hybridizes
(e.g. about, less than about, or more than about 5, 10, 15, 20, 25,
30, 35, 40, 45, 50, or more nucleotides). "Amplification" refers to
any process by which the copy number of a target sequence is
increased. Methods for primer-directed amplification of target
polynucleotides are known in the art, and include without
limitation, methods based on the polymerase chain reaction (PCR).
Conditions favorable to the amplification of target sequences by
PCR are known in the art, can be optimized at a variety of steps in
the process, and depend on characteristics of elements in the
reaction, such as target type, target concentration, sequence
length to be amplified, sequence of the target and/or one or more
primers, primer length, primer concentration, polymerase used,
reaction volume, ratio of one or more elements to one or more other
elements, and others, some or all of which can be altered. In
general, PCR involves the steps of denaturation of the target to be
amplified (if double stranded), hybridization of one or more
primers to the target, and extension of the primers by a DNA
polymerase, with the steps repeated (or "cycled") in order to
amplify the target sequence. Steps in this process can be optimized
for various outcomes, such as to enhance yield, decrease the
formation of spurious products, and/or increase or decrease
specificity of primer annealing. Methods of optimization are well
known in the art and include adjustments to the type or amount of
elements in the amplification reaction and/or to the conditions of
a given step in the process, such as temperature at a particular
step, duration of a particular step, and/or number of cycles. In
some embodiments, an amplification reaction comprises at least 5,
10, 15, 20, 25, 30, 35, 50, or more cycles. In some embodiments, an
amplification reaction comprises no more than 5, 10, 15, 20, 25,
35, 50, or more cycles. Cycles can contain any number of steps,
such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more steps. Steps can
comprise any temperature or gradient of temperatures, suitable for
achieving the purpose of the given step, including but not limited
to, strand denaturation, primer annealing, and primer extension.
Steps can be of any duration, including but not limited to about,
less than about, or more than about 1, 5, 10, 15, 20, 25, 30, 35,
40, 45, 50, 55, 60, 70, 80, 90, 100, 120, 180, 240, 300, 360, 420,
480, 540, 600, or more seconds, including indefinitely until
manually interrupted. Cycles of any number comprising different
steps can be combined in any order.
[0080] In some embodiments, amplification comprises hybridization
between sequence D at the 3' end of an amplification primer and
sequence D' of an adapted polynucleotide, extension of the
amplification primer along the adapted polynucleotide to produce a
primer extension product comprising sequence D derived from the
amplification primer and sequence D' produced during primer
extension. In some embodiments, the amplification process is
repeated one or more times by denaturing the primer extension
product from a template polynucleotide, and repeating the process
using the primer extension product as template for further primer
extension reactions. In some embodiments, the first cycle of primer
extension is repeated using the same primer as the primer used in
the first primer extension reaction, such as for about, less than
about, or more than about 5, 10, 15, 20, 25, 30, 35, 50, or more
cycles. In some embodiments, one or more primer extensions by the
amplification primer is followed by one or more amplification
cycles using a second amplification primer having a 3' end
comprising a sequence complementary to a sequence added to the
adapted polynucleotides by amplification with the first
amplification primer (e.g. complementary to the complement of
sequence C, or a portion thereof). In some embodiments, the second
amplification primer comprises sequence C, or a portion thereof, at
the 3' end. A non-limiting example of a second amplification primer
includes CGAGATCTACACGCCTCCCTCGCGCCATCAG (SEQ ID NO: 19). In some
embodiments, amplification by the second amplification primer
comprises about, less than about, or more than about 5, 10, 15, 20,
25, 30, 35, 50, or more cycles. In some embodiments, the amount of
adapted polynucleotides subjected to amplification is about, less
than about, or more than about 50 ng, 100 ng, 200 ng, 300 ng, 400
ng, 500 ng, 600 ng, 700 ng, 800 ng, 900 ng, 1000 ng, 1500 ng, 2000
ng, 2500 ng, 5000 ng, 10 .mu.g, or more (e.g. a threshold amount).
In some embodiments, the amount of adapted polynucleotides is
determined before proceeding with amplification, where
amplification is not performed if the amount is below a threshold
amount.
[0081] In some embodiments, the amplification primer comprises a
barcode. As used herein, the term "barcode" refers to a known
nucleic acid sequence that allows some feature of a polynucleotide
with which the barcode is associated to be identified. In some
embodiments, the feature of the polynucleotide to be identified is
the sample from which the polynucleotide is derived. In some
embodiments, barcodes are about or at least about 3, 4, 5, 6, 7, 8,
9, 10, 11, 12, 13, 14, 15, or more nucleotides in length. In some
embodiments, barcodes are shorter than 10, 9, 8, 7, 6, 5, or 4
nucleotides in length. In some embodiments, barcodes associated
with some polynucleotides are of different lengths than barcodes
associated with other polynucleotides. In general, barcodes are of
sufficient length and comprise sequences that are sufficiently
different to allow the identification of samples based on barcodes
with which they are associated. In some embodiments, a barcode, and
the sample source with which it is associated, can be identified
accurately after the mutation, insertion, or deletion of one or
more nucleotides in the barcode sequence, such as the mutation,
insertion, or deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more
nucleotides. In some embodiments, each barcode in a plurality of
barcodes differ from every other barcode in the plurality at at
least three nucleotide positions, such as at least 3, 4, 5, 6, 7,
8, 9, 10, or more nucleotide positions. A plurality of barcodes may
be represented in a pool of samples, each sample comprising
polynucleotides comprising one or more barcodes that differ from
the barcodes contained in the polynucleotides derived from the
other samples in the pool. Samples of polynucleotides comprising
one or more barcodes can be pooled based on the barcode sequences
to which they are joined, such that all four of the nucleotide
bases A, G, C, and T are approximately evenly represented at one or
more positions along each barcode in the pool (such as at 1, 2, 3,
4, 5, 6, 7, 8, or more positions, or all positions of the barcode).
In some embodiments, the methods of the invention further comprise
identifying the sample from which a target polynucleotide is
derived based on a barcode sequence to which the target
polynucleotide is joined. In general, a barcode comprises a nucleic
acid sequence that when joined to a target polynucleotide serves as
an identifier of the sample from which the target polynucleotide
was derived.
[0082] In some embodiments, separate amplification reactions are
carried out for separate samples using amplification primers
comprising at least one different barcode sequence for each sample,
such that no barcode sequence is joined to the target
polynucleotides of more than one sample in a pool of two or more
samples. In some embodiments, amplified polynucleotides derived
from different samples and comprising different barcodes are pooled
before proceeding with subsequent manipulation of the
polynucleotides (such as before amplification and/or sequencing on
a solid support). Pools can comprise any fraction of the total
constituent amplification reactions, including whole reaction
volumes. Samples can be pooled evenly or unevenly. In some
embodiments, target polynucleotides are pooled based on the
barcodes to which they are joined. Pools may comprise
polynucleotides derived from about, less than about, or more than
about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 25,
30, 40, 50, 75, 100, or more different samples. Samples can be
pooled in multiples of four in order to represent all four of the
nucleotide bases A, G, C, and T at one or more positions along the
barcode evenly, for example 4, 8, 12, 16, 20, 24, 28, 32, 36, 40,
44, 48, 52, 56, 60, 64, 96, 128, 192, 256, 384, and so on.
Non-limiting examples of barcodes include AGGTCA, CAGCAG, ACTGCT,
TAACGG, GGATTA, AACCTG, GCCGTT, CGTTGA, GTAACC, CTTAAC, TGCTAA,
GATCCG, CCAGGT, TTCAGC, ATGATC, and TCGGAT. In some embodiments,
the barcode is positioned between sequence D and sequence C of an
amplification primer, or after sequence C and sequence D in a 5' to
3' direction ("downstream"). In some embodiments, the amplification
primer comprises or consists of the sequence
CGAGATCTACACGCCTCCCTCGCGCCATCAGXXXXXXCACTCAGCAGCACGACGATCAC (SEQ ID
NO: 21), where each "X" represents zero, one, or more nucleotides
of a barcode sequence.
[0083] Non-limiting examples of amplification primers are provided
in Table 1:
TABLE-US-00001 TABLE 1 SEQ ID CGAGATCTACACGCCTCCCTCGCGCCATCA NO: 1
GAGGTCACACTCAGCAGCACGACGATCAC SEQ ID CGAGATCTACACGCCTCCCTCGCGCCATCA
NO: 2 GCAGCAGCACTCAGCAGCACGACGATCAC SEQ ID
CGAGATCTACACGCCTCCCTCGCGCCATCA NO: 3 GACTGCTCACTCAGCAGCACGACGATCAC
SEQ ID CGAGATCTACACGCCTCCCTCGCGCCATCA NO: 4
GTAACGGCACTCAGCAGCACGACGATCAC SEQ ID CGAGATCTACACGCCTCCCTCGCGCCATCA
NO: 5 GGGATTACACTCAGCAGCACGACGATCAC SEQ ID
CGAGATCTACACGCCTCCCTCGCGCCATCA NO: 6 GAACCTGCACTCAGCAGCACGACGATCAC
SEQ ID CGAGATCTACACGCCTCCCTCGCGCCATCA NO: 7
GGCCGTTCACTCAGCAGCACGACGATCAC SEQ ID CGAGATCTACACGCCTCCCTCGCGCCATCA
NO: 8 GCGTTGACACTCAGCAGCACGACGATCAC SEQ ID
CGAGATCTACACGCCTCCCTCGCGCCATCA NO: 9 GGTAACCCACTCAGCAGCACGACGATCAC
SEQ ID CGAGATCTACACGCCTCCCTCGCGCCATCA NO: 10
GCTTAACCACTCAGCAGCACGACGATCAC SEQ ID CGAGATCTACACGCCTCCCTCGCGCCATCA
NO: 11 GTGCTAACACTCAGCAGCACGACGATCAC SEQ ID
CGAGATCTACACGCCTCCCTCGCGCCATCA NO: 12 GGATCCGCACTCAGCAGCACGACGATCAC
SEQ ID CGAGATCTACACGCCTCCCTCGCGCCATCA NO: 13
GCCAGGTCACTCAGCAGCACGACGATCAC SEQ ID CGAGATCTACACGCCTCCCTCGCGCCATCA
NO: 14 GTTCAGCCACTCAGCAGCACGACGATCAC SEQ ID
CGAGATCTACACGCCTCCCTCGCGCCATCA NO: 15 GATGATCCACTCAGCAGCACGACGATCAC
SEQ ID CGAGATCTACACGCCTCCCTCGCGCCATCA NO: 16
GTCGGATCACTCAGCAGCACGACGATCAC
[0084] In some embodiments, target polynucleotides are hybridized
to a plurality of oligonucleotides that are attached to a solid
support, such as any apparatus described herein. Hybridization may
be before or after one or more sample processing steps, such as
adapter joining and amplification. In preferred embodiments, target
polynucleotides are hybridized to oligonucleotides on a solid
support after both adapter joining and one or more amplification
reactions. Oligonucleotides on the solid support may hybridize to
random polynucleotide sequences, specific sequences common to
multiple different target polynucleotides (e.g. one or more
sequences derived from an adapter oligonucleotide, such as
sequences D, D', or a portion thereof; one or more sequences
derived from an amplification primer, such as sequences C, C', or a
portion thereof; or combinations of these), sequences specific to
different target polynucleotides (such as represented by sequence B
as described herein), or combinations of these. In some
embodiments, the solid support comprises a plurality of different
first oligonucleotides comprising sequence A and sequence B,
wherein sequence A is common among all first oligonucleotides; and
further wherein sequence B is different for each different first
oligonucleotide, is at the 3' end of each first oligonucleotide. In
some embodiments, the plurality of first oligonucleotides comprises
about, less than about, or more than about 5, 10, 25, 50, 75, 100,
125, 150, 175, 200, 300, 400, 500, 750, 1000, 2500, 5000, 7500,
10000, 20000, 50000, or more different oligonucleotides, each
comprising a different sequence B. In some embodiments, sequence B
of one or more of the plurality of first oligonucleotides comprises
a sequence selected from the group consisting of SEQ ID NOs 22-121,
shown in FIG. 4 (e.g. 1, 5, 10, 25, 50, 75, or 100 different
oligonucleotides each with a different sequence from FIG. 4). In
some embodiments, sequence B or the target sequence to which it
specifically hybridizes comprises a causal genetic variant, as
described herein. In some embodiments, sequence B or the target
sequence to which it specifically hybridizes is within about, less
than about, or more than about 1, 2, 3, 4, 5, 6, 6, 7, 8, 9, 10,
15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 200, 500 or
more nucleotides of a causal genetic variant, as described herein.
Causal genetic variants are typically located downstream of a first
oligonucleotide, such that at least a portion of the causal genetic
variant serves as template for extension of a first
oligonucleotide. The solid support may further comprise a plurality
of second oligonucleotides comprising sequence A at the 3' end of
each second oligonucleotide, and a plurality of third
oligonucleotides comprising sequence C at the 3' end of each third
oligonucleotide, as described herein.
[0085] In some embodiments, sequence B of one or more of the
plurality of first oligonucleotides or the target sequence to which
it specifically hybridizes comprises a non-subject sequence. In
some embodiments, sequence B or the target sequence to which it
specifically hybridizes is within about, less than about, or more
than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40,
45, 50, 60, 70, 80, 90, 100, 200, 500 or more nucleotides of a
non-subject sequence. In general, a non-subject sequence
corresponds to a polynucleotide derived from an organism other than
the individual being tested or from whom a sample is taken, such as
DNA or RNA from bacteria, archaea, viruses, protists, fungi, or
other organism. Non-subject sequence can also include nucleic acids
from a fetus, such as cell-free nucleic acid (also referred to as
extracellular nucleic acid) from a fetus. A non-subject sequence
may be indicative of the identity of an organism or class of
organisms, and may further be indicative of a disease state, such
as infection. An example of non-subject sequences useful in
identifying an organism include, without limitation, rRNA
sequences, such as 16s rRNA sequences (see e.g. WO2010151842). In
some embodiments, non-subject sequences are analyzed instead of, or
separately from causal genetic variants. In some embodiments,
causal genetic variants and non-subject sequences are analyzed in
parallel, such as in the same sample (e.g. using a mixture of first
oligonucleotides, some with a sequence B that specifically
hybridizes to a sequence comprising or near a causal genetic
variant, and some with a sequence B that specifically hybridizes to
a sequence comprising or near a non-subject sequence) and/or in the
same report.
[0086] In some embodiments, sequence B of one or more of the
plurality of first oligonucleotides or the target sequence to which
it specifically hybridizes comprises an ancestry informative marker
(AIM). In some embodiments, sequence B or the target sequence to
which it specifically hybridizes is within about, less than about,
or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30,
35, 40, 45, 50, 60, 70, 80, 90, 100, 200, 500 or more nucleotides
of an AIM. An AIM may be used to classify a person as belonging to
or not belonging to one or more populations, such as a population
that is at increased risk for one of the causal genetic variants.
For example, an AIM can be diagnostic for a population in which a
trait is at increased prevalence. In certain instances the AIM may
distinguish between populations with finer granularity, for
example, between sub-continental groups or related ethnic groups.
In some embodiments, AIMs are analyzed instead of, or separately
from causal genetic variants and/or non-subject sequences. In some
embodiments, AIMs, causal genetic variants, and/or non-subject
sequences are analyzed in parallel, such as in the same sample
(e.g. using a mixture of first oligonucleotides, some with a
sequence B that specifically hybridizes to a sequence comprising or
near a causal genetic variant, and some with a sequence B that
specifically hybridizes to a sequence comprising or near an AIM)
and/or in the same report.
[0087] In some embodiments, the method further comprises performing
bridge amplification on the solid support. In general, bridge
amplification uses repeated steps of annealing of primers to
templates, primer extension, and separation of extended primers
from templates. These steps can generally be performed using
reagents and conditions known to those skilled in PCR (or reverse
transcriptase plus PCR) techniques. Thus a nucleic acid polymerase
can be used together with a supply of nucleoside triphosphate
molecules (or other molecules that function as precursors of
nucleotides present in DNA/RNA, such as modified nucleoside
triphosphates) to extend primers in the presence of a suitable
template. Excess deoxyribonucleoside triphosphates are desirably
provided. Preferred deoxyribonucleoside triphosphates are
abbreviated; dTTP (deoxythymidine nucleoside triphosphate), dATP
(deoxyadenosine nucleoside triphosphate), dCTP (deoxycytosine
nucleoside triphosphate) and dGTP (deoxyguanosine nucleoside
triphosphate). Preferred ribonucleoside triphosphates are UTP, ATP,
CTP and GTP. However, alternatives are possible. These may be
naturally or non-naturally occurring. A buffer of the type
generally used in PCR reactions may also be provided. A nucleic
acid polymerase used to incorporate nucleotides during primer
extension is preferably stable under the reaction conditions
utilized in order that it can be used several times. Thus, where
heating is used to separate a newly synthesized nucleic acid strand
from its template, the nucleic acid polymerase is preferably heat
stable at the temperature used. Such heat stable polymerases are
known to those skilled in the art. They are obtainable from
thermophilic micro-organisms, and include the DNA dependent DNA
polymerase known as Taq polymerase and also thermostable
derivatives thereof.
[0088] Typically, annealing of a primer to its template takes place
at a temperature of 25 to 90.degree. C. A temperature in this range
will also typically be used during primer extension, and may be the
same as or different from the temperature used during annealing
and/or denaturation. Once sufficient time has elapsed to allow
annealing and also to allow a desired degree of primer extension to
occur, the temperature can be increased, if desired, to allow
strand separation. At this stage the temperature will typically be
increased to a temperature of 60 to 100.degree. C. High
temperatures can also be used to reduce non-specific priming
problems prior to annealing, and/or to control the timing of
amplification initiation, e.g. in order to synchronize
amplification initiation for a number of samples. Alternatively,
the strands maybe separated by treatment with a solution of low
salt and high pH (>12) or by using a chaotropic salt (e.g.
guanidinium hydrochloride) or by an organic solvent (e.g.
formamide).
[0089] Following strand separation (e.g. by heating), a washing
step may be performed. The washing step may be omitted between
initial rounds of annealing, primer extension and strand
separation, such as if it is desired to maintain the same templates
in the vicinity of immobilized primers. This allows templates to be
used several times to initiate colony formation. The size of
colonies produced by amplification on the solid support can be
controlled, e.g. by controlling the number of cycles of annealing,
primer extension and strand separation that occur. Other factors
which affect the size of colonies can also be controlled. These
include the number and arrangement on a surface of immobilized
primers, the conformation of a support onto which the primers are
immobilized, the length and stiffness of template and/or primer
molecules, temperature, and the ionic strength and viscosity of a
fluid in which the above-mentioned cycles can be performed.
[0090] A non-limiting example of an amplification process in
accordance with the methods of the invention is illustrated in FIG.
1, and described below. First, a first oligonucleotide attached to
the solid support and comprising sequence B at its 3' end
hybridizes to a complementary target sequence B', such as a
sequence unique to a specific target polynucleotide in a plurality
of different target polynucleotides (e.g. a particular genomic DNA
sequence). In this way, sequence B serves as a probe. The target
polynucleotide in Figure lcomprises sequences derived from adapter
oligonucleotides (e.g. sequences D and D') and from amplification
primers (e.g. C and C'). Extension of the first oligonucleotide
produces a first extension product attached to the solid support,
the first extension product comprising, from 5' to 3', sequences A,
B, C', and D', where sequence C' is complementary to sequence C and
sequence D' is complementary to sequence D. The first extension
product is then separated from the target polynucleotide template
(e.g. by heat or chemical denaturation). Sequence C' of the first
extension product then hybridizes to one of a plurality of third
oligonucleotides attached to the solid support, the third
oligonucleotide comprising sequence C at its 3' end. Extension of
the third oligonucleotide produces a second extension product
attached to the solid support, the second extension product
comprising, from 5' to 3', sequences C, D, B' and A', where
sequence B' is complementary to sequence B and sequence A' is
complementary to sequence A. The two extension products form a
double-stranded polynucleotide "bridge," with one strand at both
ends attached to the solid support. The first and second extension
products are then denatured, and subsequence hybridizations between
the extension products and other oligonucleotides followed by
extension replicate the first and second extension products. For
example, each first extension product may hybridize to a further
third oligonucleotide to produce additional copies of the second
extension product. In addition, a second extension product may
hybridize to one of a plurality of second oligonucleotides attached
to the solid support, the second oligonucleotide comprising
sequence A at its 3' end. Extension of the second oligonucleotide
produces an extension product comprising the sequence of a first
extension product. Successive rounds of extension along extension
products radiates outward from an initial first extension product
to produce a cluster or "colony" of first extension products and
their complementary second extension products derived from a single
target polynucleotide. This process may be modified to accommodate
oligonucleotides comprising different sequences or sequence
arrangements, different target polynucleotides or combinations of
target polynucleotides, types of solid supports, and other
considerations depending on a particular bridge amplification
reaction. In general, this process provides for amplification on a
solid support of specific target polynucleotides from sample
polynucleotides comprising target polynucleotides and non-target
polynucleotides. Generally, target polynucleotides are selectively
amplified while non-target polynucleotides in the sample are not
amplified, or are amplified to a much lower degree, such as about
or less than about 10-fold, 100-fold, 500-fold, 1000-fold,
2500-fold, 5000-fold, 10000-fold, 25000-fold, 50000-fold,
100000-fold, 1000000-fold, or more lower than one or more target
polynucleotides.
[0091] In some embodiments, the amount of amplified polynucleotides
from a previous amplification step that is subjected to bridge
amplification is about, less than about, or more than about 50 ng,
100 ng, 500 ng, 1 .mu.g, 2 .mu.g, 3 .mu.g, 4 .mu.g, 5 .mu.g, 6
.mu.g, 7 .mu.g, 8 .mu.g, 9 .mu.g, 10 .mu.g, 11 .mu.g, 12 .mu.g, 13
.mu.g, 14 .mu.g, 15 .mu.g, 20 .mu.g, 25 .mu.g, 26 .mu.g, 27 .mu.g,
28 .mu.g, 29 .mu.g, 30 .mu.g, 40 .mu.g, 50 .mu.g, or more (e.g. a
threshold amount). In some embodiments, the amount of amplified
polynucleotides from a previous amplification step is determined
before proceeding with bridge amplification, where bridge
amplification is not performed if the amount is below a threshold
amount.
[0092] In some embodiments, bridge amplification is followed by
sequencing a plurality of oligonucleotides attached to the solid
support. General methods for sequencing polynucleotides attached to
a solid support, including reagents and reaction conditions, are
known in the art. In some embodiments, sequencing comprises or
consists of single-end sequencing. In some embodiments, sequencing
comprises or consists of paired-end sequencing. Sequencing can be
carried out using any suitable sequencing technique, wherein
nucleotides are added successively to a free 3' hydroxyl group,
resulting in synthesis of a polynucleotide chain in the 5' to 3'
direction. The identity of the nucleotide added is preferably
determined after each nucleotide addition. Sequencing techniques
using sequencing by ligation, wherein not every contiguous base is
sequenced, and techniques such as massively parallel signature
sequencing (MPSS) where bases are removed from, rather than added
to the strands on the surface are also within the scope of the
invention, as are techniques using detection of pyrophosphate
release (pyrosequencing). Such pyrosequencing based techniques are
particularly applicable to sequencing arrays of beads where the
beads have been amplified in an emulsion such that a single
template from the library molecule is amplified on each bead.
[0093] One particular sequencing method which can be used in the
methods of the invention relies on the use of modified nucleotides
that can act as reversible chain terminators. Such reversible chain
terminators comprise removable 3' blocking groups, for example as
described in WO04018497 and U.S. Pat. No. 7,057,026. Once such a
modified nucleotide has been incorporated into the growing
polynucleotide chain complementary to the region of the template
being sequenced there is no free 3'-OH group available to direct
further sequence extension and therefore the polymerase cannot add
further nucleotides. Once the identity of the base incorporated
into the growing chain has been determined, the 3' block may be
removed to allow addition of the next successive nucleotide. By
ordering the products derived using these modified nucleotides it
is possible to deduce the DNA sequence of the DNA template. Such
reactions can be done in a single experiment if each of the
modified nucleotides has attached thereto a different label, known
to correspond to the particular base, to facilitate discrimination
between the bases added at each incorporation step. Non-limiting
examples of suitable labels are described in WO/2007/135368, the
contents of which are incorporated herein by reference in their
entirety. Alternatively, a separate reaction may be carried out
containing each of the modified nucleotides added individually.
[0094] The modified nucleotides may carry a label to facilitate
their detection. In a particular embodiment, the label is a
fluorescent label. Each nucleotide type may carry a different
fluorescent label. However, the detectable label need not be a
fluorescent label. Any label can be used which allows the detection
of the incorporation of the nucleotide into the DNA sequence. One
method for detecting fluorescently labeled nucleotides comprises
using laser light of a wavelength specific for the labeled
nucleotides, or the use of other suitable sources of illumination.
Fluorescence from the label on an incorporated nucleotide may be
detected by a CCD camera or other suitable detection means.
Suitable detection means are described in WO/2007/123744, the
contents of which are incorporated herein by reference in their
entirety.
[0095] In some embodiments, a first sequencing reaction proceeds
from a 3' end created by cleavage at a cleavage site contained in
an oligonucleotide attached to the solid support, which
oligonucleotide was extended during bridge amplification. In some
embodiments, the cleaved strand is separated from its complementary
strand before sequencing by extension of the attached
oligonucleotide. In some embodiments, the attached oligonucleotide
having the newly freed 3' end created by cleavage is extended using
a polymerase having strand displacement activity, such that the
cleaved strand is displaced as the new strand is extended. In some
embodiments extension of the attached oligonucleotide proceeds
along the full length of the template extension product from the
amplification reaction, which in some embodiments includes
extension beyond a last identified nucleotide. In some embodiments,
the template extension product is then cleaved at a cleavage site
contained in an oligonucleotide attached to the solid support, and
the oligonucleotide extended during the sequencing reaction is
linearized, for produce a freed first sequencing extension product.
The 5' end of the first sequencing product may then serve as a
template for a second sequencing reaction, which can proceed by
extension of a sequencing primer (such as a sequencing primer
described herein) or by extension from the 3' end created by
cleavage at the cleavage site. In some embodiments, the average or
median number of nucleotides identified along a template
polynucleotide being sequenced is about, less than about, or more
than about 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100,
150, 200, 300, 400, 500, or more.
[0096] In some embodiments, sequencing comprises treating bridge
amplification products to remove substantially all or remove or
displace at least a portion of one of the immobilized strands in
the "bridge" structure in order to generate a template that is at
least partially single-stranded. The portion of the template which
is single-stranded will thus be available for hybridization with a
sequencing primer. The process of removing all or a portion of one
immobilized strand in a bridged double-stranded nucleic acid
structure may be referred to herein as "linearization," and is
described in further detail in WO07010251, the contents of which
are incorporated herein by reference in their entirety.
[0097] Bridged template structures may be linearized by cleavage of
one or both strands with a restriction endonuclease or by cleavage
of one strand with a nicking endonuclease. Other methods of
cleavage can be used as an alternative to restriction enzymes or
nicking enzymes, including but not limited to chemical cleavage
(e.g. cleavage of a diol linkage with periodate), cleavage of
abasic sites by cleavage with endonuclease (for example "USER," as
supplied by NEB, part number M5505S), by exposure to heat or
alkali, cleavage of ribonucleotides incorporated into amplification
products otherwise comprised of deoxyribonucleotides, photochemical
cleavage or cleavage of a peptide linker. In some embodiments, a
linearization step may be avoided, such as when the solid-phase
amplification reaction is performed with only one amplification
oligonucleotide covalently immobilized and another amplification
oligonucleotide free in solution. Following the cleavage step,
regardless of the method used for cleavage, the product of the
cleavage reaction may be subjected to denaturing conditions in
order to remove the portion(s) of the cleaved strand(s) that are
not attached to the solid support. Suitable denaturing conditions,
for example sodium hydroxide solution, formamide solution, or heat,
are known in the art, such as described in standard molecular
biology protocols (Sambrook et al., 2001, Molecular Cloning, A
Laboratory Manual, 3rd Ed, Cold Spring Harbor Laboratory Press,
Cold Spring Harbor Laboratory Press, NY; Current Protocols, eds
Ausubel et al.). Denaturation results in the production of a
sequencing template which is partially or substantially
single-stranded. A sequencing reaction may then be initiated by
hybridization of a sequencing primer to the single-stranded portion
of the template. Thus, the invention encompasses methods wherein
the nucleic acid sequencing reaction comprises hybridizing a
sequencing primer to a single-stranded region of a linearized
amplification product, sequentially incorporating one or more
nucleotides into a polynucleotide strand complementary to the
region of amplified template strand to be sequenced, identifying
the base present in one or more of the incorporated nucleotide(s)
and thereby determining the sequence of a region of the template
strand.
[0098] In some embodiments, the sequencing primer comprises a
sequence complementary to one or more sequences derived from an
adapter oligonucleotide, an amplification primer, an
oligonucleotide attached to the solid support, or a combination of
these. In some embodiments, the sequencing primer comprises
sequence D, or a portion thereof. In some embodiments, a sequencing
primer comprises sequence C, or a portion thereof. A sequencing
primer can be of any suitable length, such as about, less than
about, or more than about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50,
55, 60, 65, 70, 75, 80, 90, 100, or more nucleotides, any portion
or all of which may be complementary to the corresponding target
sequence to which the primer hybridizes (e.g. about, less than
about, or more than about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, or
more nucleotides). In some embodiments, a sequencing primer
comprises the sequence CACTCAGCAGCACGACGATCACAGATGTGTATAAGAGACAG
(SEQ ID NO: 20).
[0099] In general, extension of a sequencing primer produces a
sequencing extension product. The number of nucleotides added to
the sequencing extension product that are identified in the
sequencing process may depend on a number of factors, including
template sequence, reaction conditions, reagents used, and other
factors. In some embodiments, the average or median number of
nucleotides identified along a growing sequencing primer is about,
less than about, or more than about 10, 15, 20, 25, 30, 35, 40, 45,
50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, or more. In some
embodiments, a sequencing primer is extended along the full length
of the template primer extension product from the amplification
reaction, which in some embodiments includes extension beyond a
last identified nucleotide.
[0100] In some embodiments, the sequencing extension product is
subjected to denaturing conditions in order to remove the
sequencing extension product from the attached template strand to
which it is hybridized, in order to make the template partially or
completely single-stranded and available for hybridization with a
second sequencing primer. The second sequencing primer may be the
same as or different from the first sequencing primer. In some
embodiments, the second sequencing primer hybridizes to a sequence
located closer to the 5' end of the target nucleic acid than the
sequence to which the first sequencing primer hybridizes. In some
embodiments, the second sequencing primer hybridizes to a sequence
located closer to the 3' end of the target nucleic acid than the
sequence to which the first sequencing primer hybridizes. In some
embodiments, only one of the first and second sequencing primers is
extended along a barcode sequence, thereby identifying the
nucleotides in the barcode sequence. In some embodiments, one
sequencing primer (e.g. the first sequencing primer) hybridizes to
a sequence located 5' from the barcode (such that extension of this
sequencing primer does not generate sequence complementary to the
barcode), and another sequencing primer (e.g. the second sequencing
primer) hybridizes to a sequence located 3' from the barcode (such
that extension of this sequencing primer generates sequence
complementary to the barcode). In some embodiments, the second
sequencing primer comprises SEQ ID NO: 19.
[0101] The invention is not intended to be limited to use of the
sequencing methods outlined above, as essentially any sequencing
methodology which relies on successive incorporation of nucleotides
into a polynucleotide chain can be used. Suitable techniques
include, for example, those described in U.S. Pat. No. 6,306,597,
US20090233802, US20120053074, and US20110223601, which are
incorporated by reference in their entireties. In the cases where
strand resynthesis is employed, both strands must be immobilized to
the surface in a way that allows subsequent release of a portion of
the immobilized strand. This can be achieved through a number of
mechanisms as described in WO07010251, the contents of which are
incorporated herein by reference in their entirety. For example,
one primer can contain a uracil nucleotide, which means that the
strand can be cleaved at the uracil base using the enzyme uracil
DNA glycosylase (UDG) which removes the nucleotide base, and
endonuclease VIII that excises the abasic nucleotide. This enzyme
combination is available as USER.TM. from New England Biolabs (NEB
part number M5505). The second primer may comprise an 8-oxoguanine
nucleotide, which is then cleavable by the enzyme FPG (NEB part
number M0240). This design of primers provides complete control of
which primer is cleaved at which point in the process, and also
where in the cluster the cleavage occurs. The primers may also be
chemically modified, for example with a disulfide or diol
modification that allows chemical cleavage at specific
locations.
[0102] In some embodiments, sequencing data are generated for
about, less than about, or more than about 5, 10, 25, 50, 100, 150,
200, 250, 300, 400, 500, 750, 1000, 2500, 5000, 7500, 10000, 20000,
50000, or more different target polynucleotides from a sample in a
single reaction container (e.g. a channel in a flow cell). In some
embodiments, sequencing data are generated for a plurality of
samples in parallel, such as about, less than about, or more than
about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 24, 48, 96, 192, 384, 768, 1000, or more samples. In some
embodiments, sequencing data are generated for a plurality of
samples in a single reaction container (e.g. a channel in a flow
cell), such as about, less than about, or more than about 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 48,
96, 192, 384, 768, 1000, or more samples, and sequencing data are
subsequently grouped according to the sample from which the
sequenced polynucleotides originated. In a single reaction,
sequencing data may be generated for about or at least about
10.sup.6, 10.sup.7, 10.sup.8, 2.times.10.sup.8, 3.times.10.sup.8,
4.times.10.sup.8, 5.times.10.sup.8, 10.sup.9, 10.sup.10, or more
target polynucleotides or clusters from a bridge amplification
reaction, which may comprise sequencing data for about, less than
about, or more than about 10.sup.4, 10.sup.5, 10.sup.6,
2.times.10.sup.6, 3.times.10.sup.6, 4.times.10.sup.6,
5.times.10.sup.6, 10.sup.7, 10.sup.8, or more target
polynucleotides or clusters for each sample in the reaction. In
some embodiments, the presence, absence, or genotype of about, less
than about, or more than about 5, 10, 25, 50, 75, 100, 125, 150,
175, 200, 300, 400, 500, 750, 1000, 2500, 5000, 7500, 10000, 20000,
50000, or more causal genetic variants is determined for a sample
based on the sequencing data. The presence, absence, or genotype of
one or more causal genetic variants may be determined with an
accuracy of about or more than about 80%, 85%, 90%, 95%, 97.5%,
99%, 99.5%, 99.9% or higher.
[0103] In some embodiments, one or more, or all, of the steps in a
method of the invention are automated, such as by use of one or
more automated devices. In general, automated devices are devices
that are able to operate without human direction--an automated
system can perform a function during a period of time after a human
has finished taking any action to promote the function, e.g. by
entering instructions into a computer, after which the automated
device performs one or more steps without further human operation.
Software and programs, including code that implements embodiments
of the present invention, may be stored on some type of data
storage media, such as a CD-ROM, DVD-ROM, tape, flash drive, or
diskette, or other appropriate computer readable medium. Various
embodiments of the present invention can also be implemented
exclusively in hardware, or in a combination of software and
hardware. For example, in one embodiment, rather than a
conventional personal computer, a Programmable Logic Controller
(PLC) is used. As known to those skilled in the art, PLCs are
frequently used in a variety of process control applications where
the expense of a general purpose computer is unnecessary. PLCs may
be configured in a known manner to execute one or a variety of
control programs, and are capable of receiving inputs from a user
or another device and/or providing outputs to a user or another
device, in a manner similar to that of a personal computer.
Accordingly, although embodiments of the present invention are
described in terms of a general purpose computer, it should be
appreciated that the use of a general purpose computer is exemplary
only, as other configurations may be used.
[0104] In some embodiments, automation may comprise the use of one
or more liquid handlers and associated software. Several
commercially available liquid handling systems can be utilized to
run the automation of these processes (see for example liquid
handlers from Perkin-Elmer, Beckman Coulter, Caliper Life Sciences,
Tecan, Eppendorf, Apricot Design, Velocity 11 as examples). In some
embodiments, automated steps include one or more of fragmentation,
end-repair, A-tailing (addition of adenine overhang), adapter
joining, PCR amplification, sample quantification (e.g. amount
and/or purity of DNA), and sequencing. In some embodiments,
hybridization of amplified polynucleotides to oligonucleotides
attached to a solid surface, extension along the amplified
polynucleotides as templates, and/or bridge amplification is
automated (e.g. by use of an Illumina cBot). Non-limiting examples
of devices for conducting bridge amplification are described in
WO2008002502. In some embodiments, sequencing is automated. A
variety of automated sequencing machines are commercially
available, and include sequencers manufactured by Life Technologies
(SOLiD platform, and pH-based detection), Roche (454 platform),
Illumina (e.g. flow cell based systems, such as Genome Analyzer,
HiSeq, or MiSeq systems). Transfer between 2, 3, 4, 5, or more
automated devices (e.g. between one or more of a liquid handler,
bridge a amplification device, and a sequencing device) may be
manual or automated. In some embodiments, one or more steps in a
method of the invention (e.g. all steps or all automated steps) are
completed in about or less than about 72, 48, 24, 20, 18, 16, 14,
12, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, or fewer hours. In some
embodiments, the time from sample receipt, DNA extraction,
fragmentation, adapter joining, amplification, or bridge
amplification to production of sequencing data is about or less
than about 72, 48, 24, 20, 18, 16, 14, 12, 10, 9, 8, 7, 6, 5, 4, 3,
2, 1, or fewer hours.
[0105] In one aspect, the invention provides a method of enriching
a plurality of different target polynucleotides in a sample. In
some embodiments, the method comprises: (a) joining an adapter
oligonucleotide to each of the target polynucleotides, wherein the
adapter oligonucleotide comprises sequence Y; (b) hybridizing a
plurality of different oligonucleotide primers to the adapted
target polynucleotides, wherein each oligonucleotide primer
comprises sequence Z and sequence W; wherein sequence Z is common
among all oligonucleotide primers; and further wherein sequence W
is different for each different oligonucleotide primer, is
positioned at the 3' end of each oligonucleotide primer, and is
complementary to a sequence comprising a causal genetic variant or
a sequence within 200 nucleotides of a causal genetic variant; (c)
in an extension reaction, extending the oligonucleotide primers
along the adapted target polynucleotides to produce extended
primers comprising sequence Z and sequence Y', wherein sequence Y'
is complementary to sequence Y; and (d) exponentially amplifying
the purified extension products using a pair of amplification
primers comprising (i) a first amplification primer comprising
sequence V and sequence Z, wherein sequence Z is positioned at the
3' end of the first amplification primer; and (ii) a second
amplification primer comprising sequence X and sequence Y, wherein
sequence Y and is positioned at the 3' end of the second
amplification primer. In some embodiments, each oligonucleotide
primer comprises a first binding partner. In some embodiments, the
method further comprises, before step (d), exposing the extended
primers to a solid surface comprising a second binding partner that
binds to the first binding partner, thereby purifying the extended
primers away from one or more components of the extension reaction.
In some embodiments, one or more of sequences V, W, X, Y, and Z are
different sequences. In some embodiments, sequence V and sequence X
are the same. In some embodiments, sequence V and/or sequence X are
not included in their respective primers. In some embodiments, one
or more of sequences V, W, X, Y, and Z are about, less than about,
or more than about 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%,
80%, 90%, or more different from one or more of the other of
sequences V, W, X, Y, and Z (e.g. have less than about 10%, 20%,
30%, 40%, 50%, 60%, 70%, 80%, 90%, or more sequence identity). In
some embodiments, one or more of sequences V, W, X, Y, and Z
comprise about, less than about, or more than about 1, 2, 3, 4, 5,
6, 7, 8, 9, 10, 15, 20, or more nucleotides each. In some
embodiments, sequence V or sequence Z is equivalent to sequence A,
sequence W is equivalent to sequence B, sequence X is equivalent to
sequence C, and/or sequence Y is equivalent to sequence D, as
described with respect to other aspects of the invention.
[0106] In one aspect, the invention provides a method of enriching
a plurality of different target polynucleotides in a sample. In
some embodiments, the method comprises: (a) hybridizing a plurality
of different oligonucleotide primers to the target polynucleotides,
wherein each oligonucleotide primer comprises sequence Z and
sequence W; wherein sequence Z is common among all oligonucleotide
primers; and further wherein sequence W is different for each
different oligonucleotide primer, is positioned at the 3' end of
each oligonucleotide primer, and is complementary to a sequence
comprising a causal genetic variant or a sequence within 200
nucleotides of a causal genetic variant; (b) in an extension
reaction, extending the oligonucleotide primers along the target
polynucleotides to produce extended primers; (c) joining an adapter
oligonucleotide to each extended primer, wherein the adapter
oligonucleotide comprises sequence Y', and further wherein sequence
Y' is the complement of a sequence Y; and (d) exponentially
amplifying the purified extension products using a pair of
amplification primers comprising (i) a first amplification primer
comprising sequence V and sequence Z, wherein sequence Z is
positioned at the 3' end of the first amplification primer; and
(ii) a second amplification primer comprising sequence X and
sequence Y, wherein sequence Y and is positioned at the 3' end of
the second amplification primer. In some embodiments, each
oligonucleotide primer comprises a first binding partner. In some
embodiments, the method further comprises, before step (c),
exposing the extended primers to a solid surface comprising a
second binding partner that binds to the first binding partner,
thereby purifying the extended primers away from one or more
components of the extension reaction. In some embodiments, one or
more of sequences V, W, X, Y, and Z are different sequences. In
some embodiments, sequence V and sequence X are the same. In some
embodiments, sequence V and/or sequence X are not included in their
respective primers. In some embodiments, one or more of sequences
V, W, X, Y, and Z are about, less than about, or more than about
5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or more
different from one or more of the other of sequences V, W, X, Y,
and Z (e.g. have less than about 10%, 20%, 30%, 40%, 50%, 60%, 70%,
80%, 90%, or more sequence identity). In some embodiments, one or
more of sequences V, W, X, Y, and Z comprise about, less than
about, or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or
more nucleotides each. In some embodiments, sequence V or sequence
Z is equivalent to sequence A, sequence W is equivalent to sequence
B, sequence X is equivalent to sequence C, and/or sequence Y is
equivalent to sequence D, as described with respect to other
aspects of the invention.
[0107] Samples from which the target polynucleotides are derived
can comprise multiple samples from the same individual, samples
from different individuals, or combinations thereof. In some
embodiments, a sample comprises a plurality of polynucleotides from
a single individual. In some embodiments, a sample comprises a
plurality of polynucleotides from two or more individuals. Examples
of sources of sample polynucleotides and methods for their
purification are described herein, such as with regard to other
aspects of the invention.
[0108] In some embodiments, target polynucleotides are fragmented
into a population of fragmented polynucleotides of one or more
specific size range(s). In some embodiments, the amount of sample
polynucleotides subjected to fragmentation is about, less than
about, or more than about 50 ng, 100 ng, 200 ng, 300 ng, 400 ng,
500 ng, 600 ng, 700 ng, 800 ng, 900 ng, 1000 ng, 1500 ng, 2000 ng,
2500 ng, 5000 ng, 10 .mu.g, or more. In some embodiments, fragments
are generated from about, less than about, or more than about 1,
10, 100, 1000, 10000, 100000, 300000, 500000, or more
genome-equivalents of starting DNA. Fragmentation may be
accomplished by methods known in the art, including chemical,
enzymatic, and mechanical fragmentation. In some embodiments, the
fragments have an average or median length from about 10 to about
10,000 nucleotides. In some embodiments, the fragments have an
average or median length from about 50 to about 2,000 nucleotides.
In some embodiments, the fragments have an average or median length
of about, less than about, more than about, or between about
100-2500, 200-1000, 10-800, 10-500, 50-500, 50-250, or 50-150
nucleotides. In some embodiments, the fragments have an average or
median length of about, less than about, or more than about 200,
300, 500, 600, 800, 1000, 1500, or more nucleotides. Example
methods of fragmentation and optional end repair (including
optional A-tailing) are described herein, such as with regard to
other aspects of the invention. End repair may be performed at any
step before joining of adapter oligonucleotides, such as before or
after extension of oligonucleotide primers.
[0109] In some embodiments, fragmentation or oligonucleotide primer
extension is followed by ligation of adapter oligonucleotides to
the fragmented or extended polynucleotides (see e.g. FIGS. 5 and
7). Examples of adapter oligonucleotides, and methods for their
manipulation and joining to target polynucleotides are described
herein, such as with regard to other aspects of the invention. In
some embodiments, adapter oligonucleotides comprise one strand
comprising the sequence element sequence Y. In some embodiments,
adapter oligonucleotides comprise one strand comprising the
sequence element sequence Y', which is the complement of sequence
Y. In some embodiments, adapter oligonucleotides comprise sequence
Y hybridized to complementary sequence Y', where sequence Y' is on
the same or different strand as sequence Y. In some embodiments,
the 3' end of a target polynucleotide or extended primer is
extended along an adapter oligonucleotide to generate sequence Y or
sequence Y'. In some embodiments, fragmented polynucleotides and
adapter oligonucleotides are combined and treated (e.g. by ligation
and optionally by fragment extension) to produce double-stranded,
adapted polynucleotides comprising fragmented polynucleotide
sequence joined to adapter oligonucleotide sequences at both ends,
where both ends of the adapted polynucleotides comprise sequence Y
hybridized to sequence Y'. In some embodiments, extended primers
that are hybridized to target polynucleotides are combined and
treated (e.g. by ligation and optionally by 3'-end extension) to
produce double-stranded, adapted polynucleotides comprising
sequence Y hybridized to sequence Y' at one end. In some
embodiments, the amount of fragmented polynucleotides subjected to
further manipulation (e.g. adapter joining or oligonucleotide
primer extension) is about, less than about, or more than about 50
ng, 100 ng, 200 ng, 300 ng, 400 ng, 500 ng, 600 ng, 700 ng, 800 ng,
900 ng, 1000 ng, 1500 ng, 2000 ng, 2500 ng, 5000 ng, 10 .mu.g, or
more (e.g. a threshold amount). In some embodiments, the amount of
fragmented polynucleotides is determined before proceeding with
further manipulation, where further manipulation is not performed
if the amount is below a threshold amount.
[0110] In some embodiments, primer extension products comprising
sequences complementary to target polynucleotide sequences are
produced in an extension reaction. In general, an extension
reaction comprises extension of an oligonucleotide primer
hybridized to a target polynucleotide. Oligonucleotide primers may
be of any suitable length, such as about, less than about, or more
than about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70,
75, 80, 90, 100, or more nucleotides, any portion or all of which
may be complementary to the corresponding target sequence to which
the primer hybridizes (e.g. about, less than about, or more than
about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, or more nucleotides).
Primer extension may comprise one or more cycles of a PCR reaction,
such as denaturation, primer annealing, and primer extension, which
may be repeated any number of times with or without a reverse
primer. For example, in the absence of a reverse primer, multiple
cycles may be used to linearly amplify one or more target
polynucleotides by repeated extension of primers along the
corresponding targets, without using extended primers as templates
for further amplification. Examples of oligonucleotides useful as
primers and methods for their use in primer extension reactions
(e.g. amplification) are provided herein, such as with regard to
other aspects of the invention. An illustration of a non-limiting
example of an amplification method is provided in FIG. 2.
[0111] In some embodiments, an oligonucleotide primer comprises
sequence Z, which is common to each of a plurality of different
oligonucleotide primers in a reaction, and sequence W, which is
different for each different oligonucleotide primer and is
positioned at the 3' end of each oligonucleotide primer. In some
embodiments, the plurality of oligonucleotide primers comprises
about, less than about, or more than about 5, 10, 25, 50, 75, 100,
125, 150, 175, 200, 300, 400, 500, 750, 1000, 2500, 5000, 7500,
10000, 20000, 50000, or more different oligonucleotides, each
comprising a different sequence W. In some embodiments, sequence W
of one or more of the plurality of oligonucleotide primers
comprises a sequence selected from the group consisting of SEQ ID
NOs 22-121, shown in FIG. 4 (e.g. 1, 5, 10, 25, 50, 75, or 100
different oligonucleotides each with a different sequence from FIG.
4). In some embodiments, sequence W or the target sequence to which
it specifically hybridizes comprises a causal genetic variant, as
described herein. In some embodiments, sequence W or the target
sequence to which it specifically hybridizes is within about, less
than about, or more than about 1, 2, 3, 4, 5, 6, 6, 7, 8, 9, 10,
15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 200, 500 or
more nucleotides of a causal genetic variant, as described herein.
Causal genetic variants are typically located downstream of an
oligonucleotide primer, such that at least a portion of the causal
genetic variant serves as template for extension of an
oligonucleotide primer. Typically, extension of an oligonucleotide
primer along a target polynucleotide comprising sequence Y derived
from an adapter oligonucleotide produces a primer extension product
comprising primer-derived sequences a the 5' end and sequences
complementary to adapter-derived sequences near the 3' end (e.g.
sequence Y', the complement of Y).
[0112] In some embodiments, sequence W of one or more of the
plurality of oligonucleotide primers or the target sequence to
which it specifically hybridizes comprises a non-subject sequence.
In some embodiments, sequence W or the target sequence to which it
specifically hybridizes is within about, less than about, or more
than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40,
45, 50, 60, 70, 80, 90, 100, 200, 500 or more nucleotides of a
non-subject sequence. In general, a non-subject sequence
corresponds to a polynucleotide derived from an organism other than
the individual being tested, such as DNA or RNA from bacteria,
archaea, viruses, protists, fungi, or other organism. A non-subject
sequence may be indicative of the identity of an organism or class
of organisms, and may further be indicative of a disease state,
such as infection. An example of non-subject sequences useful in
identifying an organism include, without limitation, rRNA
sequences, such as 16s rRNA sequences (see e.g. WO2010151842). In
some embodiments, non-subject sequences are analyzed instead of, or
separately from causal genetic variants. In some embodiments,
causal genetic variants and non-subject sequences are analyzed in
parallel, such as in the same sample (e.g. using a mixture of
oligonucleotide primers, some with a sequence W that specifically
hybridizes to a sequence comprising or near a causal genetic
variant, and some with a sequence W that specifically hybridizes to
a sequence comprising or near a non-subject sequence) and/or in the
same report.
[0113] In some embodiments, sequence W of one or more of the
plurality of oligonucleotide primers or the target sequence to
which it specifically hybridizes comprises an ancestry informative
marker (AIM). In some embodiments, sequence W or the target
sequence to which it specifically hybridizes is within about, less
than about, or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15,
20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 200, 500 or more
nucleotides of an AIM. An AIM may be used to classify a person as
belonging to or not belonging to one or more populations, such as a
population that is at increased risk for one of the causal genetic
variants. For example, an AIM can be diagnostic for a population in
which a trait is at increased prevalence. In certain instances the
AIM may distinguish between populations with finer granularity, for
example, between sub-continental groups or related ethnic groups.
In some embodiments, AIMs are analyzed instead of, or separately
from causal genetic variants and/or non-subject sequences. In some
embodiments, AIMs, causal genetic variants, and/or non-subject
sequences are analyzed in parallel, such as in the same sample
(e.g. using a mixture of first oligonucleotides, some with a
sequence B that specifically hybridizes to a sequence comprising or
near a causal genetic variant, and some with a sequence B that
specifically hybridizes to a sequence comprising or near an AIM)
and/or in the same report.
[0114] In some embodiments, the oligonucleotide primers comprise a
first binding partner, such as a member of a binding pair. In
general, "binding partner" refers to one of a first and a second
moiety, wherein the first and the second moiety have a specific
binding affinity for each other. Suitable binding pairs for use in
the invention include, but are not limited to, antigens/antibodies
(for example, digoxigenin/anti-digoxigenin, dinitrophenyl
(DNP)/anti-DNP, dansyl-X-anti-dansyl, Fluorescein/anti-fluorescein,
lucifer yellow/anti-lucifer yellow, and rhodamine anti-rhodamine);
biotin/avidin (or biotin/streptavidin); calmodulin binding protein
(CBP)/calmodulin; hormone/hormone receptor; lectin/carbohydrate;
peptide/cell membrane receptor; protein A/antibody;
hapten/antihapten; enzyme/cofactor; and enzyme/substrate. Other
suitable binding pairs include polypeptides such as the
FLAG-peptide (Hopp et al., BioTechnology, 6:1204-1210 (1988)); the
KT3 epitope peptide (Martin et al., Science, 255:192-194 (1992));
tubulin epitope peptide (Skinner et al., J. Biol. Chem.,
266:15163-15166 (1991)); and the T7 gene 10 protein peptide tag
(Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. USA, 87:6393-6397
(1990)) and the antibodies each thereto. Further non-limiting
examples of binding partners include agonists and antagonists for
cell membrane receptors, toxins and venoms, viral epitopes,
hormones such as steroids, hormone receptors, peptides, enzymes and
other catalytic polypeptides, enzyme substrates, cofactors, drugs
including small organic molecule drugs, opiates, opiate receptors,
lectins, sugars, saccharides including polysaccharides, proteins,
and antibodies including monoclonal antibodies and synthetic
antibody fragments, cells, cell membranes and moieties therein
including cell membrane receptors, and organelles. In some
embodiments, the first binding partner is a reactive moiety, and
the second binding partner is a reactive surface that reacts with
the reactive moiety, such as described herein with respect to other
aspects of the invention. In some embodiments, the oligonucleotide
primers are attached to the solid surface prior to initiating the
extension reaction. Methods for the addition of binding partners to
oligonucleotides are known in the art, and include addition during
(such as by using a modified nucleotide comprising the binding
partner) or after synthesis.
[0115] In some embodiments, extension of the oligonucleotide
primers is followed by purification of extended primers on a solid
surface. In some embodiments, adapter joining is followed by
purification of extended primers on a solid surface. Typically, the
solid surface comprises a second binding partner, which is the
second member of a binding pair and binds to the first binding
partner. In some embodiments, a solid surface may have a wide
variety of forms, including membranes, slides, plates,
micromachined chips, microparticles, beads, and the like. Solid
surfaces may comprise a wide variety of materials including, but
not limited to, glass, plastic, silicon, alkanethiolate derivatized
gold, cellulose, low cross linked and high cross linked
polystyrene, silica gel, polyamide, and the like, and can have
various shapes and features (e.g., wells, indentations, channels,
etc.). The surface can be hydrophilic or capable of being rendered
hydrophilic and may comprise inorganic powders such as silica,
magnesium sulfate, and alumina; natural polymeric materials,
particularly cellulosic materials and materials derived from
cellulose, such as fiber containing papers, e.g., filter paper,
chromatographic paper, etc.; synthetic or modified naturally
occurring polymers, such as nitrocellulose, cellulose acetate,
poly(vinyl chloride), polyacrylamide, cross linked dextran,
agarose, polyacrylate, polyethylene, polypropylene,
poly(4-methylbutene), polystyrene, polymethacrylate, poly(ethylene
terephthalate), nylon, poly(vinyl butyrate), etc.; either used by
themselves or in conjunction with other materials; glass available
as Bioglass, ceramics, metals, and the like. Natural or synthetic
assemblies such as liposomes, phospholipid vesicles, and cells can
also be employed. The surface can have any one of a number of
shapes, such as strip, rod, particle, including bead, and the
like.
[0116] In some embodiments, the solid surface comprises a bead or
plurality of beads. The beads may be of any convenient size and
fabricated from any number of known materials. Example of such
materials include: inorganics, natural polymers, and synthetic
polymers. Specific examples of these materials include: cellulose,
cellulose derivatives, acrylic resins, glass, silica gels,
polystyrene, gelatin, polyvinyl pyrrolidone, co-polymers of vinyl
and acrylamide, polystyrene cross-linked with divinylbenzene or the
like (as described, e.g, in Merrifield, Biochemistry 1964, 3,
1385-1390), polyacrylamides, latex gels, polystyrene, dextran,
rubber, silicon, plastics, nitrocellulose, natural sponges, silica
gels, control pore glass, metals, cross-linked dextrans (e.g.,
Sephadex) agarose gel (Sepharose), and other solid phase supports
known to those of skill in the art. The beads are generally about 2
to about 100 .mu.m in diameter, or about 5 to about 80 pm in
diameter, in some cases, about 10 to about 40 .mu.m in diameter. In
some embodiments the beads can be magnetic, paramagnetic, or
otherwise responsive to a magnetic field. Having beads responsive
to a magnetic field can be useful for isolation and purification of
the beads having polynucleotides attached thereto, such as by the
application of a magnetic field and isolation of the beads (e.g. by
removal of the beads from solution, or removal of solution from the
beads). Non-limiting examples of beads responsive to a magnetic
field include Dynabeads, manufactured by Life Technologies
(Carlsbad, Calif.). Other methods to separate beads can also be
used. For example, the capture beads may be labeled with a
fluorescent moiety which would make the nucleic acid-bead complex
fluorescent. The target capture bead complex may be separated, for
example, by flow cytometry or fluorescence cell sorter. Beads may
also be separated by centrifugation. Isolation of polynucleotides
by attachment to beads may further comprise the step of washing the
beads, such as in a suitable wash buffer. Generally, purification
of primer extension products comprises purification away from one
or more components of the primer extension reaction, such that the
one or more components from which the extension products are
purified are reduced in amount, such as by 10-fold, 5-fold,
100-fold, 500-fold, 1000-fold, 10000-fold, 100000-fold, or more, or
below detectable levels. In some embodiments, purification includes
a denaturation step such that primer extension products are
purified away from the target polynucleotide templates to which
they were hybridized.
[0117] Extended primers may be subjected to amplification, such as
linear or exponential amplification. Methods for amplification are
known in art, examples of which are described herein, such as with
respect to other aspects of the invention. Exponential
amplification includes PCR amplification, and any other
amplification methods where primer extension products serve as
templates for further rounds of primer extension. Amplification
typically utilizes one or more amplification primers, examples of
which are described herein, such as with regard to other aspects of
the invention. Amplification primers may be of any suitable length,
such as about, less than about, or more than about 5, 10, 15, 20,
25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, or more
nucleotides, any portion or all of which may be complementary to
the corresponding target sequence to which the primer hybridizes
(e.g. about, less than about, or more than about 5, 10, 15, 20, 25,
30, 35, 40, 45, 50, or more nucleotides). In general, PCR involves
the steps of denaturation of the target to be amplified (if double
stranded), hybridization of one or more primers to the target, and
extension of the primers by a DNA polymerase, with the steps
repeated (or "cycled") in order to amplify the target sequence.
Steps in this process can be optimized for various outcomes, such
as to enhance yield, decrease the formation of spurious products,
and/or increase or decrease specificity of primer annealing.
Methods of optimization are well known in the art and include
adjustments to the type or amount of elements in the amplification
reaction and/or to the conditions of a given step in the process,
such as temperature at a particular step, duration of a particular
step, and/or number of cycles. In some embodiments, an
amplification reaction comprises at least 5, 10, 15, 20, 25, 30,
35, 50, or more cycles. In some embodiments, an amplification
reaction comprises no more than 5, 10, 15, 20, 25, 35, 50, or more
cycles. Cycles can contain any number of steps, such as 1, 2, 3, 4,
5, 6, 7, 8, 9, 10 or more steps. Steps can comprise any temperature
or gradient of temperatures, suitable for achieving the purpose of
the given step, including but not limited to, strand denaturation,
primer annealing, and primer extension. Steps can be of any
duration, including but not limited to about, less than about, or
more than about 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60,
70, 80, 90, 100, 120, 180, 240, 300, 360, 420, 480, 540, 600, or
more seconds, including indefinitely until manually interrupted.
Cycles of any number comprising different steps can be combined in
any order.
[0118] In some embodiments, amplification comprises generating
primer extension products using a pair of amplification primers.
Amplification primers may comprise sequences complementary to
complete or one or more portions of sequences derived from adapter
oligonucleotide sequences, sequences derived from oligonucleotide
primer sequences, sequences that are not complementary to template
polynucleotides (e.g. 5' non-complementary sequences), one or more
other sequence elements (e.g. sequence elements as described
herein), or combinations of these. In some embodiments, a second
amplification primer comprises sequence X and sequence Y, where
sequence Y is positioned at the 3' end of the second amplification
primer.
[0119] FIG. 2 illustrates a non-limiting example of an
amplification process. In a first step of an example exponential
amplification reaction, sequence Y of the second amplification
primer hybridizes to the complementary sequence Y' of an extended
primer from a previous oligonucleotide primer extension reaction.
Extension of the second amplification primer (e.g. by a polymerase)
produces a second-amplification-primer extension product comprising
sequences X, Y, W', and Z' in a 5' to 3' direction, where sequence
W' is the complement of sequence W, and sequence Z' is the
complement of sequence Z. The primer extension product is then
denatured, freeing the template target polynucleotide to serve as
template for hybridization with and extension of a further second
amplification primer, and the extension product for hybridization
with and extension of a first amplification primer. In some
embodiments, the first amplification primer comprises sequence V
and sequence Z, where sequence Z is positioned at the 3' end of the
first amplification primer. In this example amplification reaction,
sequence Z hybridizes to sequence Z' of a second amplification
primer extension product. Extension of the first amplification
primer (e.g. by a polymerase) produces a first-amplification-primer
extension product comprising sequences V, Z, W, Y', and X' in a 5'
to 3' direction, where sequence X' is complementary to sequence X,
which itself can serve as a template for extension of a second
amplification primer. Repeated cycles of denaturation,
hybridization, and extension thus produce duplexes of primer
extension products comprising one strand comprising sequences V, Z,
W, Y', and X' (from 5' to 3') hybridized to a second strand
comprising sequences X, Y, W', Z', and V' (from 5' to 3'). In
accordance with this example amplification reaction, target
polynucleotide sequence will generally be positioned between
sequences Z and Y' on one strand, and between sequences Z' and Y on
the other strand.
[0120] In some embodiments the oligonucleotide primer and/or one or
more amplification primers comprise a barcode. Examples of barcodes
are described herein, such as with regard to other aspects of the
invention. In some embodiments, separate amplification reactions
are carried out for separate samples using amplification primers
comprising at least one different barcode sequence for each sample,
such that no barcode sequence is joined to the target
polynucleotides of more than one sample to be analyzed in parallel.
In some embodiments, amplified polynucleotides derived from
different samples and comprising different barcodes are pooled
before proceeding with subsequent manipulation of the
polynucleotides (such as before sequencing). Pools may comprise
polynucleotides derived from about, less than about, or more than
about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30,
40, 50, 75, 100, or more different samples. Pools may subsequently
be subjected to sequencing, and the source samples of sequenced
target polynucleotides may be identified based on their associated
barcodes.
[0121] In some embodiments, exponentially amplified target
polynucleotides are sequenced. Sequencing may be performed
according to any method of sequencing known in the art, including
sequencing processes described herein, such as with reference to
other aspects of the invention. Sequence analysis using template
dependent synthesis can include a number of different processes.
For example, in the ubiquitously practiced four-color Sanger
sequencing methods, a population of template molecules is used to
create a population of complementary fragment sequences. Primer
extension is carried out in the presence of the four naturally
occurring nucleotides, and with a sub-population of dye labeled
terminator nucleotides, e.g., dideoxyribonucleotides, where each
type of terminator (ddATP, ddGTP, ddTTP, ddCTP) includes a
different detectable label. As a result, a nested set of fragments
is created where the fragments terminate at each nucleotide in the
sequence beyond the primer, and are labeled in a manner that
permits identification of the terminating nucleotide. The nested
fragment population is then subjected to size based separation,
e.g., using capillary electrophoresis, and the labels associated
with each different sized fragment is identified to identify the
terminating nucleotide. As a result, the sequence of labels moving
past a detector in the separation system provides a direct readout
of the sequence information of the synthesized fragments, and by
complementarity, the underlying template (See, e.g., U.S. Pat. No.
5,171,534).
[0122] Other examples of template dependent sequencing methods
include sequence by synthesis processes, where individual
nucleotides are identified iteratively, as they are added to the
growing primer extension product.
[0123] Pyrosequencing is an example of a sequence by synthesis
process that identifies the incorporation of a nucleotide by
assaying the resulting synthesis mixture for the presence of
by-products of the sequencing reaction, namely pyrophosphate. In
particular, a primer/template/polymerase complex is contacted with
a single type of nucleotide. If that nucleotide is incorporated,
the polymerization reaction cleaves the nucleoside triphosphate
between the .alpha. and .beta. phosphates of the triphosphate
chain, releasing pyrophosphate. The presence of released
pyrophosphate is then identified using a chemiluminescent enzyme
reporter system that converts the pyrophosphate, with AMP, into
ATP, then measures ATP using a luciferase enzyme to produce
measurable light signals. Where light is detected, the base is
incorporated, where no light is detected, the base is not
incorporated. Following appropriate washing steps, the various
bases are cyclically contacted with the complex to sequentially
identify subsequent bases in the template sequence. See, e.g., U.S.
Pat. No. 6,210,891.
[0124] In related processes, the primer/template/polymerase complex
is immobilized upon a substrate and the complex is contacted with
labeled nucleotides. The immobilization of the complex may be
through the primer sequence, the template sequence and/or the
polymerase enzyme, and may be covalent or noncovalent. For example,
immobilization of the complex can be via a linkage between the
polymerase or the primer and the substrate surface. In alternate
configurations, the nucleotides are provided with and without
removable terminator groups. Upon incorporation, the label is
coupled with the complex and is thus detectable. In the case of
terminator bearing nucleotides, all four different nucleotides,
bearing individually identifiable labels, are contacted with the
complex. Incorporation of the labeled nucleotide arrests extension,
by virtue of the presence of the terminator, and adds the label to
the complex, allowing identification of the incorporated
nucleotide. The label and terminator are then removed from the
incorporated nucleotide, and following appropriate washing steps,
the process is repeated. In the case of non-terminated nucleotides,
a single type of labeled nucleotide is added to the complex to
determine whether it will be incorporated, as with pyrosequencing.
Following removal of the label group on the nucleotide and
appropriate washing steps, the various different nucleotides are
cycled through the reaction mixture in the same process. See, e.g.,
U.S. Pat. No. 6,833,246, incorporated herein by reference in its
entirety for all purposes. For example, the Illumina Genome
Analyzer System is based on technology described in WO 98/44151,
hereby incorporated by reference, wherein DNA molecules are bound
to a sequencing platform (flow cell) via an anchor probe binding
site (otherwise referred to as a flow cell binding site) and
amplified in situ on a glass slide. A solid surface on which DNA
molecules are amplified typically comprise a plurality of first and
second bound oligonucleotides, the first complementary to a
sequence near or at one end of a target polynucleotide and the
second complementary to a sequence near or at the other end of a
target polynucleotide. This arrangement permits bridge
amplification, such as described herein. The DNA molecules are then
annealed to a sequencing primer and sequenced in parallel
base-by-base using a reversible terminator approach. Hybridization
of a sequencing primer may be preceded by cleavage of one strand of
a double-stranded bridge polynucleotide at a cleavage site in one
of the bound oligonucleotides anchoring the bridge, thus leaving
one single strand not bound to the solid substrate that may be
removed by denaturing, and the other strand bound and available for
hybridization to a sequencing primer. Typically, the Illumina
Genome Analyzer System utilizes flow-cells with 8 channels,
generating sequencing reads of 18 to 36 bases in length, generating
>1.3 Gbp of high quality data per run (see
www.illumina.com).
[0125] In yet a further sequence by synthesis process, the
incorporation of differently labeled nucleotides is observed in
real time as template dependent synthesis is carried out. In
particular, an individual immobilized primer/template/polymerase
complex is observed as fluorescently labeled nucleotides are
incorporated, permitting real time identification of each added
base as it is added. In this process, label groups are attached to
a portion of the nucleotide that is cleaved during incorporation.
For example, by attaching the label group to a portion of the
phosphate chain removed during incorporation, i.e., a .beta.,
.gamma., or other terminal phosphate group on a nucleoside
polyphosphate, the label is not incorporated into the nascent
strand, and instead, natural DNA is produced. Observation of
individual molecules typically involves the optical confinement of
the complex within a very small illumination volume. By optically
confining the complex, one creates a monitored region in which
randomly diffusing nucleotides are present for a very short period
of time, while incorporated nucleotides are retained within the
observation volume for longer as they are being incorporated. This
results in a characteristic signal associated with the
incorporation event, which is also characterized by a signal
profile that is characteristic of the base being added. In related
aspects, interacting label components, such as fluorescent resonant
energy transfer (FRET) dye pairs, are provided upon the polymerase
or other portion of the complex and the incorporating nucleotide,
such that the incorporation event puts the labeling components in
interactive proximity, and a characteristic signal results, that is
again, also characteristic of the base being incorporated (See,
e.g., U.S. Pat. Nos. 6,056,661, 6,917,726, 7,033,764, 7,052,847,
7,056,676, 7,170,050, 7,361,466, and 7,416,844; and US
20070134128).
[0126] In some embodiments, the nucleic acids in the sample can be
sequenced by ligation. This method uses a DNA ligase enzyme to
identify the target sequence, for example, as used in the polony
method and in the SOLiD technology (Applied Biosystems, now
Invitrogen). In general, a pool of all possible oligonucleotides of
a fixed length is provided, labeled according to the sequenced
position. Oligonucleotides are annealed and ligated; the
preferential ligation by DNA ligase for matching sequences results
in a signal corresponding to the complementary sequence at that
position.
[0127] In some embodiments, sequencing data are generated for a
plurality of samples in parallel, such as about, less than about,
or more than about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 24, 48, 96, 192, 384, 768, 1000, or more
samples. In some embodiments, sequencing data are generated for a
plurality of samples in a single reaction container (e.g. a channel
in a flow cell), such as about, less than about, or more than about
2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
24, 48, 96, 192, 384, 768, 1000, or more samples, and sequencing
data are subsequently grouped according to the sample from which
the sequenced polynucleotides originated (e.g. based on a barcode
sequence).
[0128] In some embodiments, sequencing data are generated for
about, less than about, or more than about 5, 10, 25, 50, 100, 150,
200, 250, 300, 400, 500, 750, 1000, 2500, 5000, 7500, 10000, 20000,
50000, or more different target polynucleotides from a sample in a
single reaction container (e.g. a channel in a flow cell). In some
embodiments, sequencing data are generated for a plurality of
samples in parallel, such as about, less than about, or more than
about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 24, 48, 96, 192, 384, 768, 1000, or more samples. In some
embodiments, sequencing data are generated for a plurality of
samples in a single reaction container (e.g. a channel in a flow
cell), such as about, less than about, or more than about 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 48,
96, 192, 384, 768, 1000, or more samples, and sequencing data are
subsequently grouped according to the sample from which the
sequenced polynucleotides originated. In a single reaction,
sequencing data may be generated for about or at least about
10.sup.6, 10.sup.7, 10.sup.8, 2.times.10.sup.8, 3.times.10.sup.8,
4.times.10.sup.8, 5.times.10.sup.8, 10.sup.9, 10.sup.10, or more
target polynucleotides or clusters from a bridge amplification
reaction, which may comprise sequencing data for about, less than
about, or more than about 10.sup.4, 10.sup.5, 10.sup.6,
2.times.10.sup.6, 3.times.10.sup.6, 4.times.10.sup.6,
5.times.10.sup.6, 10.sup.7, 10.sup.8 target polynucleotides or
clusters for each sample in the reaction. In some embodiments, the
presence or absence of about, less than about, or more than about
5, 10, 25, 50, 75, 100, 125, 150, 175, 200, 300, 400, 500, 750,
1000, 2500, 5000, 7500, 10000, 20000, 50000, or more causal genetic
variants is determined for a sample based on the sequencing data.
The presence or absence of one or more causal genetic variants may
be determined with an accuracy of about or more than about 80%,
85%, 90%, 95%, 97.5%, 99%, 99.5%, 99.9% or higher.
[0129] In some embodiments, one or more, or all, of the steps in a
method of the invention are automated, such as by use of one or
more automated devices. In general, automated devices are devices
that are able to operate without human direction--an automated
system can perform a function during a period of time after a human
has finished taking any action to promote the function, e.g. by
entering instructions into a computer, after which the automated
device performs one or more steps without further human operation.
Software and programs, including code that implements embodiments
of the present invention, may be stored on some type of data
storage media, such as a CD-ROM, DVD-ROM, tape, flash drive, or
diskette, or other appropriate computer readable medium. Various
embodiments of the present invention can also be implemented
exclusively in hardware, or in a combination of software and
hardware. For example, in one embodiment, rather than a
conventional personal computer, a Programmable Logic Controller
(PLC) is used. As known to those skilled in the art, PLCs are
frequently used in a variety of process control applications where
the expense of a general purpose computer is unnecessary. PLCs may
be configured in a known manner to execute one or a variety of
control programs, and are capable of receiving inputs from a user
or another device and/or providing outputs to a user or another
device, in a manner similar to that of a personal computer.
Accordingly, although embodiments of the present invention are
described in terms of a general purpose computer, it should be
appreciated that the use of a general purpose computer is exemplary
only, as other configurations may be used.
[0130] In some embodiments, automation may comprise the use of one
or more liquid handlers and associated software. Several
commercially available liquid handling systems can be utilized to
run the automation of these processes (see for example liquid
handlers from Perkin-Elmer, Beckman Coulter, Caliper Life Sciences,
Tecan, Eppendorf, Apricot Design, Velocity 11 as examples). In some
embodiments, automated steps include one or more of fragmentation,
end-repair, A-tailing (addition of adenine overhang), adapter
joining, PCR amplification, sample quantification (e.g. amount
and/or purity of DNA), and sequencing. In some embodiments, bridge
amplification is automated (e.g. by use of an Illumina cBot). In
some embodiments, sequencing is automated. A variety of automated
sequencing machines are commercially available, and include
sequencers manufactured by Life Technologies (SOLiD platform, and
pH-based detection), Roche (454 platform), Illumina (e.g. flow cell
based systems, such as Genome Analyzer devices). Transfer between
2, 3, 4, 5, or more automated devices (e.g. between one or more of
a liquid handler, bridge a amplification device, and a sequencing
device) may be manual or automated. In some embodiments, one or
more steps in a method of the invention (e.g. all steps or all
automated steps) are completed in about or less than about 72, 48,
24, 20, 18, 16, 14, 12, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, or fewer
hours. In some embodiments, the time from sample receipt, DNA
extraction, fragmentation, adapter joining, amplification, or
bridge amplification to production of sequencing data is about or
less than about 72, 48, 24, 20, 18, 16, 14, 12, 10, 9, 8, 7, 6, 5,
4, 3, 2, 1, or fewer hours.
[0131] In one aspect, the invention provides a method of detecting
genetic variation in a subject's genome. In some embodiments, the
method comprises generating and analyzing sequencing data. In one
embodiment, the method comprises: (a) providing a plurality of
clusters of polynucleotides, wherein (i) each cluster comprises
multiple copies of a nucleic acid duplex attached to a support;
(ii) each duplex in a cluster comprises a first molecule comprising
sequences A-B-G'-D'-C' from 5' to 3' and a second molecule
comprising sequences C-D-G-B'-A' from 5' to 3'; (iii) sequence A'
is complementary to sequence A, sequence B' is complementary to
sequence B, sequence C' is complementary to sequence C, sequence D'
is complementary to sequence D, and sequence G' is complementary to
sequence G; (iv) sequence G is a portion of a target polynucleotide
sequence from a subject and is different for each of a plurality of
clusters; and (v) sequence B' is located 5' with respect to
sequence G in the corresponding target polynucleotide sequence; (b)
sequencing sequence G' by extension of a first primer comprising
sequence D to produce an R1 sequence for each cluster; (c)
sequencing sequence B' by extension of a second primer comprising
sequence A to produce R2 sequence for each cluster; (d) performing
a first alignment using a first algorithm to align all R1 sequences
to one or more first reference sequences; (e) performing a second
alignment using a second algorithm to locally align R1 sequences
identified in said first alignment as likely to contain an
insertion or deletion with respect to said one or more first
reference sequences, to produce a single consensus alignment for
each insertion or deletion; (f) performing an R2 alignment by
aligning all R2 sequences to one or more second reference
sequences; and (g) transmitting a report identifying sequence
variation identified by steps (d) to (f) to a receiver. In some
embodiments, sequence A, B, C, and D correspond to sequence A, B,
C, and D, respectively, as described with regard to other aspects
of the invention.
[0132] In some embodiments, the method comprises: (a) providing
sequencing data for a plurality of clusters of polynucleotides,
wherein (i) each cluster comprised multiple copies of a nucleic
acid duplex attached to a support; (ii) each duplex in a cluster
comprised a first molecule comprising sequences A-B-G'-D'-C' from
5' to 3' and a second molecule comprising sequences C-D-G-B'-A'
from 5' to 3'; (iii) sequence A' is complementary to sequence A,
sequence B' is complementary to sequence B, sequence C' is
complementary to sequence C, sequence D' is complementary to
sequence D, and sequence G' is complementary to sequence G; (iv)
sequence G is a portion of a target polynucleotide sequence from a
subject and is different for each of a plurality of clusters; (v)
sequence B' is located 5' with respect to sequence G in the
corresponding target polynucleotide sequence; (viii) the sequencing
data comprises R1 sequences generated by extension of a first
primer comprising sequence D; and (vi) the sequencing data
comprises R2 sequences generated by extension of a second primer
comprising sequence A; (b) performing a first alignment using a
first algorithm to align all R1 sequences to one or more first
reference sequences; (c) performing a second alignment using a
second algorithm to locally align R1 sequences identified in said
first alignment as likely to contain an insertion or deletion with
respect to said one or more first reference sequences, to produce a
single consensus alignment for each insertion or deletion; (d)
performing an R2 alignment by aligning all R2 sequences to one or
more second reference sequences; and (e) transmitting a report
identifying sequence variation identified by steps (b) to (d) to a
receiver. In some embodiments, sequence A, B, C, and D correspond
to sequence A, B, C, and D, respectively, as described with regard
to other aspects of the invention.
[0133] In general, a cluster of polynucleotides comprises multiple
copies of a nucleic acid duplex that co-localize to a position on a
support. A variety of suitable solid supports and support materials
are known in the art, non-limiting examples of which are provided
herein, such as with regard to other aspects of the invention.
Clusters of polynucleotides may be produced by bridge
amplification. Suitable methods and apparatuses for performing
bridge amplification are provided herein, such as with regard to
other aspects of the invention. In some embodiments, a solid
support comprises a plurality of clusters, with each cluster in the
plurality formed by amplification of a different target
polynucleotide sequence. The portion of a target polynucleotide
sequence to be amplified, such as a sequence G, may be bound to a
support in a process comprising extension of a first
oligonucleotide immobilized on the support. In some embodiments,
the solid support comprises a plurality of different first
oligonucleotides comprising sequence A and sequence B, wherein
sequence A is common among all first oligonucleotides; and further
wherein sequence B is different for each different first
oligonucleotide, and is at the 3' end of each first
oligonucleotide. In some embodiments, the plurality of first
oligonucleotides comprises about, less than about, or more than
about 5, 10, 25, 50, 75, 100, 125, 150, 175, 200, 300, 400, 500,
750, 1000, 2500, 5000, 7500, 10000, 20000, 50000, or more different
oligonucleotides, each comprising a different sequence B. In some
embodiments, sequence B of one or more of the plurality of first
oligonucleotides comprises a sequence selected from the group
consisting of SEQ ID NOs 22-121, shown in FIG. 4 (e.g. 1, 5, 10,
25, 50, 75, or 100 different oligonucleotides each with a different
sequence from FIG. 4). In some embodiments, sequence B or the
target sequence to which it specifically hybridizes comprises a
causal genetic variant, as described herein. In some embodiments,
sequence B or the target sequence to which it specifically
hybridizes is within about, less than about, or more than about 1,
2, 3, 4, 5, 6, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60,
70, 80, 90, 100, 200, 500 or more nucleotides of a causal genetic
variant, as described herein. Causal genetic variants are typically
located downstream of a first oligonucleotide, such that at least a
portion of the causal genetic variant serves as template for
extension of a first oligonucleotide. The solid support may further
comprise a plurality of second oligonucleotides comprising sequence
A at the 3' end of each second oligonucleotide, and a plurality of
third oligonucleotides comprising sequence C at the 3' end of each
third oligonucleotide, as described herein. An example of bridge
amplification of a portion of a target polynucleotide sequence
using bound first, second, and third oligonucleotides to produce
clusters of duplexes is illustrated in FIG. 1, with sequence G'
represented by the black line between sequences B and D', and
sequence G represented by the black line between sequence B' and
D.
[0134] In some embodiments, sequence B of one or more of the
plurality of first oligonucleotides or the target sequence to which
it specifically hybridizes comprises a non-subject sequence. In
some embodiments, sequence B or the target sequence to which it
specifically hybridizes is within about, less than about, or more
than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40,
45, 50, 60, 70, 80, 90, 100, 200, 500 or more nucleotides of a
non-subject sequence. In general, a non-subject sequence
corresponds to a polynucleotide derived from an organism other than
the individual being tested or from whom a sample is taken, such as
DNA or RNA from bacteria, archaea, viruses, protists, fungi, or
other organism. Non-subject sequence can also include nucleic acids
from a fetus, such as cell-free nucleic acid (also referred to as
extracellular nucleic acid) from a fetus. A non-subject sequence
may be indicative of the identity of an organism or class of
organisms, and may further be indicative of a disease state, such
as infection. An example of non-subject sequences useful in
identifying an organism include, without limitation, rRNA
sequences, such as 16s rRNA sequences (see e.g. WO2010151842). In
some embodiments, non-subject sequences are analyzed instead of, or
separately from causal genetic variants. In some embodiments,
causal genetic variants and non-subject sequences are analyzed in
parallel, such as in the same sample (e.g. using a mixture of first
oligonucleotides, some with a sequence B that specifically
hybridizes to a sequence comprising or near a causal genetic
variant, and some with a sequence B that specifically hybridizes to
a sequence comprising or near a non-subject sequence) and/or in the
same report.
[0135] In some embodiments, sequence B of one or more of the
plurality of first oligonucleotides or the target sequence to which
it specifically hybridizes comprises an ancestry informative marker
(AIM). In some embodiments, sequence B or the target sequence to
which it specifically hybridizes is within about, less than about,
or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30,
35, 40, 45, 50, 60, 70, 80, 90, 100, 200, 500 or more nucleotides
of an AIM. An AIM may be used to classify a person as belonging to
or not belonging to one or more populations, such as a population
that is at increased risk for one of the causal genetic variants.
For example, an AIM can be diagnostic for a population in which a
trait is at increased prevalence. In certain instances the AIM may
distinguish between populations with finer granularity, for
example, between sub-continental groups or related ethnic groups.
In some embodiments, AIMs are analyzed instead of, or separately
from causal genetic variants and/or non-subject sequences. In some
embodiments, AIMs, causal genetic variants, and/or non-subject
sequences are analyzed in parallel, such as in the same sample
(e.g. using a mixture of first oligonucleotides, some with a
sequence B that specifically hybridizes to a sequence comprising or
near a causal genetic variant, and some with a sequence B that
specifically hybridizes to a sequence comprising or near an AIM)
and/or in the same report.
[0136] In some embodiments, one or more sequences of a plurality of
clusters are sequenced. Example methods of sequencing are described
herein, such as with regard to other aspects of the invention.
Sequencing data may be produced by extension of one or more
sequencing primers for each cluster. A sequencing primer can be of
any suitable length, such as about, less than about, or more than
about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,
80, 90, 100, or more nucleotides, any portion or all of which may
be complementary to the corresponding target sequence to which the
primer hybridizes (e.g. about, less than about, or more than about
5, 10, 15, 20, 25, 30, 35, 40, 45, 50, or more nucleotides). A
sequencing primer, primer D, may comprise or consist of sequence D,
such that it specifically hybridizes to complementary sequence D'.
In some embodiments, the first nucleotide downstream of sequence D'
is the first nucleotide of sequence G', such that the first
nucleotide added in extension of primer D corresponds to sequence
G. A sequencing primer, primer C, may comprise or consist of
sequence C, such that it specifically hybridizes to complementary
sequence C'. In some embodiments, the first nucleotide downstream
of sequence C' is the first nucleotide of a barcode sequence, such
that the first nucleotide added in extension of primer C
corresponds to a barcode sequence. A sequencing primer, primer A,
may comprise or consist of sequence A, such that it specifically
hybridizes to complementary sequence A'. In some embodiments, the
first nucleotide downstream of sequence A' is the first nucleotide
of sequence B', such that the first nucleotide added in extension
of primer A corresponds to sequence B. In some embodiments, a
sequencing primer comprises the sequence
CACTCAGCAGCACGACGATCACAGATGTGTATAAGAGACAG (SEQ ID NO: 20).
[0137] Two or more different sequencing primers may be used in
successive sequencing reactions to produce multiple sequencing
reads for each cluster. For example, successive sequencing
reactions may be performed for each of primers A, C, and D, in any
order (e.g. primer D, then primer C, then primer A). A sequencing
reaction may be preceded by one or more of: strand cleavage, strand
denaturation, or a wash step to remove one or more components of a
previous reaction (e.g. a sequencing primer). A sequencing reaction
may comprise multiple cycles of individual nucleotide primer
extension, with each addition followed by an identification step to
determine the identity of the added base. The number of cycles of
individual nucleotide extension may be about or more than about 1,
2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 500, or more, such
as for each of a plurality of sequencing primers used in successive
sequencing reactions, or collectively for all sequencing primers
used in successive sequencing reactions. In some embodiments, the
number of cycles of individual nucleotide extension is selected
based on the length of the sequence to be identified, such as a
barcode or probe sequence, and may be less than about 30, 25, 20,
15, 10, 9, 8, 7, 6, 5, or fewer cycles. The number of cycles for
each of a plurality of sequencing primers used in successive
sequencing reactions may be different. For example, 59 cycles of
extension of primer D may be followed by 6 cycles of extension of
primer C, which may then be followed by 15 cycles of extension of
primer A, for 80 total cycles of extension.
[0138] Extension of a first sequencing primer, second sequencing
primer, and a third primer that is an indexing primer may produce
an R1, an R2, and a barcode sequence, respectively, for each
cluster. In general, multiple sequences are identified as
originating from a single cluster based on physical co-localization
of successive extension reactions, such as a position on an array
of clusters. In some embodiments, sequencing data (e.g. R1 and/or
R2 sequences) are generated for about, less than about, or more
than about 5, 10, 25, 50, 100, 150, 200, 250, 300, 400, 500, 750,
1000, 2500, 5000, 7500, 10000, 20000, 50000, or more different
target polynucleotides from a sample in a single reaction container
(e.g. a channel in a flow cell), such as by extension of one or
more sequencing primers. In some embodiments, sequencing data are
generated for a plurality of samples in parallel, such as about,
less than about, or more than about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 48, 96, 192, 384, 768,
1000, or more samples. In some embodiments, sequencing data are
generated for a plurality of samples in a single reaction container
(e.g. a channel in a flow cell), such as about, less than about, or
more than about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 24, 48, 96, 192, 384, 768, 1000, or more samples,
and sequencing data are subsequently grouped according to the
sample from which the sequenced polynucleotides originated (e.g.
based on a barcode sequence). Grouping of sequencing data based on
barcode sequences may be performed before or after performing one
or more alignments, such as described herein, and optionally before
removing one or more sequences from analysis. In general, once
sequencing reads are grouped based on a barcode, each group of
reads is further processed independently of other groups. In some
embodiments, each barcode differs from every other barcode in a
plurality of different barcodes analyzed in parallel. Typically, a
barcode sequence is associated with a single sample in a pool of
samples sequenced in a single reaction. In some embodiments, each
of a plurality of barcode sequences is uniquely associated with a
single sample in a pool of samples sequenced simultaneously. In
some embodiments, a barcode sequence is located 5' from sequence
D'.
[0139] In a single reaction, sequencing data (e.g. R1 and/or R2
sequence) may be generated for about or at least about 10.sup.6,
10.sup.7, 10.sup.8, 2.times.10.sup.8, 3.times.10.sup.8,
4.times.10.sup.8, 5.times.10.sup.8, 10.sup.9, 10.sup.10, or more
target polynucleotides or clusters from a bridge amplification
reaction, which may comprise sequencing data for about, less than
about, or more than about 10.sup.4, 10.sup.5, 10.sup.6,
2.times.10.sup.6, 3.times.10.sup.6, 4.times.10.sup.6,
5.times.10.sup.6, 10.sup.7, 10.sup.8 target polynucleotides or
clusters for each sample in the reaction. A sequencing system may
output sequencing data in any of a variety of output data file
types or formats, including, but not limited to, *.fasta,
*.csfasta, *seq.txt, *qseq.txt, *.fastq, *.sff, *prb.txt, *.sms,
*srs and/or *.qv. In some embodiments, the presence or absence of
about, less than about, or more than about 5, 10, 25, 50, 75, 100,
125, 150, 175, 200, 300, 400, 500, 750, 1000, 2500, 5000, 7500,
10000, 20000, 50000, or more causal genetic variants is determined
for a sample based on the sequencing data. The presence, absence,
or allele ratio of one or more causal genetic variants may be
determined with an accuracy of about or more than about 80%, 85%,
90%, 95%, 97.5%, 99%, 99.5%, 99.9% or higher. In some embodiments,
the presence, absence, or quantity of one or more non-subject
sequence and/or one or more AIM is determined with an accuracy of
about or more than about 80%, 85%, 90%, 95%, 97.5%, 99%, 99.5%,
99.9% or higher.
[0140] In some embodiments, sequences identified in one or more
sequencing reactions for a plurality of clusters are aligned to a
reference sequence. In general, alignment involves placing one
sequence along another sequence, iteratively introducing gaps along
each sequence, scoring how well the two sequences match, and
preferably repeating for various positions along the reference. The
best-scoring match is deemed to be the alignment and represents an
inference about the degree of relationship between the sequences.
In some embodiments, a reference sequence to which sequencing reads
are compared is a reference genome, such as the genome of a member
of the same species as the subject. A reference genome may be
complete or incomplete. In some embodiments, a reference genome
consists only of regions containing target polynucleotides. In some
embodiments, a reference sequence comprises or consists of a human
genome. In some embodiments, a reference sequence comprises or
consists of sequences of polynucleotides of one or more organisms
other than the individual being tested or from whom a sample is
taken, such as sequences from one or more bacteria, archaea,
viruses, protists, fungi, or other organism. In some embodiments, a
reference sequence comprises or consists of a plurality of known
sequences, such as all probe sequences used to amplify target
polynucleotide sequences (e.g. every sequence B and/or sequence B'
for every different target polynucleotide). Sequencing data
generated from the extension of one primer (e.g. R1 sequences from
primer D) may be aligned to the same or different reference
sequence as sequencing data generated from the extension of another
primer (e.g. R2 sequences from primer A). Sequencing data generated
from the extension of one primer may be aligned to a reference
sequence two or more times, with each alignment using a different
alignment algorithm. R1 sequences may be aligned independently of
R2 sequences. A first alignment of R1 and R2 sequences may use the
same alignment algorithm.
[0141] In an alignment, a base in the sequencing read alongside a
non-matching base in the reference indicates that a substitution
mutation has occurred at that point. Similarly, where one sequence
includes a gap alongside a base in the other sequence, an insertion
or deletion mutation (an "indel") is inferred to have occurred.
When it is desired to specify that one sequence is being aligned to
one other, the alignment is sometimes called a pairwise alignment.
Multiple sequence alignment generally refers to the alignment of
two or more sequences, including, for example, by a series of
pairwise alignments. In some embodiments, scoring an alignment
involves setting values for the probabilities of substitutions and
indels. When individual bases are aligned, a match or mismatch
contributes to the alignment score by a substitution probability,
which could be, for example, 1 for a match and 0.33 for a mismatch.
An indel deducts from an alignment score by a gap penalty, which
could be, for example, -1. Gap penalties and substitution
probabilities can be based on empirical knowledge or a priori
assumptions about how sequences mutate. Their values affect the
resulting alignment. Examples of algorithms for performing
alignments include, without limitation, the Smith-Waterman (SW)
algorithm, the Needleman-Wunsch (NW) algorithm, algorithms based on
the Burrows-Wheeler Transform (BWT), and hash function aligners
such as Novoalign (Novocraft Technologies; available at
www.novocraft.com), ELAND (Illumina, San Diego, Calif.), SOAP
(available at soap.genomics.org.cn), and Maq (available at
maq.sourceforge.net).
[0142] In some embodiments, an alignment according to the invention
is performed using a computer program. One exemplary alignment
program, which implements a BWT approach, is Burrows-Wheeler
Aligner (BWA) available from the SourceForge web site maintained by
Geeknet (Fairfax, Va.). BWT typically occupies 2 bits of memory per
nucleotide, making it possible to index nucleotide sequences as
long as 4G base pairs with a typical desktop or laptop computer.
The pre-processing includes the construction of BWT (i.e., indexing
the reference) and the supporting auxiliary data structures. BWA
includes two different algorithms, both based on BWT. Alignment by
BWA can proceed using the algorithm bwa-short, designed for short
queries up to about 200 bp with low error rate (<3%) (Li H. and
Durbin R. Bioinformatics, 25:1754-60 (2009)). The second algorithm,
BWA-SW, is designed for long reads with more errors (Li H. and
Durbin R. (2010). Fast and accurate long-read alignment with
Burrows-Wheeler Transform. Bioinformatics, Epub.). One skilled in
the art will recognize that bwa-sw is sometimes referred to as
"bwa-long", "bwa long algorithm", or similar.
[0143] An alignment program that implements a version of the
Smith-Waterman algorithm is MUMmer, available from the SourceForge
web site maintained by Geeknet (Fairfax, Va.). MUMmer is a system
for rapidly aligning entire genomes, whether in complete or draft
form (Kurtz, S., et al., Genome Biology, 5:R12 (2004); Delcher, A.
L., et al., Nucl. Acids Res., 27:11 (1999)). For example, MUMmer
3.0 can find all 20-basepair or longer exact matches between a pair
of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a
2.4 GHz Linux desktop computer. MUMmer can also align incomplete
genomes; it can easily handle the 100 s or 1000 s of contigs from a
shotgun sequencing project, and will align them to another set of
contigs or a genome using the NUCmer program included with the
system.
[0144] Other non-limiting examples of alignment programs include:
BLAT from Kent Informatics (Santa Cruz, Calif.) (Kent, W. J.,
Genome Research 4: 656-664 (2002)); SOAP2, from Beijing Genomics
Institute (Beijing, Conn.) or BGI Americas Corporation (Cambridge,
Mass.); Bowtie (Langmead, et al., Genome Biology, 10:R25 (2009));
Efficient Large-Scale Alignment of Nucleotide Databases (ELAND) or
the ELANDv2 component of the Consensus Assessment of Sequence and
Variation (CASAVA) software (Illumina, San Diego, Calif.); RTG
Investigator from Real Time Genomics, Inc. (San Francisco, Calif.);
Novoalign from Novocraft (Selangor, Malaysia); Exonerate, European
Bioinformatics Institute (Hinxton, UK) (Slater, G., and Birney, E.,
BMC Bioinformatics 6:31(2005)), Clustal Omega, from University
College Dublin (Dublin, Ireland) (Sievers F., et al., Mol Syst Biol
7, article 539 (2011)); ClustalW or ClustalX from University
College Dublin (Dublin, Ireland) (Larkin M. A., et al.,
Bioinformatics, 23, 2947-2948 (2007)); and FASTA, European
Bioinformatics Institute (Hinxton, UK) (Pearson W. R., et al., PNAS
85(8):2444-8 (1988); Lipman, D. J., Science 227(4693):1435-41
(1985)).
[0145] In some embodiments, any or all of the steps of the
invention are automated. For example, a Perl script or shell script
can be written to invoke any of the various programs discussed
above (see, e.g., Tisdall, Mastering Perl for Bioinformatics,
O'Reilly & Associates, Inc., Sebastopol, Calif. 2003; Michael,
R., Mastering Unix Shell Scripting, Wiley Publishing, Inc.,
Indianapolis, Ind. 2003). Alternatively, methods of the invention
may be embodied wholly or partially in one or more dedicated
programs, for example, each optionally written in a compiled
language such as C++ then compiled and distributed as a binary.
Methods of the invention may be implemented wholly or in part as
modules within, or by invoking functionality within, existing
sequence analysis platforms. In certain embodiments, methods of the
invention include a number of steps that are all invoked
automatically responsive to a single starting queue (e.g., one or a
combination of triggering events sourced from human activity,
another computer program, or a machine). Thus, the invention
provides methods in which any or the steps or any combination of
the steps can occur automatically responsive to a queue. The output
can be provided in the format of a computer file. In certain
embodiments, the output is a FASTA file, VCF file, text file, or an
XML file containing sequence data such as a sequence of the nucleic
acid aligned to a sequence of the reference genome. In other
embodiments, the output contains coordinates or a string describing
one or more mutations in the subject nucleic acid relative to the
reference genome. Alignment strings known in the art include Simple
UnGapped Alignment Report (SUGAR), Verbose Useful Labeled Gapped
Alignment Report (VULGAR), and Compact Idiosyncratic Gapped
Alignment Report (CIGAR) (Ning, Z., et al., Genome Research
11(10):1725-9 (2001)). In some embodiments, the output is a
sequence alignment--such as, for example, a sequence alignment map
(SAM) or binary alignment map (BAM) file--comprising a CIGAR string
(the SAM format is described, e.g., in Li, et al., The Sequence
Alignment/Map format and SAMtools, Bioinformatics, 2009,
25(16):2078-9). In some embodiments, CIGAR displays or includes
gapped alignments one-per-line. CIGAR is a compressed pairwise
alignment format reported as a CIGAR string.
[0146] In some embodiments, R1 sequence from a cluster comprises
sequence G from a plurality of different target polynucleotides and
R2 sequence from a cluster comprises sequence B, where sequence B
is a probe sequence used to generate a cluster of amplified
duplexes. When each sequence B is selected to target a specific
target polynucleotide, its sequence and location within the
reference sequences (e.g. reference genome) is generally known, and
R1 sequences from the same cluster may be expected to fall within
an anticipated nucleotide distance. An anticipated nucleotide
distance may be based on an average or median fragment length for
samples comprising fragmented sample polynucleotides, or an upper
threshold distance representing an unlikely fragment length based
on such median or average fragment length. Thus, in some
embodiments, an R1 sequence that aligns to a position further away
than the threshold distance from the R2 sequence from the same
cluster may be erroneous and is discarded. In some embodiments, the
upper threshold distance along a reference sequence between aligned
R1 and R2 sequences from the same cluster, above which sequence
reads for a cluster are discarded, is about, or more than about
1000, 2500, 5000, 7500, 10000, 12500, 15000, 20000 or more base
pairs. In some embodiments, alignments of R1 sequences to
non-unique regions of a reference sequence (e.g. a reference
genome) are discarded and the sequences re-aligned to a smaller
subset of unique sequences within the reference sequence.
[0147] Typically, a base quality score is determined for each
nucleotide in a sequencing result, and relates to the probability
that a particular base call is wrong. An example of a base quality
score is a Phred quality score Q, where Q=-10 log.sub.10 P, and
where P represents the probability that the corresponding base call
is incorrect. In some embodiments, base quality scores are used to
evaluate alignments of sequencing reads to a reference sequence,
such as by determining a mapping quality score for each of a
plurality of alignments. Methods for calculating mapping quality
scores are known in the art. For example, alignments having a
quality score below a threshold value may be discarded, re-aligned,
or replaced with an alternative alignment having a higher score. In
some embodiments, an alignment with a mapping quality score below a
threshold value and having more than one optimal alignment is
re-aligned to a subset of sequences within the reference sequence,
such as only regions of a reference genome containing target
polynucleotides. In some embodiments, a threshold mapping quality
score is about, or less than about 100, 75, 50, 25, 20, 10, 5, 4,
3, 2, 1, or 0.
[0148] In some embodiments, sequencing reads likely to be
duplicative are removed following an initial alignment. When
sequencing reads are mapped, duplicative reads may be marked as
duplicates by the alignment algorithm. For example, a mark
duplicates subroutine within the alignment algorithm examines all
of the records in a file of aligned sequences (e.g. a *.BAM file)
and decides which reads are duplicates of other reads. Generally
speaking, there are two types of duplicates: optical duplicates,
which are typically caused by defects in the primary analysis
software, and PCR duplicates, which are caused by duplicative PCR
reactions. However from a computational point of view, optical
duplicates and PCR duplicates are indistinguishable. One way to
determine if two sequence reads are duplicates or not is to compare
the base sequences--two duplicate reads should have duplicate base
sequences. However, due to sequencing errors, it may be the case
that two duplicate reads are sequenced such that a sequencing error
for one read will cause its base sequence to differ significantly
from the other read. Therefore, rather than compare base sequences
to determine if two reads are duplicates, their alignments can be
compared instead. If two reads are duplicates, then the entire set
of alignments for both reads will generally be the same. In some
embodiments, duplicates are marked for removal and/or discarded
using one or more algorithms distinct from the alignment algorithm.
In general, when barcode sequences are used, sequencing reads are
only deleted when occurring within the same barcode sequence
grouping.
[0149] In some embodiments, a second alignment using a second
algorithm is performed after a first alignment using a first
algorithm. The second alignment may be with respect to the same
reference sequence as the first alignment, a different reference
sequence from that used in the first alignment, or without use of a
reference sequence (such as when all sequencing reads overlapping a
particular region are aligned with one another). For example,
sequences identified in a first alignment as likely to contain an
insertion and/or deletion (indel) with respect to the first
reference sequence may be locally aligned to produce a single
consensus sequence for an insertion and/or deletion contained in a
target polynucleotide. A first alignment may align individual
sequences to a reference sequence independently. In some cases, a
sequencing read with a true indel may be aligned with multiple
mismatches rather than an indel when an alignment model with
multiple mismatches scores higher than the indel-containing
alignment. Typically, multiple sequences are aligned as overlapping
a single nucleotide position (such as in a tiled fashion).
Overlapping regions containing more than a predicted amount of
sequence variation (for example, more than two alleles for a unique
locus in a genome of a human subject) may indicate the likely
presence of an indel. The location of some indels for a particular
reference sequence may be known, such that sequences overlapping
the location of a known indel identifies the sequence as likely to
contain an indel. The likelihood of containing an indel may be
expressed numerically, based on one or more such factors, such as a
likelihood of at least about 60%, 70%, 80%, 90%, 95%, 99%, or more.
In some embodiments, all sequences overlapping a region of
interest, such as a causal genetic variant, and optionally also
containing or likely to contain an indel are locally aligned using
a second algorithm in order to produce a single consensus sequence
for the region of interest. A region of interest may be of any
suitable size, such as about, less than about, or more than about
5, 10, 15, 20, 25, 50, 100, 250, 500, or more nucleotides in
length. A second alignment may be a local multiple-sequence
alignment of all sequencing reads overlapping one or more
nucleotide positions. In some embodiments, the second alignment
identifies a single consensus sequence by optimizing the alignment
of all sequencing reads at a position. In some embodiments, the
consensus sequence produced by the second alignment contains at
least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 fewer nucleotide
mismatches with respect to the reference sequence than one or more
of the sequences realigned to produce the consensus sequence. In
some embodiments, the algorithm used to perform the second
alignment is capable of identifying an insertion and/or a deletion
of about, or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20,
25, or more nucleotides relative to the reference sequence with an
accuracy of about or more than about 80%, 85%, 90%, 95%, 97%, 99%,
or higher.
[0150] Typically, the second algorithm is different from the first
algorithm, and the second algorithm may require more resources of
the system (e.g. a computer system) running the algorithm to
perform the same number of alignments. For example, performing the
first alignment with a system using the first algorithm may take
less time to align all R1 reads than would be taken if the system
used the second algorithm to perform the first alignment of all R1
reads. In some embodiments, performing the first alignment with the
first algorithm takes about or less than about 90%, 80%, 70%, 60%,
50%, 40%, 30%, 25%, 20%, 15%, 10%, 5%, or less of the time that
would be taken by the same system to perform the first alignment
using the second algorithm. As a further example, performing the
first alignment with a system using the first algorithm may use
less system memory to align all R1 reads than would be used if the
system used the second algorithm to perform the first alignment of
all R1 reads. In some embodiments, performing the first alignment
with the first algorithm uses about or less than about 90%, 80%,
70%, 60%, 50%, 40%, 30%, 25%, 20%, 15%, 10%, 5%, or less memory
than would be used by the same system to perform the first
alignment using the second algorithm. The first algorithm may
perform the first alignment using heuristics. In some embodiments,
the first algorithm is based on the Burrows-Wheeler transform, such
as the Burrows-Wheeler Aligner. In some embodiments, the second
algorithm is based on the Smith-Waterman algorithm.
[0151] In some embodiments, an amplified sequence derived from one
or more target polynucleotides from a sample (e.g. sequence G from
at least 75%, 80%, 85%, 90%, 95%, or 100% of all clusters) is from
1 nucleotide in length to about, less than about, or more than
about 10, 25, 50, 100, 250, 500, 1000, 2000, 5000, or more
nucleotides in length. In general, if an amplified sequence derived
from a target polynucleotide for a cluster (e.g. sequence G) is
shorter than the number of cycles of nucleotide extension performed
in sequencing the amplified sequence (also referred to as the "read
length"), then sequence data returned for that sequencing read will
likely contain sequence of a first oligonucleotide used to
initially capture the amplified sequence (e.g. sequence B or B').
When sequence B or B' exists in the reference sequence (e.g.
reference genome), the sequence may correctly align, but any true
mutation in the target polynucleotide may be masked or inferred
with lower confidence. To avoid negative effects of first
oligonucleotide sequence contained in an R1 sequence, base calls
likely to correspond to sequence B or B' for a cluster may be
deleted. Sequence B or B' for a cluster may be identified in a
separate sequencing reaction, such as producing R2 sequence. R1
sequence may then be compared to R2 sequence for the same cluster
to determine whether or not one or more nucleotides of R1
correspond to sequence B or B'. If no R2 sequence (or no R2
sequence comprising any sequence B) is obtained for a cluster,
deleting first oligonucleotide sequence may comprise deleting a
portion of an R1 sequence for a cluster when the portion of R1
sequence to be deleted is identical to at least a portion of any
sequence B' (such as any B' found in any cluster, or corresponding
to any sequence B used to amplify a target polynucleotide), the
portion includes either the 5' or 3' nucleotide of R1, and either
(i) no R2 sequence was produced for the cluster or (ii) R2 sequence
produced is not identical to any sequence B. In general, nucleotide
sequence comprising sequence B or B' found in the interior of an R1
sequence (that is, not including the 5' or 3' end of the sequencing
read) indicates that the amplified sequence was captured using a
more distant sequence B.
[0152] In some embodiments, genetic variation detected by a method
of the invention is used to calculate a plurality of probabilities.
Each probability may be a probability of a subject or a subject's
present or future offspring having or developing a disease or
trait. In some embodiments, each probability is based on the R1
sequences for the subject, and one or more such probabilities may
be included in a report of analysis results. In general,
calculation of a probability that the tested subject has or will
develop a disease or trait is based on a level of risk associated
with one or more tested causal genetic variants, non-subject
sequences, and/or AIMs. For example, if two causal genetic variants
contribute to the risk of developing a disease in an additive
fashion, then the presence of both causal genetic variants in a
subject would indicate that the risk of that disease in the subject
is increased by the value resulting from adding the risks
associated with each. In general, calculation of a probability that
an offspring of the subject will have a disease or trait is based
on a level of risk associated with one or more tested causal
genetic variants and/or AIMs, and the probability that an offspring
will inherit the causal genetic variants and/or AIMs. Risk
calculations may be based on risk correlations maintained in one or
more databases, which databases may be updated based on external
reports and/or records of genotyping results and associated
phenotypes of tested subjects. In some embodiments, the
calculations are performed by a computer in accordance with
instructions contained in a computer readable medium. In some
embodiments, the statistical confidence of a probability that the
subject or subject's offspring will have or develop a disease or
trait is at least about 70%, 80%, 85%, 90%, 95%, 97.5%, 99%, or
higher. Confidence may be based on a number of factors, such as
confidence in sequencing accuracy, number of associated genetic
variants tested, and confidence in the risk associate with each
genetic variant. Example methods for calculating probabilities are
described in US20100022406.
[0153] In some embodiments of any aspect of the invention, a
computer system is used to execute one or more steps of the
described methods. FIG. 8 illustrates a non-limiting example of a
computer system useful in the methods of the invention. In some
embodiments, the computer system is integrated into and is part of
an analysis system, like a liquid handler, bridge amplification
system (e.g. an Illumina cBot), and/or a sequencing system (e.g. an
Illumina Genome Analyzer, HiSeq, or MiSeq system). In some
embodiments, the computer system is connected to or ported to an
analysis system. In some embodiments, the computer system is
connected to an analysis system by a network connection. A computer
system (or digital device) may be used to receive and store
results, analyze the results, and/or produce a report of the
results and analysis. The computer system may be understood as a
logical apparatus that can read instructions from media (e.g.
software) and/or network port (e.g. from the internet), which can
optionally be connected to a server having fixed media. A computer
system may comprise one or more of a CPU, disk drives, input
devices such as keyboard and/or mouse, and a display (e.g. a
monitor). Data communication, such as transmission of instructions
or reports, can be achieved through a communication medium to a
server at a local or a remote location. The communication medium
can include any means of transmitting and/or receiving data. For
example, the communication medium can be a network connection, a
wireless connection, or an internet connection. Such a connection
can provide for communication over the World Wide Web. It is
envisioned that data relating to the present invention can be
transmitted over such networks or connections (or any other
suitable means for transmitting information, including but not
limited to mailing a physical report, such as a print-out) for
reception and/or for review by a receiver. The receiver can be but
is not limited to an individual, a health care provider, a health
care manager, or electronic system (e.g. one or more computers,
and/or one or more servers). In some embodiments, a
computer-readable medium includes a medium suitable for
transmission of a result of an analysis of a biological sample. The
medium can include a result regarding analysis of an individual's
genetic profile, wherein such a result is derived using the methods
described herein. The data and or results may be displayed at any
time on a display, such as a monitor, and may also be stored or
printed in the form of a genetic report.
[0154] Causal genetic variants associated with phenotypes may be
obtained from scientific literature and sent to a computer system
for comparison with sequence results for a sample from a subject.
Genotypes of causal genetic variants and results from biological
samples may be sent to, stored, and analyzed by a computer system
(or other digital device), which produces a report of the results
and analyses of genomic data. The results and analyses may be
accessed online by a receiver, such as a health care provider, via
an online portal or website. The results and analyses may be viewed
online, saved on a receiver's computer, printed, or be mailed to a
receiver. The results may be used for personalized health
management, such as at the direction of a physician or other health
professional. For example, the subject may be referred to or
contacted by a genetic counselor to receive genetic counseling.
[0155] The database may have one or more of a variety of optional
components that, for example, provide more information about the
sequencing results produced by methods of the invention. In some
embodiments there is provided a computer readable medium encoded
with computer executable software that includes instructions for a
computer to execute functions associated with the identified causal
genetic variants. Such computer system may include any combination
of such codes or computer executable software, depending upon the
types of evaluations desired to be completed. The computer system
may also have code for linking each of the sequences (e.g.
genotypes for causal genetic variants) to at least one phenotype,
such as a condition, for example, a medical condition, including
but not limited to a risk for having or developing the phenotype.
Each medical condition in turn can be linked to at least one
recommendation by a medical specialist and code for generating a
report comprising the recommendation. The system can also have code
for generating a report. Different types of reports can be
generated, for example, reports based on the level of detail a
receiver may want or have paid for. For example, a receiver may
have ordered analysis for a single phenotype, such as a condition,
and thus a report may comprise the results for that single
phenotype, such as a condition. Another receiver may have requested
a genetic profile for a panel or an organ system, or another
individual may have requested a comprehensive genetic profile that
includes analysis of all clinically relevant causal genetic
variants. Reports may comprise one or more of: subject information
(e.g. name, date of birth, ethnicity, sample type, date of sample
collection, and/or date of sample receipt); description of analysis
method(s); results for all causal genetic variants tested; results
for all disease or traits tested; results for diseases or traits
having a positive score (e.g. a risk above a threshold level, such
as about or more than about 1/50000, 1/25000, 1/10000, 1/5000,
1/2500, 1/1000, 1/500, 1/100, 1/50, 1/10, or higher); results for
causal genetic variants associated with a disease or trait having a
positive score; results for two or more individuals (such as
individuals that are parents or planning to have children); risk of
having or developing a disease or trait; risk of a present or
future child having or developing a disease or trait; risk of a
fetus having or developing a disease or trait; methods of risk
calculation; and recommendations for further action.
[0156] The report generated can be reviewed and further analyzed by
a genetic counselor and/or other medical professional, such as a
managing doctor or licensed physician, or other third party. The
genetic counselor or medical professional or both, or other third
party, can meet with the individual to discuss the results,
analysis, and the genetic report. Discussions can include
information about: the causal genetic variant(s), such as the
causal genetic variant(s) that is or are tested (presence, absence,
and/or genotype), how the causal genetic variant(s) can be
inherited or transmitted (for example using the pedigree generated
from a questionnaire), the prevalence of the causal genetic
variant(s); prevalence or incidence of associated phenotypes; and
information about associated phenotypes (for example, specific
conditions or traits, such as medically or clinically relevant
conditions), such as how the phenotype may affect the individual,
and preventative measures that may be taken. The genetic counselor
or medical professional may incorporate other information, such as
other genetic information or information from questionnaires in
their analysis and discussion with the individual. Information
about the phenotype, such as condition or trait, can include
recommendations, such as follow-up suggestions such as further
genetic counseling, predictive medicine recommendations, or
preventive medicine recommendations for the individual's personal
physician or other healthcare provider. Screening information, such
as methods of breast cancer screening, may be discussed for example
if an individual was found to be at a higher risk of breast cancer.
Other topics that may be discussed include lifestyle modifications
and medications. For example, lifestyle modifications may be
suggested such as dietary changes and specific diet plans may be
recommended or an exercise regimen may be suggested and specific
exercise facilities or trainers may be referred to the individual.
Common misconceptions may also be included, allowing the individual
to be aware of preventive measures or other interventions that may
be thought of as being helpful or useful but that have been shown
in published literature to either not be beneficial or to actually
be harmful. Alternative therapies may also be included, such as
alternative medicines, such as dietary supplements, or alternative
therapies, such as acupuncture or yoga. Family planning options may
also be included, as well as monitoring options, such as such as
screening exams or laboratory tests that may detect or help monitor
for the presence of a phenotype, or the progression of a phenotype.
Medications that may prevent, limit the onset, or delay the
progression of a phenotype, such as a disease to which the
individual is predisposed, or a medication with high efficacy and
low side effects may be suggested for an individual, or medications
or classes of medications that an individual should avoid due to
possibility of adverse reaction(s). For example, the medical
professional may make an assessment of the individual's likely drug
response including metabolism, efficacy and/or safety. The medical
professional can also discuss therapeutic treatments, such as
prophylactic treatments and monitoring (such as doctor visits and
exams, radiologic exams, self exams, or laboratory tests) for
potential need of treatment or effects of treatment based on
information from the individual's genetic profile either alone or
in combination with information about the individual's
environmental factors (such as lifestyle, habits, diagnosed medical
conditions, current medications, and others). Additional resources
may also be listed, such as including information for the
individual or the individual's physician or other healthcare
professional to acquire additional information about the phenotype,
the causal genetic variant(s), or both, such as links to websites
that contain information on the phenotype, such as an internal
website from the company that produces the genetic report or
external websites, such as national organizations for the
phenotype. Additional resources may also include reference to
telephone numbers, books, or people that the individual may seek
out to acquire more information about the phenotype, the causal
genetic variant(s) or both.
[0157] In one aspect, the invention provides a method comprising
offering a first and optionally a second service, wherein: a) the
first service comprises predicting the probability that an
offspring of the couple will have each of a plurality of traits
caused by causal genetic variants, wherein the prediction is based
on the respective genotypes of the two individuals in the couple;
and b) the second service comprises predicting the probable
phenotype of an offspring of the couple for a plurality of traits,
wherein the probability is determined based on the respective
phenotypes and/or the family history of the individuals in the
couple. In one embodiment at least one prediction is further based
on the respective genetically inferred ancestries of the
individuals. In another embodiment the first service is offered as
a service for a fee and the second service is offered as a free
service.
[0158] In one aspect this invention provides a system comprising:
a) computer readable medium configured to store family history
information from each member of a couple; b) computer readable
medium configured to store data comprising genetic information
about each member of the couple; c) computer readable medium
comprising computer code that, when executed: i) predicts each
individual's carrier status with respect to traits caused by
alleles identified in the genetic information; or ii) predicts
probable traits of offspring of the couple determinable by the
family histories and/or the genetic information; and d) a display
that displays: i) carrier status of at least one member of the
couple or ii) probable traits of the offspring. In some embodiments
the system further comprises e) a webpage configured to accept an
offer to purchase a DNA test kit. In some embodiments the display
is electronic, for example, a webpage. In some embodiments the
system further comprises e) a display that displays referrals to a
genetic counselor and/or other medical professional (for example,
medical geneticists or obstetrician/gynecologist) based on the
genetic information.
[0159] The internet and the world wide web offer access to and
distribution of information. In some embodiments, a website can be
particularly suited to efficiently providing various functionality
for allowing customers to purchase genetic testing and receive the
results of genetic testing. The system typically will include a
server on which the website resides. Users use an interface
connected to the server, such as a computer monitor or a telephone
screen, to interact with the website by clicking or rolling over
links that pop up information or direct the user to another
webpage. Websites typically are interactive, allowing the user to
input information or a query and obtain a response on the
interface.
[0160] In some embodiments of a system and business method, a
website can allow a customer to purchase, manage, and view the
results of genetic testing as well as to learn more generally about
the probability that potential offspring will develop a disease or
trait. For example, a customer can be a couple of prospective
parents who seek to learn whether their offspring will be at risk
for developing Mendelian disease. A customer can be presented with
the offer to purchase genetic testing to determine one or more of:
(i) the carrier status of the customer; (ii) the likelihood that
the customer will develop one or more diseases or traits; and (iii)
the probability that an offspring of the customer will develop one
or more diseases or traits, based on causal genetic variants
identified in the customer's DNA.
[0161] If the customer chooses to purchase genetic testing, then
the customer may pay a fee, for example through an online credit
card transaction, in exchange for genetic testing, direct phone
consultation with a genetic counselor on the company's staff and/or
referrals to genetic counselors and/or other relevant medical
professionals. The genetic testing and referrals can be paid for by
a fee at the point of purchase or can be included in an initial
user registration fee. In some embodiments, the services are free
and revenue is generated by the company by advertising other
products in conjunction with a particular product. For example,
after a customer places an order online, the order is sent to a
server for processing. Once payment has been verified, the order
processing server can send an electronic notification to a shipping
vendor to mail a DNA collection kit to the customer. In an
embodiment, the DNA collection kit is separate from the genetic
testing service, or the user or customer already has or obtains the
DNA collection kit from another source. Notifications can also
periodically be sent electronically to the customer comprising
order confirmation and updates on order and shipping status. In
some embodiments of a business method of the invention, a customer
can deposit a sample into the collection kit. Any sample that would
be obvious to one skilled in the art can be deposited into or onto
a collection kit. A sample can be any material containing nucleic
acid to be analyzed that would be obvious to one skilled in the
art, such as bodily fluid like saliva or blood. The collection kit
can then be returned to the company for sending to a genotyping lab
or can be returned directly to a genotyping lab for processing. A
genotyping lab, either internal within the company, contracted to
work with the company, or external from the company, can isolate
the customer's DNA from the provided sample. After the DNA has been
isolated from the sample, a genotyping device (such as an apparatus
described herein) can be used to test the DNA for the presence of
one or more of (i) ancestry informative markers, (ii) causal
genetic variants, and (iii) non-subject sequences (one or more of
which are also referred to herein as, Raw Genotypic Information).
In some embodiments, the DNA does not have to be isolated from the
sample to test the DNA for the presence of Raw Genotypic
Information.
[0162] Raw Genotypic Information can be sent electronically to a
server for storage and processing. Computer code on the server can
execute on the Raw Genotypic Information to infer the ancestry of
the customer and/or to confirm the presence of causal genetic
variants and/or non-subject sequences, if any. The processed
genotypic information can then be electronically sent to a server,
where computer code on the server can execute on the processed
genotypic information to predict the probability that an offspring
of the customer will have each of a plurality of traits caused by
causal genetic variants found to be present in the customer's
processed genotypic information. Results can then be electronically
transmitted to a server for storage.
[0163] In an example, a notification can be sent to the customer to
alert the customer to the availability of the results. The
notification can be electronic, non-limiting examples of which
include a text message, an email, or other data packet; or the
notification can be non-electronic, non-limiting examples of which
include a phone call from a genetic counselor or printed
communication such as a report sent through the mail. The results
provided to a customer can inform the customer of the carrier
status of the customer for one or more diseases or traits and/or
the chances that the customer or customer's future offspring will
develop one or more diseases or traits. After the customer has
received results and referrals, the customer's order can be
considered fulfilled, and results and referrals can remain
accessible to the customer through an online website account. The
customer can then choose to further pursue a referral offline if
the customer so desires but outside of the purview of the
website.
[0164] In one aspect, the invention provides compositions that can
be used in the above described methods. Compositions of the
invention can comprise any one or more of the elements described
herein. For example, compositions may include one or more of the
following: one or more solid supports comprising oligonucleotides
attached thereto, one or more oligonucleotides for attachment to a
solid support, one or more adapter oligonucleotides, one or more
amplification primers, one or more oligonucleotide primers
comprising a first binding partner, one or more solid surfaces
(e.g. beads) comprising a second binding partner, one or more
sequencing primers, reagents for utilizing any of these, reaction
mixtures comprising any of these, and instructions for using any of
these.
[0165] In one aspect, the invention provides kits containing any
one or more of the elements disclosed in the above methods and
compositions. In some embodiments, a kit comprises a composition of
the invention, in one or more containers. For example, kits may
include one or more of the following: one or more solid supports
comprising oligonucleotides attached thereto, one or more
oligonucleotides for attachment to a solid support, one or more
adapter oligonucleotides, one or more amplification primers, one or
more oligonucleotide primers comprising a first binding partner,
one or more solid surfaces (e.g. beads) comprising a second binding
partner, one or more sequencing primers, reagents for utilizing any
of these, and instructions for using any of these. In some
embodiments, the kit further comprises one or more of: (a) a DNA
ligase, (b) a DNA-dependent DNA polymerase, (c) an RNA-dependent
DNA polymerase, (d) random primers, (e) primers comprising at least
4 thymidines at the 3' end, (f) a DNA endonuclease, (g) a
DNA-dependent DNA polymerase having 3' to 5' exonuclease activity,
(h) a plurality of primers, each primer having one of a plurality
of selected sequences, (i) a DNA kinase, (j) a DNA exonuclease, (k)
magnetic beads, and (1) one or more buffers suitable for one or
more of the elements contained in the kit. The adapters, primers,
other oligonucleotides, and reagents can be, without limitation,
any of those described herein. Elements of the kit can further be
provided, without limitation, in any amount and/or combination
(such as in the same kit or same container). The kits may further
comprise additional agents for use according to the methods of the
invention. The kit elements can be provided in any suitable
container, including but not limited to test tubes, vials, flasks,
bottles, ampules, syringes, or the like. The agents can be provided
in a form that may be directly used in the methods of the
invention, or in a form that requires preparation prior to use,
such as in the reconstitution of lyophilized agents. Agents may be
provided in aliquots for single-use or as stocks from which
multiple uses, such as in a number of reaction, may be
obtained.
EXAMPLES
[0166] The following examples are given for the purpose of
illustrating various embodiments of the invention and are not meant
to limit the present invention in any fashion. The present
examples, along with the methods described herein are presently
representative of preferred embodiments, are exemplary, and are not
intended as limitations on the scope of the invention. Changes
therein and other uses which are encompassed within the spirit of
the invention as defined by the scope of the claims will occur to
those skilled in the art.
Example 1
Sample Preparation and Sequencing Process
[0167] Genomic DNA (gDNA) is extracted in 96-well format, leaving
wells A1, G12, and H12 empty (which will later contain a
no-template control, the universal negative standard containing
Coriell sample NA12878 genomic DNA lacking every causal genetic
variant tested, and a sample comprising one of a plurality of known
causal genetic variants, respectively). 50 .mu.L from each well are
transferred into a corresponding well of an absorbance plate.
Absorbance at 260 nm is measured using a Tecan M200 plate reader to
calculate DNA quantity. 50 .mu.L of gDNA are transferred from the
absorbance plate into an Eppendorf twin.tec plate. Control samples
are added to their respective position on the twin.tec plate. The
gDNA and controls are fragmented in a SonicMan (Matrical, Spokane
Wash.) sonicator, according to the following protocol at 10.degree.
C.: Pre-chill 180 s, cycles 100, sonication 3.0s, power 35%, lid
chill 1.0 s, plate chill 0, post chill 0. A 2 .mu.L sample is
analyzed for fragmentation size distribution using a Fragment
Analyzer (Advanced Analytical Technologies, Ames Iowa). Samples
having a median fragment size of at least 200 base pairs and no
more than 1000 bp are subjected to further processing. Samples with
a median fragment size below 200 bp are discarded and reprocessed
from extracted gDNA. Samples with a median fragment size above 1000
bp are either subjected to further sonication to reach the desired
size range, or are discarded and reprocessed from extracted
gDNA.
[0168] Sonicated gDNA is transferred into a round-bottomed sample
plate for use in conjunction with the Beckman Biomek FXP. The
Biomek automates the processes of end-repair, addition of adenine
overhangs, and adapter ligation. The Biomek system comprises an
Agencourt SPRIPlate Super Magnet Plate, a Biomek FXP Dual-Arm
System with Multichannel Pipettor and Span-8 Pipettor (with pump
control module, computer and monitor, peltier controller, two waste
containers, and two water containers), and BioMek FXP Control
Software. This process utilizes the SPRIworks HT Fragmentation
Library Kit, which contains end-repair buffer and enzyme, a-tailing
buffer and enzyme, ligation buffer and enzyme, and Agencourt AMPure
XP beads. After each reaction, processed gDNA is cleaned using
magnetic bead separation. Adapter ligation is followed by
quantifying DNA in the processed sample using absorbance at 260 nm,
as measured by the Tecan M200. Samples with less than 900 ng are
not processed further, but are instead reprocessed from the
original extracted sample. After the absorbance reading, the sample
plate is returned to the Biomek FXP for PCR amplification. The
first step is division of each sample into four separate samples on
a 384-well plate, such that amplification for each sample source is
performed in quadruplicate. Amplification primers comprise a
barcode sequence to allow identification of the sample source of a
sequence. PCR includes the use of an ABI GeneAmp PCR system 9700
with dual 384-well blocks, 1.5 mL tube racks, 24-channel 200 .mu.L
multichannel pipettor, and 96-well aluminum plate holder. Samples
are automatically thermally cycled according to following protocol:
95 C for 5 minutes; 27 cycles of 98 C for 20 seconds, 65 C for 15
seconds, 72 C for 1 minute. When amplification is complete, the
four sub-samples from each sample source are recombined into a
single well of a 96-well plate.
[0169] Amplified polynucleotides are purified by magnetic bead
separation. 1.8 sample volumes of magnetic beads are added to each
sample, which are allowed to sit at room temperature for about 5
minutes. The plate is placed on a magnetic separator for about 2
minutes, until the slurry is completely clear and all beads have
been collected on the side of each well. Buffer solution is then
aspirated, and 200 .mu.L of 70% ethanol are added. The ethanol is
allowed to sit at room temperature for about 30 seconds before
being aspirated. The plate is then removed from the magnet and DNA
is eluted in about 40 .mu.L of elution buffer (EB; 10 mM Tris-HCl,
pH 8.5). The plate is returned to the magnet and allowed to sit at
room temperature for about 2 minutes, until the beads have
collected on the sides of the well. The 40 .mu.L sample from each
well is then transferred to a corresponding well of a new
absorbance quantitation plate. DNA quantity in each well is checked
by measuring absorbance at 260 nm as above. Samples having a
concentration of at least 500 ng/.mu.L are further processed for
sequencing. Wells with lower concentrations are failed, and the
corresponding samples are re-amplified.
[0170] Amplified samples are pooled across rows of the 96-well
plate, to produce pools of 12 samples, where amplified
polynucleotides of each sample comprise a barcode unique to that
sample among the 12 samples in the pool. The volume of each sample
added to the pool is calculated such that the total amount of DNA
in the sample submitted for sequencing is approximately 11.25
.mu.g. Each pool is concentrated by cleanup on magnetic beads, as
above, with elution in 38.5 .mu.L EB. 1 .mu.L of each pool is used
to quantify total DNA on a NanoDrop machine (Thermo Scientific,
Wilmington Del.). Samples below 10 .mu.g are failed, and pooling
and cleanup are repeated. Samples having at least 10 .mu.g are
further processed for sequencing.
[0171] Before polynucleotides in each pool are attached, bridge
amplified, and sequenced, a cBot reagent plate is prepared. Reagent
plates are prepared ten at a time, using commercially supplied
Phusion High-Fidelity PCR Master Mix with HF Buffer (New England
Biolabs), Detergent-free Phusion HF Buffer Pack (New England
Biolabs), 0.1N NaOH, HT1 buffer (5.times.SSC+0.05% Tween 20), and
HT2 buffer (0.3.times.SSC+0.05% Tween 20). Five Nova Biostorage
8-tube strips are placed into positions 1, 2, 3, 7, and 10 of ten
separate Nova Biostorage RoBo Racks. 1.25 mL of Phusion master mix
are added to a 15 mL tube, followed by addition of 1.25 mL of
RNase- and DNase-free water, and vortexing for 10 seconds to
generate 1.times. Phusion master mix. 440 .mu.L of 5.times. Phusion
HF buffer are added to another 15 mL tube labeled "HF," followed by
addition of 1760 .mu.L of RNase- and DNase-free water, and mixed to
generate 1.times.HF buffer. Reagents are dispensed into rows of the
reagent plates as follows: Row 1--720 .mu.L HT1 buffer; Row 2--230
.mu.L Phusion master mix; Row 3--200 .mu.L 1.times.HF buffer; Row
7--300 .mu.L HT2 buffer; and Row 10--215 .mu.L 0.1N NaOH. Each tube
strip is then covered with Nova Biostage tube caps, and all plates
are frozen until needed.
[0172] Each sample pool is then prepared for sequencing by
attachment to a flow cell. The system for attachment and bridge
amplification comprises a cBot system, a NanoDrop Absorbance
Spectrometer, Applied Biosystems Veriti 96-well Thermal Cycler (0.2
mL), Veriti Thermocycler Program, and cBot attachment and bridge
amplification programs. Samples are heated to 95.degree. C. for 5
minutes. 12.5 .mu.L of 4.times. Hybridization buffer
(10.times.SSC+0.2% Tween-20) is added to each sample, which are
placed on ice until loaded on the Illumina cBot machine. A sipper
comb, flowcell, reagent plate, and sample tubes are then loaded on
the cBot. For each sample pool, polynucleotides are attached to a
channel of the flow cell by extension of oligonucleotides attached
to the surface of the channel ("target capture" step of FIG. 1).
The attached oligonucleotides comprise a collection of different
oligonucleotides that specifically hybridize to members of a
collection of about 5000 different interrogation positions located
upstream of selected causal genetic variants. Clusters of bridge
amplified sequences are then generated on the cBot using standard
procedures.
[0173] Clusters are sequenced using a Genome Analyzer IIx (GAIIx;
Illumina, San Diego Calif.). The sequencing system comprises a
Genome Analyzer IIx, a Paired-End Module, Sequencing Control
Software, GAIIx programs (sequencing, pre-wash, prime, post-wash),
500 mL capacity plastic beakers, a large square ice bucket, and a
scale with 0.1 g tolerance. Sequencing is performed in two rounds.
In a first round, sequencing data is generated from a first primer
that hybridizes downstream of (3' along the extended strand) the
barcode and adjacent to the target genomic DNA sequences, thereby
generating sequencing data for the target gDNA regions comprising
causal genetics variants. In the second round, sequencing data is
generated from a second primer that hybridizes upstream of (5'
along the extended strand) the barcode sequence, such that barcode
sequence data is produced for each cluster. The order of these
sequencing reactions could be reversed. Barcodes for each cluster
are then matched to their corresponding gDNA sequence, such that
the sample source for each gDNA sequence can be identified. The raw
data from the GAIIx is combined into individual reads, each with
quality scores, using standard Illumina software. Reads are aligned
to a reference genome using a Burrows-Wheeler Aligner, and variants
are found from this alignment using the genome analysis toolkit
GATK. The output file from the GATK listing all found discrepancies
between the sequencing reads and the reference assembly is then
used to generate a genotype report, which is sent securely to the
ordering physician for a consultation with the patient that
provided the sample.
Example 2
Amplification and Sequencing Process
[0174] Example processes for the amplification of a plurality of
different target polynucleotides are illustrated in FIGS. 2 and 5,
which differ primarily in the inclusion of a solid-phase
purification step in FIG. 2. FIG. 7 also illustrates an example
amplification process, and differs from the process illustrated in
FIG. 2 primarily in that oligonucleotide primer extension is
performed before adapter joining, instead of after adapter joining.
Amplification may or may not include a solid-phase purification
step. FIG. 6 illustrates an amplification process as in FIG. 5, and
also example bridge amplification and sequencing processes. The
amplification process illustrated in FIG. 6 may be used in
conjunction with any bridge amplification method and associated
sequencing method.
[0175] First, a partially single-stranded adapter is ligated to
fragmented polynucleotides. The partially single-stranded adapter
has a double-stranded region at one end (sequence U hybridized to
complementary sequence U') and the single-stranded sequence Y that
does not hybridize to the target polynucleotide under the
hybridization and extension conditions used. Ligation adds sequence
Y to both 5' ends of the target polynucleotides. Next, a plurality
of different oligonucleotide primers, each having a different
target-specific sequence W at the 3' end, are hybridized to their
respective target polynucleotides, and extended, producing an
extended oligonucleotide with sequence Y' (complement of Y) at the
3' end. Extension may be performed before adapter ligation, such as
illustrated in FIG. 7. The oligonucleotide primers may lack a first
binding partner, as in FIG. 5, or may comprise a first binding
partner, as the in the small overhanging circle in FIGS. 2 and 7.
If the extended oligonucleotides do comprise a binding partner,
they may be purified by selectively binding to a solid surface
comprising a second binding partner that binds to the first binding
partner, as in the bead (larger circle) in FIG. 2. Bound and
extended oligonucleotides may be purified, such as by holding in
place on a magnetically responsive bead in the presence of a
magnetic field while reaction solution is removed, beads washed,
and new reaction solution added (e.g. components of a further
amplification reaction). Extended oligonucleotides, purified or
not, are then amplified with a pair of amplification primers. One
amplification primer comprises sequence X and sequence Y, with
sequence Y at the 3' end for hybridization to sequence Y'. The X-Y
primer is extended along the extended oligonucleotides to produce a
plurality of extended X-Y oligonucleotides comprising sequences X,
Y, W', and Z' (5' to 3'; where W' is the complement of W, and Z' is
the complement of Z). Another amplification primer comprises
sequences V and Z, with Z at the 3' end for hybridization to
sequence Z' of an extended X-Y primer. The V-Z primer is extended
along the extended X-Y primer to produce a plurality of sequences
comprising V, Z, Y', and X' (5' to 3'; where X' is the complement
of X), which may then serve as a template for extension of a
further X-Y primer, which may then serve as a template for
extension of a further V-Z primer, and so on for each successive
primer extension reaction in the amplification process. The
predominant amplified sequences comprise a plurality of different
target polynucleotides, each contained in a polynucleotide
comprising one strand comprising sequences V, Z, W, Y', and X'
(from 5' to 3'), and another strand comprising sequences X, Y, W',
Z', and V' (from 5' to 3'), with target polynucleotide sequence
located between Z/Y' and between Z'/Y. These amplified
polynucleotides may then be subjected to sequencing.
[0176] Sequencing may follow the process illustrated in the lower
half of FIG. 6. A first bound oligonucleotide is hybridized to a
sequence near or at the 3' end of an amplified polynucleotide,
typically by complementarity to a sequence added during the
exponential amplification step (thereby specifically amplifying,
and ultimately sequencing, exponentially amplified products).
Extension of each first bound oligonucleotide provides nucleation
points for bridge amplification to produce clusters of
double-stranded bridge polynucleotides with the same sequence.
Extension products of first bound oligonucleotides are denatured to
remove the hybridized templates. An extended first bound
oligonucleotide then hybridize to a second bound oligonucleotide,
typically by complementary to a sequence at or near the 3' end and
derived from sequence added during the exponential amplification
step. Extended second bound oligonucleotides may then serve as
templates for extension of further first oligonucleotides, which
may then serve as templates for extension of further second
oligonucleotides, and so on. Here, some or all first
oligonucleotides comprise a cleavage site, which is cleaved after
completing the bridge amplification process. Bound polynucleotides
are then subjected to denaturing conditions, such as heating (e.g.
about 95.degree. C.) or chemically denatured, to remove one strand
of a plurality of bound bridge polynucleotides. The remaining,
bound strands are then free for hybridization with a sequencing
primer, illustrated above "first read" in FIG. 6. Sequencing data
is then generated by sequential steps of nucleotide extension and
detection, extending the sequencing primer. The extended first
sequencing primer may then be denatured and removed from the
template, in order to repeat the sequencing process from a second
sequencing primer that is different from the first. Where one
sequencing primer is used only to generate enough sequencing data
to identify a barcode sequence, that sequencing reaction may be
significantly shorter than the other sequencing reaction (e.g. less
than about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more
cycles of nucleotide addition). While FIG. 6 only illustrates
bridge amplification and sequencing of a single target
polynucleotide, bridge amplification and sequencing typically
involves a plurality of different target polynucleotides amplified
in a previous amplification step, all of which are bridge amplified
and sequenced in parallel.
Example 3
Identification of Non-Subject Sequences
[0177] Polynucleotides (e.g. DNA and/or RNA) are extracted from a
sample from a subject suspected to contain viral and/or bacterial
polynucleotides using standard methods known in the art. Sample
polynucleotides are fragmented, end-repaired, and A-tailed, such as
in Example 1. Adapter oligonucleotides comprising sequence D are
then joined to the sample polynucleotides, which are then amplified
using amplification primers comprising sequence C, sequence D, and
a barcode. Amplified target polynucleotides are hybridized to a
plurality of different first oligonucleotides that are attached to
a solid surface. Each first oligonucleotide comprises sequence A
and sequence B, where sequence B is different for each different
first oligonucleotide, is at the 3' end of each first
oligonucleotide, and is complementary to a sequence comprising a
non-subject sequence or a sequence within 200 nucleotides of a
non-subject sequence. Specifically, the first oligonucleotides are
selected to amplify sequences having high depth outside the
subject's genome, such as viral or bacterial sequences unique to a
particular class, order, family, genus, species or other taxonomic
group of virus or bacteria. Sequences amplified may include 16s
rRNA sequences. Polynucleotides from a healthy control are
processed simultaneously. Target polynucleotides are then bridge
amplified and sequenced, according to methods of the invention.
Sequencing data produced for the non-subject sequences may be used
to identify an infectious agent. Sequencing data produced for the
non-subject sequences may be used to detect relative levels of
different taxonomic groups of bacteria (e.g. ratios of one or more
taxonomic groups to one or more other taxonomic groups), or shifts
in these. The identities or relative levels of bacteria or
infectious agent are then used as the basis for making a medical
recommendation or taking medical action.
Example 4
Alignment of Nucleic Acid Sequences for Detecting Genetic
Variation
[0178] This example sequence manipulation and alignment procedure
("pipeline") begins with raw data from Genome Analyzer IIx (GAIIx)
or HiSeq sequencers (Illumina; San Diego, Calif.) to infer
genotypes and compute metrics from patient samples. Sequencing data
is generated from runs of barcoded samples in a 12.times.
multiplexed configuration per Flowcell lane according to a method
of the invention. The sequencer raw data includes basecalls (BCL
files) and various quality-control and calibration metrics. The raw
basecalls and metrics are first compiled into QSEQ files and then
filtered, merged, and demultiplexed (based on barcode sequences)
into sample-specific FASTQ files. FASTQ reads are aligned to the
HG19 genome to create an initial BAM file. This BAM file undergoes
several transformations to filter, clip, and refine alignments, and
to recalibrate quality metrics. The final BAM file is used to infer
genotypes for known variants and to discover novel ones, producing
a callset. The callset (VCF files) is then filtered using various
call metrics to create a final set of high-confidence (such as
about or more than about 80%, 85%, 90%, 95%, 99%, or higher
confidence) variant calls per sample. Finally, various metrics are
computed per sample, lane, and batch and the calls and metrics are
loaded into a laboratory information management system (LIMS) for
visualization, review, and final report generation. The pipeline
can be run (in whole or in part) locally and/or using cloud
computing, such as on the Amazon cloud. Users may interact with the
pipeline using any suitable communication mechanism. For example,
interaction may be via Django management commands (Django Software
Foundation, Lawrence, Kans.), a shell script for executing each
step of the pipeline, or an application programming interface
written in a suitable programming language (e.g. PHP, Ruby on
Rails, Django, or an interface like Amazon EC2). Overviews of the
operation of this example pipeline are illustrated in FIGS. 10 and
11.
[0179] Sequencing occurs on a flowcell with 8 lanes. Each lane has
12 (or more with HiSeq) samples, each with a unique 6-7 nucleotide
barcode sequence. Each lane is subdivided into some number of tiles
(120 for GAIIx, 48 for HiSeq). The sequencer outputs 3 reads per
flowcell cluster. Read1 (R1) is the sequence of one edge of a gDNA
fragment (59 bp), generated by extension of a first primer. Read2
is the barcode sequence (6 bp) generated by extension of a third
primer. Read3 (R2) is part of the probe sequence (15 bp), generated
by extension of a second primer.
[0180] The raw sequencing data processed in the first step of the
pipeline (creating FASTQ files) is typically large (such as about
or more than about 100 GB, 150 GB, 200 GB, 250 GB, 300 GB, 400 GB,
500 GB, 1000 GB, or more). Accordingly, it can be advantageous to
utilize cloud computing for some or all of the analysis steps. In
this example, the first step is run locally, and the resulting
FASTQ files are uploaded to Amazon S3 (an online storage web
service provided by Amazon; Seattle, Wash.) and processed using
Amazon EC2 instances (a cloud computing web service provided by
Amazon; Seattle, Wash.). Amazon's Simple Queue Service (SQS) is
used to assign tasks. The final calls and metrics are then
downloaded and loaded into a local database. The EC2 instances pull
tasks and FAQSTQ files from SQS and S3, respectively, process them,
and upload the results to S3. Instances may be initiated and/or
terminated manually, or may be partially or fully automated.
[0181] FIG. 10 shows an example of temporary and archival storage
space utilized and processing runtime for the pipeline on Illumina
GAIIx sequencing data. The BCL2FASTQ step is run on the entire
batch and subsequent steps are run per sample. To reduce processing
time, BCL2QSEQ is run locally and then the remaining steps are run
on 96 Amazon EC2 instances, one per sample. Running the pipeline
using the cloud takes 7 to 10 hours depending on the batch yield.
Use of cloud computing for one or more of the data processing steps
may reduce the total time needed to generate final alignments for a
sample by more than about 10%, 25%, 50%, 75%, 90%, or more.
[0182] FIG. 11 shows an example sequencing data manipulation
process. The BCL2FASTQ process converts raw basecalls into
filtered, merged, and demultiplexed reads, and comprises bcl2qseq
and process_lane steps. The input for bcl2qseq is the rawdata
directory for a sequencing batch, which are converted to QSEQ files
(one per tile and read number) using an Illumina tool--this is run
locally on the entire batch. The QSEQ files are processed in
process_lane to filter out poor reads (using the Illumina "chastity
filter"), merge reads from different tiles, and demultiplex read1
and read3 into sample-specific FASTQ files using the barcodes in
read2. Each lane may be run in parallel.
[0183] The FASTQ2BAM process aligns reads to the genome and further
processes the alignment. Format changing, sorting, and indexing are
performed as needed. All steps are run on files for individual
samples, and all samples represented in a batch may be run in
parallel on different machines. The steps in FASTQ2BAM include
align_bwa, fix_align, mark_duplicates, realign_bam,
recalibrate_bam, and clip_alignment. In the align_bwa step, reads
in a FASTQ file are aligned to the reference genome using the BWA
aligner. This step is called twice, once to align read1 to a
reference genome and once to align read3 to a collection of the
probe sequences used to amplify target polynucleotides. The output
sequence alignment/map (SAM) file is converted to a binary
alignment/map (BAM) file and then sorted and indexed. In order to
improve detection of indels, the default BWA parameters are
modified as follows: decrease seed length to 16; increase number of
allowed gaps in alignment to 3; decrease the gap open and extension
penalties to 6 and 2, respectively; increase the number of allowed
gap extensions to 20 (for larger variants, custom contigs may be
added to the genome to infer their presence). The fix_alignment
step then modifies some of the alignments to improve their accuracy
and remove alignments likely to be erroneous. Because read3
includes probe-derived sequence at variable distances from read1 in
this scenario, it does not fit some of the statistical assumptions
made by aligners (such as expected distance between reads), and
customary paired-end mapping would be less efficient. To improve
alignment accuracy, read1 and read3 are aligned independently
(which is generally faster than paired-end mapping), and then the
fix_alignment step processes the results to: discard any reads
where read1 and read3 are on different strands or positioned more
than 10000 base pairs away from each other (read1 not filtered if
read3 does not map); and remap reads with multiple best-scoring
positions to a subset of the genome consisting only of regions of
interest (ROI; e.g. regions containing a causal genetic variant,
non-subject sequence, or AIM; typically near a probe sequence).
FIGS. 12A and 12B illustrate an example alignment of reads in a
CFTR exon with a non-unique region before and after fix_align,
respectively, which closes an artificial gap in the illustrated
sequence pileup.
[0184] The mark_duplicates step identifies and tags PCR and optical
duplicates using a tool from the Picard toolset (java-based
command-line utilities for processing sequencing data in BAM
format; available from the SourceForge web site maintained by
Geeknet (Fairfax, Va.)). Without discarding duplicates, non-uniform
PCR efficiency between the reference and alternate allele could
lead to allelic bias, where the counts of reference and alternate
alleles for a variant may be biased by PCR. Without additional
information, it is assumed that two reads from a sample that map to
the same position are duplicates and thus, all except one are
marked as duplicates and excluded from subsequent analysis. Depth
of coverage may be increased by using primers with different
barcodes in the same sample, such that an additional read having
the same sequence as another would not be discarded if the
associated barcodes from the respective clusters were
different.
[0185] The realign_bam step performs multiple sequence
Smith-Waterman alignment around indels, and typically has the
effects of better identifying true indels, and reducing or
eliminating the number of false-positive SNPs. The initial aligner
(BWA or any similar tool) aligns each read independently and
heuristically. A read with a true INDEL may align as a read with a
cluster of SNPs because that alignment model scores better than one
with the INDEL given the set of parameters and heuristics used. In
multiple sequence alignment of the same reads, the aligner tries to
optimize the score of an alignment model of all reads (to the
reference and to each other); thus, unless the same cluster of SNPs
can align all reads, the true alignment will typically score
higher. The realignment step performs a multiple-sequence exact
realignment around any INDELs found in the ROI. FIGS. 13A and 13B
show the same reads before and after local realignment. A
realignment may be performed around any indel in an ROI.
Alternatively or additionally, a realignment may be performed
around known indels, such as around indels in one or more reference
sets of indels (such as sets reported in Mills et al., Genome Res.
(2011) June; 21(6): 830-839; Durbin et al., Nature (2010) October
28; 467(7319): 1061-1073; and Bhangale et al., Nature Genetics
(2006) 38, 1457-1462).
[0186] The recalibrate_bam step recalibrates base qualities using
empirical batch data. Illumina software estimates a quality value
for each base using various quality control metrics using a simple
model of the sequencing chemistry--it does not take specific error
modes into account. In this step, a GATK tool that uses
high-scoring alignments is used to determine empirical base
quality, analyze the covariation in empirical quality between many
features of a sequenced base (reported quality, surrounding bases,
read position, etc), and recalibrate all qualities using the
covariation model. This step provides more accurate base qualities
which leads to more accurate calling statistics.
[0187] The clip_alignment step removes bases from aligned reads
that include probe sequence from the corresponding cluster. For
amplified sequences from a subject that are shorter than the
read-length, read1 will typically contain sequences from the
corresponding probe. When probe sequences are derived from the
reference genome, these reads will align to the genome but will
mask out any true SNPs, thus introducing an allelic bias towards
the reference sequence. This step identifies when a read overlaps
its own probe and selectively removes the overlapping bases from
the read. For all reads where both read1 and read3 map and where
read1 overlaps the probe, the overlapping bases of read1 are
removed from the alignment ("clipped"). If read3 of a read doesn't
map, then read1 is clipped if it overlaps any probe, but only if
the overlap occurs at either end of the read (probe sequence that
does not include a terminal base indicates the read was not
generated from that probe). In either case, clipping is performed
by modifying the CIGAR alignment string to include the "S"
operation for the clipped bases, updating the start position and
setting the base qualities of the clipped bases to 0. Thus, the
sequence still exists, but the alignment is modified to exclude the
clipped bases.
[0188] The BAM2VCF process uses the final alignments (BAM files
from the FASTQ2BAM process) to determine genotypes using a Bayesian
method to compute probability of variants given sequencing data and
prior knowledge. All steps are run on files for individual samples
and can be run in parallel and on different machines. The strategy
for variant identification ("calling") is to create an initial set
of identified variants (a "callset") using very lenient thresholds
to maximize sensitivity and then to filter it based on call metrics
and other criteria. The steps in the BAM2VCF process include
genome_whitelist, genotype_novel, and hardfilter_vcf steps. The
genome_whitelist step infers genotypes for an input BAM file based
on a comparison to a given a reference list of known variant
positions and alleles at those positions. In this step, a computer
algorithm programmed to identify variants (a "caller") is
configured to output all variants and to skip any confidence-based
filtering. The output of this step is a variant call format (VCF)
file, which is further processed in additional steps.
[0189] The genotype_novel step identifies variant sites within the
ROI that differ from the reference genome, and infers the genotypes
at those sites. In this step, the caller is configured to output
only genotypes not included in the reference list of known variants
used in the previous step, and to skip any confidence-based
filtering. Calls from the genotype_novel step may contain many
false positives. The hard_filter_vcf step filters genotype
determinations using several call metrics. These metrics fall into
two broad categories: (1) those that quantify the confidence of the
base calls, mapping, variant, or genotype determination and (2)
those that quantify the likelihood of common sources of errors such
as strand bias, position bias, or presence of sequence features
such as homopolymer runs that are known to cause Illumina chemistry
errors. Modified thresholds may be based on recommendations by the
Genome Analysis Tool Kit (GATK). Alternatively or additionally, a
machine learning approach may be used to identify thresholds for a
desired sensitivity and specificity.
[0190] To aid the evaluation of the processes in this example, a
record for each sample is made of the number of: reads with
corresponding barcode, reads mapped to the genome, reads after
fix_align step, reads after excluding PCR/optical duplicates, reads
where read1 and read3 map more than 10000 bp apart, reads in
non-unique regions that the fix_align step attempts to remap, reads
successfully remapped, reads that are clipped and have a
corresponding read3, reads that are clipped and do not have a
corresponding read3, reads in X and Y chromosomes (which may be
used to infer sex), and SNP calls that match the SNP identity in
the reference genome. Thresholds as to any one or combination of
these metrics may be set, such that results for any sample falling
below the threshold are discarded. Any one or combination of these
metrics may also be aggregated for an entire sequencing lane, in
addition to the total number of reads per lane and the number of
reads passing an initial filter. Thresholds as to any one or
combination of sequencing lane metrics may also be set for the
exclusion of data resulting from lanes failing to pass the
threshold(s). Concordance and discordance between any two callsets
may be analyzed for validation studies or for setting thresholds
for future sample analyses.
[0191] For any genomic variants identified, a pileup image may be
generated, which illustrates an alignment of all reads underlying
any variant call. A pileup image may be produced using a genomics
data visualizer, such as the Integrative Genomics Viewer (IGV;
provided by the Broad Institute, Cambridge, Mass.). To do this, an
IGV script is generated that (1) loads the genome and BAM files and
(2) iterates through each variant position and outputs a snapshot
PNG of the pileups. IGV is run under a virtual framebuffer (e.g.
xvfb) and the resulting PNG files are cropped (using command line
Imagick tool) to remove IGV chrome.
Example 5
Selecting Probe Sequences
[0192] An algorithm is used in a process of selecting optimal probe
sequences for initial capture of target sequence for amplification
and sequencing (a process also referred to as "probe design"). The
probe sequences may then be used in the production of a collection
of oligonucleotide primers or first oligonucleotides bound to a
solid support. The probe design process may be repeated, such as to
incorporate additions to the list of variants and corresponding
target sequences to be sequenced. Accordingly, the algorithm allows
the addition of previously designed regions of interest (ROIs) and
probes so that regions that are already covered by a previously
designed ROI are not redesigned.
[0193] The initial unit of probe design is the Region of Interest
(ROI), which can be a list of the exons of a gene, a single genomic
base, regions or points that are non-coding, or combinations of
these that can possibly overlap. The first step in the process is
to load and then reconcile all of the different regions for which
probes are to be designed. The "design engine" class keeps track of
all ROIs to be considered and, later, all of the probes that have
been designed for each ROI. Small ROIs, such as variants initially
entered as point mutations, are padded to a length of 100 bp before
being processed further. Then, all overlapping ROIs are combined
into single ROIs so that duplicate probes are not designed.
[0194] Two ROIs are merged if and only if they reduce the number of
ROI Tiles covering the combined ROIs. The number of tiles covering
the two separate areas is calculated along with the number of tiles
to cover a hypothetically joined ROI. The case that requires the
fewest tiles is used for subsequent steps of probe design. An
algorithm is used to determine the number of tiles covering a given
genomic region.
[0195] Once ROIs have been padded and merged, all ROIs are at least
100 bp long and none overlap. The resulting ROIs are long (e.g.
longer than a specified tile length) or short (e.g. less than or
equal to a specified tile length). Long ROIs are subdivided into
ROI tiles, which are unit lengths of sequence for which a probe
will be designed. Short ROIs, being less than or equal to the tile
length, are not subdivided. Each potential ROI tile is evaluated on
how well the probes designed from it perform. The maximum number of
tiles is also calculated as the upper bound on this calculation.
All tile numbers between the minimum and the maximum number of
tiles possible are considered in order from least number of tiles
to greatest. These numbers of tiles are equal to the ceiling of the
number of bases in the ROI to be split divided by the min or max
length of the ROI, depending on what number is being calculated.
These numbers are ROI_TILE (250 bases) and MAX_ROI_TILE, where
MAX_ROI_TILE=(TILE_SIZE)-(READ_LENGTH)-(RECESS). TILE_SIZE is
between 300-440 bases long. READ_LENGTH is 40-60 bases long. RECESS
is set at 10 bases in length. Once a number of tiles whose probe
design yields all valid probes is found, the iteration ends. This
in effect minimizes the number of tiles required to cover a region
while at the same time ensuring the best probes are chosen
according to the criteria below.
[0196] The probe design algorithm works on a given ROI tile in
isolation from other ROI tiles, so the ROI tile can be considered
the fundamental unit of this probe design process. Each ROI tile
will have a forward and reverse tile designed for it, so that all
bases may be evidenced from either strand upon sequencing. The
probe design algorithm works by considering the forward and reverse
primers for every READ_LENGTH tile in a "probe design window" that
is calculated for each ROI tile. Each probe in this window is then
scored based on criteria described below to create a set of scores
from most important to least important where, for all scores, a
lower score is better. Therefore, the best probe is merely the one
that appears first in a multiple-field ascending sort of the probe
score sets. Each ROI tile partition causes the probe design
algorithm to be run for each of the possible ROI tiles. The
iteration starts with the condition of the fewest ROI tiles and, if
such a partition doesn't yield valid probes (conditions of which
are described below), the number of ROI tiles is increased and the
partition is re-done.
[0197] The probe window is defined as follows: (1) the length of
the probe window is defined as (TILE_SIZE)-(length of the current
ROI tile)-(RECESS); (2) the start coordinate is then defined as
RECESS by away from the end of the ROI itself, and the stop
coordinate is calculated by adding the length of the probe window
above to the RECESS coordinate; and (3) all 40mers in this range
are then considered as probes for evaluation. FIG. 19 provides an
illustration of the positional relationship of sequence regions
considered in this step.
[0198] Criteria used to evaluate each probe, in the order
considered, include uniqueness of the "near 24-mer," overlap with
any common SNPs in the near 24mer, mappability of the entire 40mer,
NtBspQI overlap, repeat masking, overlap with any common SNPs in
entire 40mer, near 24mer overlap with disease variant, 40mer
overlap with disease variant, GC %, and Distance to ROI. While an
ideal probe is unique across the genome, sometimes finding such a
location near an arbitrary site is not possible. To compensate, the
"near 24-mer" (defined as the 3'-most 24 bases of the
oligonucleotide comprising the probe sequence or its complement) is
selected to be as unique as possible. Because the extension of the
captured genomic species occurs from 5' to 3', the quality of the
basepair binding site nearest the double-stranded to
single-stranded junction has a large effect on the efficiency of
the capture--a stronger bond making it more likely that the
captured sequence will be extended. To measure binding quality, the
University of California Santa Cruz 24mer mappability track
(available through the UCSC genome browser) is used, which gives,
for each base in the genome, the mapping score of the 24mer
beginning at that base. The score is given as 1/N, where N is the
number of matches to that 24mer in the genome. Only two results out
of this test are considered: whether the score equals 1 (i.e. is
unique) or is less than one (i.e. has multiple binding sites). The
first case is preferred.
[0199] Overlap with common SNPs in the near 24-mer is not desired.
Any mismatch in the capture probe binding site reduces binding
efficiency. Because nearby SNPs are often in linkage
disequilibrium, this difference in binding efficiency would
introduce a great deal of allelic bias. It is therefore desirable
for any allele found to have the greatest chance possible of having
the same probe binding site as other alleles in that gene. The UCSC
Common SNP Track is used to make this calculation. There are two
categories: those with no overlaps and those with one or more
overlaps. The former is greatly preferred.
[0200] The mappability of the entire 40mer determines the same
score with the same categories as the 24mer mappability, but using
the UCSC 40mer Mappability track instead of the 24mer track. This
new track has a similar definition, only 40mer mappability is
considered instead of 24mer mappability.
[0201] The enzyme NtBspQI may be useful in oligonucleotide
synthesis or manipulation. Accordingly, the number of bases of
overlap between the probe and the recognition site of the enzyme is
scored.
[0202] In evaluating repeat masking, the UCSC repeat mask track
(annotated repeats) is used to calculate the weighted average of
the values for the bases that makeup the each 40mer. The repeat
mask track assigns values 0 or 1 to each base depending on whether
it is masked or not. Thus, the higher the score, the more it is
masked. Designing probes for masked bases is not desired, so a
lower, ideally 0, score is better. These scores are divided into
quartiles: so, up to 25% masked comprises a class (scored as 0), up
to 50% another, as does 75% and 100%.
[0203] Just as overlap of a probe` near-24mer with any common SNP
is evaluated, so too is overlap of the entire 40mer probe sequence
with any common SNP evaluated and scored.
[0204] Whether or not the near-24mer overlaps a disease variant is
also evaluated. This test is similar to the common SNP overlap
test, except the near-24mer is evaluate for overlap with any causal
genetic variants to be sequenced. A score of 0 is given for no
overlap, and a score of 1 is given for the presence of overlap. A
similar analysis is then performed for the entire 40-mer.
[0205] The GC % of a probe sequence received one of two scores--0
for a GC % between 20-80%, and 1 for outside this range. Finally,
distance to the ROI is evaluated. All other things being equal, the
probe closest to the ROI is preferred. The score for ROI distance
is equal to the number of base pairs between the end of the probe
and the start of the ROI it targets.
[0206] A valid probe is a probe that meets all of the following
criteria and for which no further iteration of probe design for the
ROI is required: (1) mappability of the near 24mer.gtoreq.1/3.5;
(2) Mappability of the entire 40mer.gtoreq.1/3.5; (3) repeat
fraction .ltoreq.0.25; (4) no overlaps with common SNPs in the near
24-mer; no NtBspQI recognition site in the probe sequence.
Example 6
Sample Collection and Analysis
[0207] Exemplary processes of delivering a probability that a user
is a carrier of rare genetic disease are demonstrated in FIGS.
14-17. FIGS. 14-15 illustrate pipelines for order fulfillment for
web and medical customers respectively. An order can be placed by a
physician or a consumer. An order can be placed for a single test
or for a couple or family. The order can be accepted through a web
site. The ordering system can accept contact information,
demographic details and billing information. Contact information
can include, without limitation, name, address, telephone number,
and email addresses. Demographic information can include, without
limitation, sex, date of birth, and self-reported ethnicity. An
order confirmation notification can be sent using the provided
contact information. Acceptable orders are added to a database, and
the states of these orders can be subsequently maintained by a
state machine.
[0208] A sample collection kit is then sent to the user. A sample
is collected that is any human tissue or fluid. The sample can also
be isolated DNA from a human. Examples of samples useful for this
example include, but are not limited to: saliva, blood, urine,
buccal cells, amniotic fluid, cell scrapings, and cell culture. The
sample is then genotyped using a device described herein. Phenotype
solicitation, for example, retrieving self-identification of
phenotypic traits of a user, can be performed in parallel with
sample processing.
[0209] Sample collection can be performed at home, in a physician's
office, or at a specialized collection site. Sample collection and
return can be tracked by advancing the state of the order-tracking
state machine. Samples received by the accessioning facility can be
registered in the database system by advancing their state in the
state machine. After acceptance at the accessioning facility,
samples can be delivered to the genotyping facility. The genotyping
facility can return raw genome data to a secure data storage server
by secure file transfer protocols. File upload can trigger an
advance of the state machine. This advance can trigger a server
configured to perform genotype calling to retrieve the raw genome
data from the data storage server as well as any phenotype data
associated with the order. The genotyping algorithm can produce a
fully probabilistic genotype call.
[0210] FIGS. 16-17 illustrate a high level sample processing
pipeline and detailed computational pipeline respectively. Batches
of samples are received and measured for quality control purposes
(Batch passes QC). Information such as family history, gender, or
self-reported ancestry is used to serve as an independent check on
calling for each sample (Phenotype data retrieved for batch
samples). In parallel with this process, a report with child
predictions is constantly updated. First pre-test risk calculations
are delivered, based on phenotype (such as family history and other
answers to an online questionnaire). Once a genotype sample is
received and processed, post-test calculations are given. The
report is then generated and sent to the final stages of the
pipeline, for laboratory staff and physician approval as shown in
FIG. 16.
[0211] Quality control metrics can be generated from the calling
process. An example quality control metric is the percentage of
probabilistic genotype calls in which at least one genotype has a
posterior probability greater than a threshold value. A batch of
samples is processed together. When processed as a batch, the
individual probabilistic genotype calls can be used to generate
batch-level quality control statistics. Probabilistic genotype
calls can be stored in a database. Successful genotype calling can
trigger an advance of the order state. For a couple or family
order, the state machine can hold for completion of the entire
order, else single orders can be passed to the next state. If
phenotype data is required for risk calculation, then the state
machine can delay processing until all phenotype data is collected.
The state machine can also trigger a notification to the patient
that phenotype data is required. If all genotype and phenotype data
are ready, then the state machine can advance, trigger the risk
calculation server to perform risk calculation. The results of risk
calculation can be serialized and transferred to a results
reporting system. This is a machine-readable format of the results.
The state machine can advance the order when the transfer is
completed. The results reporting server can combine the
probabilistic risk calculation with appropriate text and formatting
to generate a human-readable report. This human readable report can
be further formatted for display on a website. This human readable
report can be formatted for other media such as PDF files for
printing. The final results reports can be automatically released
using an auto-verification system. A human can review the reports
for release. The reviewers may be a clinical laboratory scientist
and a physician. The results are accessed via a web portal which
links to a view of the results and a summary of the quality control
metrics. Acceptance of the report by the clinical laboratory
scientist releases the results to the physician. The physician can
review the results in a similar portal and approve the final
release of the results.
[0212] FIG. 18 illustrates exemplary input and output steps for
report generation for two hypothetical parents: Mama Hen and Papa
Hen. A child prediction is produced that incorporates mother and
father genotypes, mother and father phenotypes, and relative
genotypes and phenotypes. Any or all of these variables can be
missing values, with defaults initialized from demographically
similar individuals (and if this is not known, from the world
population). The resulting child prediction may include not only
disease or trait risk, but also other variables such as height and
weight. Different variables in the child prediction will use
different weights of genotype and phenotype.
[0213] While preferred embodiments of the present invention have
been shown and described herein, it will be obvious to those
skilled in the art that such embodiments are provided by way of
example only. Numerous variations, changes, and substitutions will
now occur to those skilled in the art without departing from the
invention. It should be understood that various alternatives to the
embodiments of the invention described herein may be employed in
practicing the invention. It is intended that the following claims
define the scope of the invention and that methods and structures
within the scope of these claims and their equivalents be covered
thereby.
Sequence CWU 1
1
123159DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 1cgagatctac acgcctccct cgcgccatca gaggtcacac
tcagcagcac gacgatcac 59259DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 2cgagatctac acgcctccct
cgcgccatca gcagcagcac tcagcagcac gacgatcac 59359DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
3cgagatctac acgcctccct cgcgccatca gactgctcac tcagcagcac gacgatcac
59459DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 4cgagatctac acgcctccct cgcgccatca gtaacggcac
tcagcagcac gacgatcac 59559DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 5cgagatctac acgcctccct
cgcgccatca gggattacac tcagcagcac gacgatcac 59659DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
6cgagatctac acgcctccct cgcgccatca gaacctgcac tcagcagcac gacgatcac
59759DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 7cgagatctac acgcctccct cgcgccatca ggccgttcac
tcagcagcac gacgatcac 59859DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 8cgagatctac acgcctccct
cgcgccatca gcgttgacac tcagcagcac gacgatcac 59959DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
9cgagatctac acgcctccct cgcgccatca ggtaacccac tcagcagcac gacgatcac
591059DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 10cgagatctac acgcctccct cgcgccatca gcttaaccac
tcagcagcac gacgatcac 591159DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 11cgagatctac acgcctccct
cgcgccatca gtgctaacac tcagcagcac gacgatcac 591259DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
12cgagatctac acgcctccct cgcgccatca ggatccgcac tcagcagcac gacgatcac
591359DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 13cgagatctac acgcctccct cgcgccatca gccaggtcac
tcagcagcac gacgatcac 591459DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 14cgagatctac acgcctccct
cgcgccatca gttcagccac tcagcagcac gacgatcac 591559DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
15cgagatctac acgcctccct cgcgccatca gatgatccac tcagcagcac gacgatcac
591659DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 16cgagatctac acgcctccct cgcgccatca gtcggatcac
tcagcagcac gacgatcac 591742DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 17cactcagcag
cacgacgatc acagatgtgt ataagagaca gt 421841DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 18gtgagtcgtc gtgctgctag tgtctacaca tattctctgt c
411931DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 19cgagatctac acgcctccct cgcgccatca g
312041DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 20cactcagcag cacgacgatc acagatgtgt ataagagaca g
412159DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 21cgagatctac acgcctccct cgcgccatca gnnnnnncac
tcagcagcac gacgatcac 592240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 22gaggattcag
gagtcaatga ctgaggatgg gactccttga 402340DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 23tgagggcctg gaccaaattc ttcaagcaaa acagaaaaca
402440DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 24actggaccgc cccctccacg ccctcccacc
gcgggcccct 402540DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 25tcttttttcc gagacaaact
tcattctgga aaggctgtca 402640DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 26ttttgctgag
cttacagtgg aaatgctatt aaattctttc 402740DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 27acttagaaag ttaaagtaag aaattattaa tatctcctat
402840DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 28tcagaagggg caaagcttgc ttcctcctgc
atccctcatg 402940DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 29tttattttgt ctctgctgtt
catggcatag tttggtggcg 403040DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 30aatggcctgc
cacctgagaa tctattgttt atggcaagac 403140DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 31agagcaaaga ggacctggga ggtgcctgca ccccatacca
403240DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 32caaatagaaa tgctcttata gatgagtatc
aaaaataaat 403340DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 33tcctccgctc ctcctgcgcg
gggtgctgaa acagcccggg 403440DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 34acccgggcct
gagccgtcgc tgggcccgtc gccttccccg 403540DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 35ttctacctgt ggaccaggaa tctaggacac agtccctgac
403640DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 36tgccctgctg cagacctaca cgcccccacc
atgtgcccac 403740DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 37gggcgtcctg ctgctgggcc
tggtgggcta ctacatcttc 403840DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 38gagcgtgatt
aggtactgga cacctgccaa gtgctgggct 403940DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 39ctgggatttg agggttttca ttacacttct gctaggataa
404040DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 40taaaatttaa aaaatacagt taaaaatcat
ggtcatataa 404140DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 41ccgctgcact gacttcattt
ccttagacaa gacacagtgt 404240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 42actgcaacat
tttcaaagca aaagaatccc gttgctgtcg 404340DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 43cttagctcag ctccaggctg tgcagcagaa gtacagggac
404440DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 44attttagatt caaaattggt agccgattac
attttctcaa 404540DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 45aggcaagctg tcctccaggt
ctttatcaga cagtgccccc 404640DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 46tttaaggttt
ctgtgacctt tgttagaaag tttttaaatg 404740DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 47aatagtaggc tgttggtaca tttctcaact tacttataaa
404840DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 48aaccagtttc tgcctgtctg taactgccct
gtctgccaca 404940DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 49cctgaaatct cttctcgagg
ctgagctgag ggcccttggg 405040DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 50ctattttctc
tctcttattt tcagaattag aaagcaattc 405140DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 51cacggacata cgcataccgg cccagtgaca cgtcaggcaa
405240DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 52atgccttatc aacagtaaaa caatgaatca
ccatagtaca 405340DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 53tcctttggaa cagtgtggac
cccaggtcat ggctcccaga 405440DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 54tgtacaggat
gttactgtac tggatgttgc aggcaactat 405540DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 55cactgctgca tgaggagtgg gcctggggcc actaaacccg
405640DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 56cctgcagtgg gatttcctct gaagagagca
cagtgagcag 405740DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 57aacttattat tttatacctg
cttcattgtt gaaaagaaaa 405840DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 58agccactgtg
cccggctgca gatattcttt cagtaaatga 405940DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 59cattgcctgt gagtgccctc agtttacata gtgctatctt
406040DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 60taattttatt cgccattagg atgaaatcca
tattcacaaa 406140DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 61tcaagccagc ctggaaggga
gatggaaaag ctgcgtgcgc 406240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 62tgctgttaag
atgttacttt ctttaaaaaa gatgggttat 406340DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 63aaaaattatg cctattagaa tcaaaatatg atagcaaaac
406440DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 64gttaatattt ttatgctaat gcagacaata
tatattactg 406540DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 65gctgtacaga gctatatatc
ataattattt ctatactatg 406640DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 66caggaggatc
agtctctgta gaggcaggga ggagctgggg 406740DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 67tattttcagg tactgaattc tgaaatgata gcattttgtg
406840DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 68tgttgagttt ttcagtttct ctgaaaagtc
atactctaga 406940DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 69tgtagcccct ttgagcatga
ggtatgcata gaacataatg 407040DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 70cttgcaatca
agtaaggtga aatattcata tactggttct 407140DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 71cggcgggccg cctagggtga ttggctgctg cagcccaccc
407240DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 72tttcgggagg agggagaggg tggggtggcg
ggtgcagact 407340DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 73cctcagccac aaccattagc
tgcaacggtc caggctcgtg 407440DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 74atctctcgcc
atttctgctg aggcctgttc tttttttctt 407540DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 75cccgggcagt cctgggcttg aacgtgtgtg tcagccgcgc
407640DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 76ggaacaaggg gtcttccgag cagcccccag
ccctcccctc 407740DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 77gcaccttccc cgcaggcggt
gggtgagccc tgggagctga 407840DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 78aaggttttca
agaagttaaa ttggaataga aacattttgg 407940DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 79aaatcaattt ctgtttctta agtaatttct tcatgagcat
408040DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 80taggcacttc cacgtggtgt caatccctga
tcactgggag 408140DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 81cagaaactta taaaatattg
ataggcagct tctttgggag 408240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 82ccagcttggg
actatgccca tgagtgcccg gccatgcccg 408340DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 83gcgcccccag agtcccaggc aaagccagca agggccaggc
408440DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 84gttctggagg aattcgtcct cggggaggca
gtgggccagg 408540DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 85tgtcatcccc agcctcatcc
tctcactgtc tcagttttcc 408640DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 86aggactgtct
gtggcattcc ccctgggatc tgaatgatgg 408740DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 87ccggaggaaa aaatctctca tcttttgaag ctatttgaag
408840DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 88atatggtgag tattttgaat atctcataca
attatgccta 408940DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 89gggctgtggt tgtcacccgt
gacgatctgc gtgcatgcca 409040DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 90tactagtgtt
ttcattggta ttaagcttga tgtaatattt 409140DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 91agccaccacg cctggcccag actcagagaa tgaatacaat
409240DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 92gtggcgagaa gcatgaggaa tggagatgga
ggaggagcag 409340DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 93tctcagtttg gctgagaagc
agggtggggg cctgaaccca 409440DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 94caacatagca
agaccccgtc actataaaaa tgaaaaagcc 409540DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 95ccagtgggtg ggagcccggg tggggagggg gcgtgggctc
409640DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 96ttatttttta tggatgtaaa cagcctcttt
gtagtttata 409740DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 97tcctgaaaca agcattaaag
agggaattaa cttaaataaa 409840DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 98ttattgtatt
gaaacatgat tgtgtatcaa atgtgagttt 409940DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 99cttttctttt ataaaggagg actcttttgc ctgatatctg
4010040DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 100cctgaagtct cagtttccat tacattatac
cctcactacc 4010140DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 101cccacccgtg ggtccctggg
ggcctgggat cccagatggt 4010240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 102acggggatga
ggagggcgtg tggtgctatg tggccgggaa 4010340DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 103cctcggattg aagaaagtct ggtactcact ggtggcggta
4010440DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 104gtttaaaaaa ttgtccttta ttgtccaaat
gtctgccttc 4010540DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 105taatgtgtaa tgataggtct
tgtcaaatag tttaataagt 4010640DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 106gagtccgagt
gccgctgact gtcactgcca ccattcatcc 4010740DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 107ctgaatgttg caaatctaaa taaacatgtt ccagaggaga
4010840DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 108gcctttattc
cgtttccact cctccttccc tagttcatcc 4010940DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 109tcaggaaatc ctacagtcca cactccagtc agccccagga
4011040DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 110ccttctcgga tctcaaacga gcaagggtta
acactcatga 4011140DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 111ggggcgcggc ccctcaagtc
cgaggacctc ccttctgggg 4011240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 112agttcctcca
gggcgccctg tggcggcgcc gcctgcacct 4011340DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 113acgaccctat tactctcata acgatgagtc tagcaagtac
4011440DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 114acaaaaaaag gtaactatgt aaagacatat
gttaattagc 4011540DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 115cttcgagaaa ttctgaaaaa
ctgcaaaggt ttgattgtgt 4011640DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 116ctatttgaag
atttgtcatc aaatattgat gcatgatagg 4011740DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 117ttccaggcaa agcagtagcc taagggttta cagctgatga
4011840DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 118cccatccaag gaaaatttag aaaagggaag
gggatgtgta 4011940DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 119gaagtgggag gggtaaaagg
gctataaaaa aaaatctaaa 4012040DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 120ccaatcattg
cacaaacaga aacagctctg acagagaagg 4012140DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 121aatttggagg acaccagtgg catcaggtct cctgtgttgc
4012210DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 122cagctaccat 1012310DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 123caggtaccat 10
* * * * *
References