U.S. patent application number 16/411908 was filed with the patent office on 2020-03-05 for methods for rapid multiplexed amplification of target nucleic acids.
The applicant listed for this patent is ANDE Corporation. Invention is credited to Heidi Susanne Giese, Gregory John Kellogg, Heung Chuan Lam, Richard F. Selden, Eugene Tan, John A. Wright.
Application Number | 20200070173 16/411908 |
Document ID | / |
Family ID | 39591889 |
Filed Date | 2020-03-05 |
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United States Patent
Application |
20200070173 |
Kind Code |
A1 |
Selden; Richard F. ; et
al. |
March 5, 2020 |
METHODS FOR RAPID MULTIPLEXED AMPLIFICATION OF TARGET NUCLEIC
ACIDS
Abstract
A fast, multiplexed PCR system is described that can rapidly
generate amplified nucleic acid products, for example, a full STR
profile, from a target nucleic acid. Such systems include, for
example, microfluidic biochips and a custom built thermal cycler,
which are also described. The resulting STR profiles can satisfy
forensic guidelines for signal strength, inter-loci peak height
balance, heterozygous peak height ratio, incomplete non-template
nucleotide addition, and stutter.
Inventors: |
Selden; Richard F.;
(Lincoln, MA) ; Tan; Eugene; (Arlington, MA)
; Lam; Heung Chuan; (Newton, MA) ; Giese; Heidi
Susanne; (Newburyport, MA) ; Kellogg; Gregory
John; (Cambridge, MA) ; Wright; John A.;
(Billerica, MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
ANDE Corporation |
Waltham |
MA |
US |
|
|
Family ID: |
39591889 |
Appl. No.: |
16/411908 |
Filed: |
May 14, 2019 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15350605 |
Nov 14, 2016 |
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16411908 |
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13040156 |
Mar 3, 2011 |
9494519 |
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15350605 |
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12080746 |
Apr 4, 2008 |
8425861 |
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13040156 |
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60921802 |
Apr 4, 2007 |
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60964502 |
Aug 13, 2007 |
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61028073 |
Feb 12, 2008 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
B01L 2300/0816 20130101;
B01L 2300/0864 20130101; B01L 3/50273 20130101; G01N 27/44791
20130101; G01N 21/6402 20130101; G01N 2021/6441 20130101; B01L
2200/0684 20130101; B01L 2300/0627 20130101; G01N 2201/06113
20130101; B01L 2300/0819 20130101; C12Q 1/686 20130101; B01L
3/502753 20130101; G01N 27/44782 20130101; Y10T 436/2575 20150115;
B01L 2200/147 20130101; B01L 2300/1844 20130101; B01L 2300/069
20130101; B01L 2200/10 20130101; B01L 2300/0654 20130101; B01L
2300/1822 20130101; B01L 2300/16 20130101; G01N 21/6486 20130101;
G01N 21/6428 20130101; C12Q 1/6869 20130101; B01L 2400/0421
20130101; B01L 2300/0887 20130101; B01L 2300/1894 20130101; G01N
27/44726 20130101; B01L 3/502715 20130101; B01L 7/52 20130101; G01N
27/44743 20130101; G01N 21/6452 20130101 |
International
Class: |
B01L 7/00 20060101
B01L007/00; C12Q 1/686 20060101 C12Q001/686; G01N 27/447 20060101
G01N027/447; G01N 21/64 20060101 G01N021/64; C12Q 1/6869 20060101
C12Q001/6869; B01L 3/00 20060101 B01L003/00 |
Claims
1-69 (canceled)
70. A method for simultaneously amplifying of a plurality of loci
in a nucleic acid solution comprising: providing in a single
solutions contained in at least two reaction chambers located in a
biochip, samples having at least ten target nucleic acid loci to be
amplified, with at least ten different primer pairs, each primer
pair hybridizing to one of the at least ten loci to be amplified,
said solution further comprising: (i) one or more buffers; (ii) one
or more salts; (iii) a nucleic acid polymerase; and (iv)
nucleotides; and providing a thermal control system comprised of
(i) a TCE having a first surface in thermal communication with said
at least two reaction chambers, said TCE further comprising a means
for heating and cooling, (ii) at least one thermosensor, (iii) a
controller that receives signals from said at least one
thermosensor and (iv)a power supply, said at least one thermosensor
positioned and configured to measure the effective temperature of
each of the single solutions in the reaction chambers of the
biochip and to provide feedback to the TCE to heat or cool the
solution to set or maintain the solution at a desired temperature;
obtaining, with said controller of the thermal control system, a
target sample solution temperature, from a control algorithm that
stores the target sample temperature, for a sample for a first
sub-step of a plurality of predetermined processing sub-steps, to
be performed on the samples, where in the first sub-step of the
processing step is one of a denaturing, an annealing or an
extending of a replication of a polymerase chain reaction;
obtaining with said controller from said control algorithm, a time
and temperature profile representing a comparison between the
target sample temperature as measured by said thermosensor in
thermal communication with said at least two reaction chambers, and
a plurality of different temperatures for said TCE, wherein the
plurality of different temperatures are different from each other
and different from the target sample temperature and correspond to
different time points, of a predetermined set of time points, of
the first sub-step; identifying, with the controller from said
control algorithm, for a first time point of the different time
points for the first sub-step, a first temperature of the plurality
of different temperatures using the time and temperature profile;
and controlling, with the controller from said control algorithm, a
temperature of the TCE at the first time point of the first
sub-step to be the first temperature, wherein the TCE is in thermal
communication with said at least two reaction chambers and controls
a temperature of said samples.
71. The method of claim 70, further comprising: identifying, for a
second time point of the different time points for the first
sub-step, a second temperature of the plurality of different
temperatures using the time and temperature profile; and
controlling the temperature of the TCE at the second time point of
the sub-step to be the second temperature.
72. The method of claim 71, further comprising: maintaining a
temperature of at least one reaction chamber at approximately a
same temperature for the first and second time points of the
sub-step by changing the temperature of the TCE from the first
temperature at the first time point to the second temperature at
the second time point.
73. The method of claim 71 further comprising: identifying, for at
least one additional time point of the different time points, at
least one additional temperature of the plurality of different
temperatures using the time and temperature profile and the
plurality of different temperatures and the at least one additional
time point; and controlling the temperature of the TCE at the at
least one additional time point of the sub-step to be the at least
one additional temperature.
74. The method of claim 73 wherein the controlling of the
temperature includes gradually changing the temperature from the
second temperature to the at least one additional temperature.
75. The method of claim 73 further comprising: maintaining a
temperature of the at least one reaction chamber at approximately a
same temperature for the first, the second and the at least one
additional time points of the sub-step by changing the temperature
of the TCE from the first temperature at the first time point to
the second temperature at the second time point to the at least one
additional temperature at the at least one additional time
point.
76. The method of claim 75 wherein maintaining the temperature of
the at least one reaction chamber maintains an approximately
constant temperature of the sample.
77. The method of claim 76 wherein the approximately constant
temperature is a temperature from a group consisting of 95 degrees;
59 degrees; and 72 degrees Celsius.
78. The method of claim 70 wherein the processing step is a DNA
sequencing step.
79. The method of claim 70, wherein for each of the denaturing, the
annealing and the extending of replication, the temperature of the
sample is approximately constant.
80. The method of claim 70, further comprising: controlling, with
the controller, the temperature of the TCE to set a temperature of
a reaction chamber at the target sample temperature; measuring with
the at least one thermosensor positioned and configured to measure
the effective temperatures of each of the single solutions in the
reaction chambers, a temperature of the at least two reaction
chambers concurrently with controlling the temperature of the TCE
which results in the temperature of each of the single solutions in
the reaction chambers being at the target sample temperature.
81. The method of claim 70 further comprising: obtaining at least
one additional target sample temperature wherein the time and
temperature profile provides at least one additional target sample
temperature and at least one additional set of temperatures of the
TCE for at least one additional sub-step of the processing step;
identifying, for a time point of the at least one additional
sub-step, a temperature of the at least one additional set of
temperatures using at least one additional time and temperature
profile generated using the at least one additional target sample
temperatures and the at least one set of additional temperatures
and the time point of the at least one additional sub-set; and
controlling the temperature of the TCE at the time point of the at
least one additional sub-set at the at least one additional set of
temperatures.
82. An apparatus comprising: a controller of a thermal control
system configured to: obtain a target sample temperature, from a
controller that stores the target sample temperature, for a sample
for a first sub-step, of a plurality of predetermined sub-steps, of
a processing step, of a plurality of predetermined processing
steps, to be performed on the sample, wherein the first sub-step of
the processing step is one of a denaturing, an annealing or an
extending of a replication of a polymerase chain reaction sub-step;
obtain a time and temperature profile, from the controller wherein
the profile provides a correlation between the target sample
temperature, as measured by a thermosensor in thermal communication
with a reaction chamber, with a target sample temperature applied
to the reaction chamber, and a plurality of different temperatures
for a TCE, wherein the plurality of different temperatures are
different from each other and different from the target sample
temperature and correspond to different time points, of a
predetermined set of time points, of the firsts sub-step; identify,
for a first time point of the different time points for the first
sub-step, a first temperature of the plurality of different
temperatures using a temperature profile between the target sample
temperature and the plurality of different temperatures and the
first time point; and control a temperature of the TCE at the first
time point of the first sub-step to be the first temperature;
wherein the TCE is in thermal communication with a reaction chamber
and controls a temperature of the sample.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of the filing date,
under 35 U.S.C. .sctn. 119(e), of U.S. Provisional Application Ser.
No. 60/921,802 filed 4 Apr. 2007; U.S. Provisional Application Ser.
No. 60/964,502 filed 13 Aug. 2007; and U.S. Provisional Application
Ser. No. 61/028,073 filed 12 Feb. 2008, each of that is hereby
incorporated by reference in its entirety. This application also
incorporates by reference, in their entireties, two U.S. Patent
applications filed on even date herewith; the first entitled
"INTEGRATED NUCLEIC ACID ANALYSIS", Attorney Docket No. 07-801-US;
and the second entitled "PLASTIC MICROFLUIDIC SEPARATION AND
DETECTION PLATFORMS", Attorney Docket No. 07-865-US.
FIELD OF THE INVENTION
[0002] The present invention generally relates to methods for the
rapid amplification of one or more loci within a nucleic acid
sample, as well as thermal cyclers and systems useful for
performing the methods.
BACKGROUND OF THE INVENTION
[0003] The polymerase chain reaction (PCR) is an enzymatic reaction
that facilitates rapid exponential amplification of nucleic acid
sequences in vitro. In forensics, PCR can be utilized to identify
individuals based on the amplification of small regions of the
human genome containing a class of repeated DNA known as Short
Tandem Repeats (STRs). The unit length of a given STR repeat ranges
between 2-10 base pairs, and STRs generally fall within non-coding
and flanking sequences but occasionally within coding regions
(Edwards et al., Am. J. Hum. Genet. 1991, 49, 746-756). There are
several hundred thousand STR loci in the human genome, occurring on
average every 6-10 kb (Beckman and Weber, Genomics 1992, 12,
627-631) and appearing to be highly polymorphic (Edwards et al.,
Trans. Assoc. Am. Physicians 1989, 102, 185-194). STR analysis has
become a major tool in the forensic armamentarium with a growing
set of applications including paternity testing, human
identification in mass disasters, and routine typing of
children.
[0004] While several commercially available STR kits have been
developed for synthesizing the desired PCR products with high
specificity, there are significant areas in which current STR
technologies can be improved. Most importantly, the average time to
complete multiplex PCR using commercial STR typing kits is
approximately 2.14 hours; the time-consuming and labor-intensive
nature of these assays has contributed to backlogs in forensic
laboratories. While the advent of automated instrumentation to
simultaneously process multiple samples has helped to alleviate a
significant bottleneck in typing throughput, the increasing number
of samples to be analyzed will require further acceleration of the
process. Furthermore, there is a need to increase the sensitivity
of STR assays as well as to improve the detection of the amplified
products (Gill, Croat. Med. J. 2001, 42, 229-32). Currently
available STR kits contain nine to sixteen loci and work is
underway in the field to increase the number of loci that can be
detected. Certain applications of STR analysis in the field can be
conducted using 4 or more loci.
[0005] PCR can also be applied in a wide range of clinical
settings. For example, PCR can be utilized to diagnose bacterial
infections such as those caused by Group A Streptococci,
methicillin resistant S. aureus, and vancomycin resistant
Enterococci and is generally more sensitive than culture-based
diagnostic techniques. Fungal infections can be similarly
diagnosed. PCR can be used to diagnose respiratory viruses (e.g.,
respiratory syncytial virus, adenovirus, and influenza and
parainfluenza viruses), .sub.Benito-urinary viruses (e.g., herpes
simplex virus and typing human papilloma viruses), meningitis
(e.g., herpes simplex virus, Epstein-Barr virus, varicella-zoster
virus, and enteroviruses), and hepatitis (e.g., hepatitis B and C).
PCR is also useful in preimplantation genetic diagnosis including
the assessment of aneuploidy as well as the diagnosis of inherited
diseases. From oncology to rheumatology and from hematology to
gastroenterology, it would be difficult to find an area of medicine
not impacted by PCR.
[0006] PCR has also been applied in a variety of non-clinical
settings including veterinary identification (analogous to human
STR typing), veterinary diagnostics, assessment of food safety,
detection of agricultural pathogens and pharmacogenomics. An
application of growing importance concerns the identification of
biological weapons agents in clinical and environmental samples.
Real-time PCR, a close relative of PCR that allows quantitation of
the amount of product present in a reaction following each
amplification cycle, is utilized in essentially the same
applications as PCR itself (see, Espy et al., Clinical Microbiology
Reviews 2006, 19, 1656-256).
[0007] Most commercially available thermal cycling instruments are
limited in that they receive temperature feedback directly from and
control the block temperature as opposed to the PCR solution
temperature. As a consequence, the temperature profile of the
solution, which is critical to the success of the PCR, is likely to
be grossly different from the desired profile. Moreover, much of
the literature on increasing PCR speed and sensitivity has focused
on amplification of one particular locus at a time ("singleplex
assays") and only limited success has been reported in simultaneous
amplification of multiple loci ("multiplex assays") as required for
forensic STR typing, clinical diagnostic and non-clinical
applications. For example, a 160 nL chamber coupled to an
integrated heater has been shown to be capable of amplification and
separation of 4 STRs contained in a Y-STR assay in 80 minutes with
a detection limit of 20 copies of template DNA. (Liu et al., Anal.
Chem. 2007, 79, 1881-1889). Increased PCR sensitivity due to
reduced PCR reaction volume has also been reported for the
PowerlPlex.RTM. 16 System, although no attempt was made to increase
reaction speed (Schmidt et al., Int. J. Legal Med. 2006, 120,
42-48). However, neither report provided for the significantly
shorter amplification times needed in the art. Hopwood et al.,
(International Congress Series 1288 (2006) 639-641) report a one
hundred minute amplification using a set of 11 STR primers. With
respect to clinical diagnostics, a panel of seven common
respiratory viruses was amplified using a nanochip system in a PCR
assay requiring 97.5 minutes (Takahashi et al., J. Clin. Microbiol
2008, doi:10.1128/JCM.01947-07).
[0008] Many of the applications of PCR (and real time PCR) such as
forensic human . identification by STR typing, clinical
diagnostics, and biological weapons agent detection are extremely
time sensitive and many of the applications are best performed in a
multiplex setting. In addition, many of these applications are
utilized in settings in which limited sample is available (e.g., a
small number of pathogens from a clinical or environmental sample
or a small number of human cells from a forensic sample) and
sensitivity of the reaction is critical.
[0009] Notably, Horsman et al., (J. Forensic Sci., 2007, 52,
784-799) Id. at 792 stated that "PCR has been a common pursuit
among analytical microchip researchers, as demonstrated by the
wealth of literature on the topic. However, for forensic DNA
analysis, there remain a number of avenues for development.
Extensive work has not been shown using the commercially available
forensic STR kits or, further, multiple STR amplifications on a
single device. When fully developed, however, microchip PCR will
undoubtedly be a considerable time and cost savings to the forensic
community." Therefore, there exists a need in the art for rapid and
sensitive methods to successfully provide simultaneous
amplification of a plurality of loci within a nucleic acid sample
for a broad range of applications.
SUMMARY OF THE INVENTION
[0010] The instruments, biochips, methods and systems of the
invention provide the capability of heating and cooling a PCR
solution rapidly, controllably, and reproducibly through monitoring
and controlling the thermal cycler based on, at least in part, the
actual temperature of the solution. The inventive instruments,
biochips, methods and systems disclosed herein provide the ability
to monitor and/or accurately control the reaction temperature of a
solution within a biochip to avoid over- or under-heating through
the specific incorporation of thermosensors that are not present in
commercial thermal cyclers. The ability to rapidly heat and cool
reaction solutions to such temperatures allows ramping and settling
times to be minimized and incubation time at the desired
temperature to dominate the total step time. Further, the
instruments, biochips, methods and systems of the invention
provided herein impart the ability to rapidly alter and equilibrate
the temperature of a reaction solution, thereby greatly increasing
the speed at which an amplification reaction may proceed.
[0011] Fast multiplex PCR amplification times as short as seventeen
minutes have been achieved using instruments, biochips, methods and
systems of the invention. Additional time reductions are possible
based on the teachings of this invention. Further, the fast PCR
methods of the invention are effective over a wide dynamic range,
are extremely sensitive and are compatible with a wide range of
commercially available enzymes and reagents. For forensic
applications, the instruments, biochips, methods and systems of the
invention enable significant reductions in the time required to
generate full profiles that satisfy interpretation guidelines for
STR analysis.
[0012] In a first aspect, the invention provides thermal cyclers
comprising a temperature control element (TCE) wherein a first
surface of said TCE is adapted to receive a sample chamber
containing a solution and a sensing chamber containing a
thermosensor, wherein the thermosensor provides feedback to the TCE
to set or maintain the sample at a desired temperature. In a second
aspect, the invention provides thermal cyclers further comprising a
second thermosensor positioned to monitor the temperature of the
first surface of the TCE.
[0013] In a second aspect, the invention provides systems
comprising a biochip comprising one or a plurality of reaction
chambers comprising a portion of the biochip having a volume,
wherein each reaction chamber further comprises a microfluidic
inlet channel and a microfluidic outlet channel, wherein each
reaction chamber is less than 200 .mu.m from a contact surface of
the biochip substrate; the system further comprising a theimal
cycler, comprising a temperature control element (TCE) wherein a
first surface of the TCE is adapted to receive a substrate
containing a sample, and a thermosensor positioned to measure the
temperature of sample in the substrate and provide feedback to the
TCE to set or maintain the sample at a desired temperature said
thermal cycler in thermal communication with the contact surface of
the biochip substrate. In a third aspect, the invention provides
systems comprising a biochip, comprising one or a plurality of
reaction chambers, wherein each reaction chamber comprising a
portion of the biochip having a volume, further comprising a
microfluidic inlet channel and a microfluidic outlet channel,
wherein each reaction chamber is less than 100 .mu.m from a contact
surface of the biochip substrate; and a thermal cycler, comprising
a temperature control element (TCE) wherein a first surface of the
TCE is adapted to receive a substrate containing a sample, and a
thermosensor positioned to measure the temperature of sample in the
substrate and provide feedback to the TCE to set or maintain the
sample at a desired temperature, said thermal cycler in thermal
communication with the contact surface of the biochip
substrate.
[0014] In a fourth aspect, the invention provides methods for
simultaneously amplifying of a plurality of loci in a nucleic acid
solution comprising providing one or a plurality of reaction
chambers wherein each reaction chamber comprises (i) a nucleic acid
solution comprising at least one copy of at least one target
nucleic acid to be amplified; (ii) one or more buffers; (iii) one
or more salts; (iv) a primer set corresponding to each of the
plurality of loci to be amplified; (v) a nucleic acid polymerase;
and (vi) nucleotides, sequentially thermally cycling the
temperature of the nucleic acid solution in each reaction chamber
between a denaturing state, an annealing state, and an extension
state for a predetermined number of cycles at heating and a cooling
rates of about 4-150.degree. C./sec, to yield a plurality of
amplified loci in each reaction chamber in about 97 minutes or
less.
[0015] In a fifth aspect, the invention provides methods for
simultaneously amplifying of a plurality of loci in a nucleic acid
solution comprising providing one or a plurality of reaction
chambers wherein each reaction chamber comprises (i) a nucleic acid
solution comprising at least one copy of at least one target
nucleic acid to be amplified; (ii) one or more buffers; (iii) one
or more salts; (iv) a primer set corresponding to each of the
plurality of loci to be amplified; (v) a nucleic acid polymerase;
and (vi) nucleotides, sequentially theiiiially cycling the
temperature of the nucleic acid solution in each reaction chamber
for a predetermined number of cycles at heating and a cooling rates
of about 4-150.degree. C./sec, to yield a plurality of amplified
loci in each reaction chamber in about 97 minutes or less.
[0016] In a sixth aspect, the invention provides methods for
simultaneously amplifying 5 or more loci in a nucleic acid solution
comprising providing one or a plurality of reaction chambers
wherein each reaction chamber comprises (i) a nucleic acid solution
comprising at least one copy of at least one target nucleic acid to
be amplified; (ii) one or more buffers; (iii) one or more salts;
(iv) a primer set corresponding to the 5 or more loci to be
amplified; (v) a nucleic acid polymerase; and (vi) nucleotides,
sequentially thermally cycling the temperature of the nucleic acid
solution in each reaction chamber between a denaturing state, an
annealing state, and an extension state for a predetermined number
of cycles at heating and a cooling rates of about 4-150.degree.
C./sec, to yield 5 or more amplified loci in each reaction
chamber.
[0017] In a seventh aspect, the invention provides integrated
biochips systems comprising a biochip comprising at least two
reaction chambers in microfludic communication, wherein a first
reaction chamber is in thermal communication with a thermal cycler,
comprising: a temperature control element (TCE) wherein a first
surface of the TCE is adapted to receive a substrate containing a
sample, and a thermosensor positioned to measure the temperature of
sample in the substrate and provide feedback to the TCE to set or
maintain the sample at a desired temperature wherein a contact
surface of the biochip is in thermal communication with the first
surface of the thermal cycler; and a second reaction chamber in
fluid connection with the first reaction chamber and adapted for
nucleic acid extraction, nucleic acid purification, pre-PCR nucleic
acid cleanup, post-PCR cleanup, pre-sequencing cleanup, sequencing,
post-sequencing cleanup, nucleic acid separation, nucleic acid
detection, reverse transcription, pre-reverse transcription
cleanup, post-reverse transcription cleanup, nucleic acid ligation,
nucleic acid hybridization, or quantification, wherein the first
reaction chamber is less than 200 .mu.m from a contact surface of
the biochip.
[0018] Specific preferred embodiments of the present invention will
become evident from the following more detailed description of
certain preferred embodiments and the claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[0019] FIG. 1A is a photograph of an embodiment of the thermal
cycler of the invention.
[0020] FIG. 1B is a photograph showing an embodiment of a 16-lane
microfluidic biochip for use with the thermal cycler shown in FIG.
1A.
[0021] FIG. 2A is a graph showing the temperature profiles of block
and reaction solution for one thermal cycle of the standard STR
cycling protocol described herein (total cycling time: 145.1
minutes).
[0022] FIG. 2B is a graph showing the temperature profiles of block
and reaction solution for one thermal cycle of the fast cycling
protocol described herein (total cycling time: 19.56 minutes).
[0023] FIG. 3 is a graph showing temperature profiles of the heat
pump and the reaction solution for one thea inial cycle for a
thermal cycler of the invention using fast cycling conditions
(total cycling time: 17.3 minutes).
[0024] FIG. 4A is a graph showing the STR profile generated in
biochip reactions according to the invention using 0.5 ng template
DNA.
[0025] FIG. 4B is a graph showing the STR profile generated in tube
reactions according to the invention using 0.5 ng template DNA.
[0026] FIG. 5A is a graph showing the effect of DNA template level
on signal strength in biochip reactions.
[0027] FIG. 5B is a graph showing the effect of DNA template level
on signal strength in tube reactions.
[0028] FIG. 6A is a graph showing the effect of DNA template level
on heterozygous peak height ratio (PHR) in biochip reactions.
[0029] FIG. 6B is a graph showing the effect of DNA template level
on PHR in tube reactions.
[0030] FIG. 7A is a graph showing the effect of DNA template level
on non-template nucleotide addition (NTA) in biochip reactions.
[0031] FIG. 7B is a graph showing the effect of DNA template level
on NTA in tube reactions
[0032] FIG. 8A is a graph showing the effect of DNA template level
on stutter in biochip reactions.
[0033] FIG. 8B is a graph showing the effect of DNA template level
on stutter in tube reactions
[0034] FIG. 9A is a graph showing the profile for biochip (top) and
tube reaction (bottom) generated with the COfiler.TM. primer set
using ing template DNA.
[0035] FIG. 9B is a graph showing the profile for biochip (top) and
tube reaction (bottom) generated with the Identifiler.TM. primer
set using ing template DNA.
[0036] FIG. 10 is a graph showing the profile for an embodiment of
a sequencing reaction, as described in Example 5.
DETAILED DESCRIPTION OF THE INVENTION
[0037] In order to achieve fast multiplexed nucleic acid
amplification, such as PCR, the invention provides thermal cycling
instrumentation, reaction vessels, and reaction conditions that can
be used to amplify a plurality of loci within a target nucleic acid
sample. As is illustrated by the examples provided herein, fast
thermal cycling methods of the invention can be perfoiiiied in
microfluidic biochips using the thermal cycler of the invention and
the methods described herein.
[0038] The methods provided by the invention are capable of rapid
multiplex amplification in applications in addition to those
utilizing the biochips and thermal cyclers described herein. For
example, the use of thin walled tubes in conventional thermal
cyclers (for example block based thermal cyclers and the Roche
LightCycler.TM.) and the use of amplification methods other than
temperature cycled PCR (for example isothermal PCR or rolling
circle amplification) are specifically contemplated.
[0039] The methods, biochips, and thermal cyclers provided by the
invention are capable of amplifying a plurality of loci in under
100 minutes within a given nucleic acid solution present at amounts
of at least 0.006 ng of human genomic DNA (the approximate amount
of DNA in a single nucleated human cell) containing the target
nucleic acid locus or loci). In other embodiments the amplification
occurs in less than 90 min., less than 80 min., less than 70 min.,
less than 60 min., less than 50 min., less than 40 min., less than
30 min., less than 20 min., less that 17.7 min., less than 15 min.,
less than 10 min., or less than 5 min.
[0040] In other embodiments, a plurality of loci within a
bacterial, viral, fungal, animal, or plant-derived genome can be
amplified starting from at least one copy of the target nucleic
acid locus or loci. For example, a sample to be analyzed can
comprise less than 1000 copies, less than 400 copies, less than 200
copies, less than 100 copies, less than 50 copies, less than 30
copies, less than 10 copies or at least 1 copy of a target nucleic
acid prior to the multiplexed amplification reaction. In addition,
less than a single genome equivalent of DNA can be utilized for
amplification if the target nucleic acid locus is present in more
than one copy in the genome. Generally, at least two loci, and up
to approximately 250 loci can be simultaneously amplified within
each target nucleic acid in a sample according to the methods
described herein. Further, at least two loci and up to
approximately 250 loci can be simultaneously amplified in a
plurality of target nucleic acids according to the methods
described herein.
[0041] The target nucleic acids utilized herein can be any nucleic
acid, for example, human nucleic acids, bacterial nucleic acids, or
viral nucleic acids. The target nucleic acid sample can be, for
example, a nucleic acid sample from one or more cells, tissues, or
bodily fluids such as blood, urine, semen, lymphatic fluid,
cerebrospinal fluid, or amniotic fluid, or other biological
samples, such as tissue culture cells, buccal swabs, mouthwashes,
stool, tissues slices, biopsy aspiration, and archeological samples
such as bone or mummified tissue. Target nucleic acids can be, for
example, DNA, RNA, or the DNA product of RNA subjected to reverse
transcription. Target samples can be derived from any source
including, but not limited to, eukaryotes, plants, animals,
vertebrates, fish, mammals, humans, non-humans, bacteria, microbes,
viruses, biological sources, serum, plasma, blood, urine, semen,
lymphatic fluid, cerebrospinal fluid, amniotic fluid, biopsies,
needle aspiration biopsies, cancers, tumors, tissues, cells, cell
lysates, crude cell lysates, tissue lysates, tissue culture cells,
buccal swabs, mouthwashes, stool, mummified tissue, forensic
sources, autopsies, archeological sources, infections, nosocomial
infections, production sources, drug preparations, biological
molecule productions, protein preparations, lipid preparations,
carbohydrate preparations, inanimate objects, air, soil, sap,
metal, fossils, excavated materials, and/or other terrestrial or
extra-terrestrial materials and sources. The sample may also
contain mixtures of material from one source or different sources.
For example, nucleic acids of an infecting bacterium or virus can
be amplified along with human nucleic acids when nucleic acids from
such infected cells or tissues are amplified using the disclosed
methods. Types of useful target samples include eukaryotic samples,
plant samples, animal samples, vertebrate samples, fish samples,
mammalian samples, human samples, non-human samples, bacterial
samples, microbial samples, viral samples, biological samples,
serum samples, plasma samples, blood samples, urine samples, semen
samples, lymphatic fluid samples, cerebrospinal fluid samples,
amniotic fluid samples, biopsy samples, needle aspiration biopsy
samples, cancer samples, tumor samples, tissue samples, cell
samples, cell lysate samples, crude cell lysate samples, tissue
lysate samples, tissue culture cell samples, buccal swab samples,
mouthwash samples, stool samples, mummified tissue samples, autopsy
samples, archeological samples, infection samples, nosocomial
infection samples, production samples, drug preparation samples,
biological molecule production samples, protein preparation
samples, lipid preparation samples, carbohydrate preparation
samples, inanimate object samples, air samples, soil samples, sap
samples, metal samples, fossil samples, excavated material samples,
and/or other terrestrial or extra-terrestrial samples. Types of
forensics samples include blood, dried blood, bloodstains, buccal
swabs, fingerprints, touch samples (e.g., epithelial cells left on
the lip of a drinking glass, the inner rim of a baseball cap, or
cigarette butts), chewing gum, gastric contents, saliva, nail
scrapings, soil, sexual assault samples, hair, bone, skin, and
solid tissue. Types of environmental samples include unfiltered and
filtered air and water, soil, swab samples from surfaces,
envelopes, and powders.
[0042] For example, the methods herein can provide amplified
nucleic acid samples whose analysis yields data suitable for
forensic interpretation, and in particular, data that satisfies
forensic interpretation guidelines. Such guidelines include signal
strength, inter-loci peak height balance, heterozygous peak height
ratio (PHR), incomplete non-template nucleotide addition (NTA), and
stutter (Scientific Working Group on DNA Analysis Methods, Short
Tandem Repeat (STR) Interpretation Guidelines. Forensic Science
Communications, 2000, 2(3)).
[0043] The phrase "fluid communication" as used herein, refers to
two chambers, or other components or regions containing a fluid,
connected together so that a fluid can flow between the two
chambers, components, or regions. Therefore, two chambers that are
in "fluid communication" can, for example, be connected together by
a microfluidic channel between the two chambers, such that a fluid
can flow freely between the two chambers. Such microfluidic
channels can optionally include one or more valves therein which
can be closed or occluded, in order to block and/or otherwise
control fluid communication between the chambers.
[0044] The term "poly(methyl methacrylate) or "PMMA," as used
herein, means the synthetic polymers of methyl methacrylate,
including but not limited to, those sold under the tradenames
Plexiglas.TM., Limacryl.TM., R-Cast.TM., Perspex.TM., Plazcryl.TM.,
Acrylex .TM., ACrylite.TM., ACrylplast.TM., Altuglas.TM.,
Polycast.TM. and Lucite.TM., as well as those polymers described in
U.S. Pat. Nos. 5,561,208, 5,462,995, and 5,334,424, each of which
are hereby incorporated by reference.
[0045] The term "polycarbonate" as used herein means a polyester of
carbonic acid and glycol or a divalent phenol. Examples of such
glycols or divalent phenols are p-xylyene glycol,
2,2-bis(4-oxyphenyl)propane, bis(4-oxyphenyl)niethane,
1,1-bis(4-oxyphenyl)ethane, 1,1-bis(oxyphenyl)butane,
1,1-bis(oxyphenyl)cyclohexane, 2,2-bis(oxyphenyl)butane, and
mixtures thereof, including but not limited to, those sold under
the tradenames Calibre.TM., Makrolon.TM., Panlite.TM.,
Makroclear.TM., Cyrolon.TM., Lexan.TM. and Tuffak.TM..
[0046] As used herein the term "nucleic acid" is intended to
encompass single- and double-stranded DNA and RNA, as well as any
and all forms of alternative nucleic acid containing modified
bases, sugars, and backbones. The term "nucleic acid" thus will be
understood to include, but not be limited to, single- or
double-stranded DNA or RNA (and forms thereof that can be partially
single-stranded or partially double-stranded), cDNA, aptamers,
peptide nucleic acids ("PNA"), 2'-5' DNA (a synthetic material with
a shortened backbone that has a base-spacing that matches the A
conformation of DNA; 2'-5' DNA will not normally hybridize with DNA
in the B form, but it will hybridize readily with RNA), and locked
nucleic acids ("LNA"). Nucleic acid analogues include known
analogues of natural nucleotides that have similar or improved
binding, hybridization of base-pairing properties. "Analogous"
forms of purines and pyrimidines are well known in the art, and
include, but are not limited to aziridinylcytosine,
4-acetylcytosine, 5-fluorouracil, 5-bromouracil,
5-carboxymethylaminomethyl-2-thiouracil,
5-carboxymethylaminomethyluracil, inosine,
N.sup.6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil,
1-methyl guanine, 1-methylinosine, 2,2-dimethylguanine,
2-methyladenine, 2-methylguanine, 3-methylcytosine,
5-methylcytosine, N.sup.6-methyl adenine, 7-methylguanine,
5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil,
beta-D-mannosylqueosine, 5-methoxyuracil,
2-methylthio-N-6-isopentenyladenine, uracil-5-oxyacetic acid
methyles ter, pseudouracil, queosine, 2-thiocytosine,
5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil,
uracil-5-oxyacetic acid, and 2,6-diaminopurine. DNA backbone
analogues provided by the invention include phosphodiester,
phosphorothioate, phosphorodithioate, methylphosphonate,
phosphoramidate, alkyl phosphotriester, sulfamate, 3'-thioacetal,
methylene(methylimino), 3'-N-carbamate, morpholino carbamate, and
peptide nucleic acids (PNAs), methylphosphonate linkages or
alternating methylphosphonate and phosphodiester linkages
(Strauss-Soukup, 1997, Biochemistry 36:8692-8698), and
benzylphosphonate linkages, as discussed in U.S. Pat. No.
6,664,057; see also OLIGONUCLEOTIDES AND ANALOGUES, A PRACTICAL
APPROACH, edited by F. Eckstein, IRL Press at Oxford University
Press (1991); Antisense Strategies, Annals of the New York Academy
of Sciences, Volume 600, Eds. Baserga and Denhardt (NYAS 1992);
Milligan, 1993, J. Med. Chem. 36:1923-1937; Antisense Research and
Applications (1993, CRC Press). The nucleic acids herein can be
extracted from cells or synthetically prepared according to any
means known to those skilled in the art; for example, the nucleic
acids can be chemically synthesized or transcribed or reverse
transcribed from cDNA or mRNA, among other sources.
[0047] The term "via" as used herein means a through-hole formed in
a solid material to allow fluidic connection between the top and
bottom surfaces of the material.
[0048] The terms "locus" and "loci" (plural) as used herein mean
one or more specific positions on one or more nucleic acids (e.g.,
one or more chromosomes), as defined herein.
[0049] The terms "STR locus" and "STR loci" as used herein means a
nucleotide sequence consisting of a repeating pattern of two or
more nucleotides at a given locus of a target nucleic acid. The
repeating pattern can range in length from 2 to 10 base pairs (bp),
and is typically in the non-coding intron region.
[0050] According to one aspect of the invention, a thermal cycler
is provided having the capability of heating and cooling a reaction
solution rapidly, controllably, and reproducibly. An example of an
embodiment of the thermal cycler of the invention is shown in FIG.
1A. The ability to rapidly heat and cool the reaction solution
temperatures allows ramping and settling times to be minimized and
incubation time at the desired temperature to dominate the total
step time, enabling minimization of multiplex cycling times.
[0051] High heating and cooling rates can be achieved by utilizing
a temperature control element (TCE), either alone or in fluid
communication with a heat sink. A TCE comprises a means for heating
and cooling, a thermosensor, a controller that receives signals
from the thennosensor, and a power supply. In a preferred
embodiment, a first surface of the TCE can be adapted to receive a
sample chamber containing a solution and a sensing chamber
containing an additional thermosensor. In this setting, the
thermosensor is positioned within the sensing chamber mounted to
the TCE such that it simulates the conditions within the sample
chamber. This sensing chamber is fabricated such that it has the
same material stack-up as the sample chamber. A thermocouple
mounted within the temperature sensor is embedded in the structure
at an analogous position to that of the sample in the sample
chamber. This sensor reports the effective temperature of the
solutions in the sample chamber. Commercially-available Type-T or
Type-K thermocouples (from Omega Engineering, Stamford, Conn.) are
most applicable but other types of thermocouple and thermosensor
may be used including thermisters, semiconductors, and infrared.
The thermosensor within the sensing chamber provides feedback to
the TCE to set or maintain the sample at the desired temperature.
In this way, the sample temperature can be measured indirectly and
controlled without inserting a thermosensor into the reaction
chamber itself. Alternatively, a thermosensor can be placed
directly into the reaction chamber and used to set and maintain
sample temperature, eliminating the need for the sensing chamber.
As one skilled in the art will appreciate, other types of sensors
such as pressure sensors may be utilized according to the teachings
of this invention.
[0052] The first surface of the TCE can be adapted to accept an
essentially flat substrate by, for example, forming a recess in the
first surface for accepting a substrate (e.g., a biochip, infra).
Alternatively, the TCE can be adapted to accept one or more
thin-walled tubes, defined as tubes with wall diameters with
regions less than 200 .mu.m thick. Preferably, the heat sink is a
high efficiency heat sink, such as, but not limited to, fan-cooled
heat sinks with copper bases and cooling fins. More preferably, the
heat sink can be a fan cooled copper base and fins having a thermal
resistance of about 0.4.degree. C./W or less. A particular and
non-limiting example of a high efficiency heat sink is
E1U-N7BCC-03-GP (Coolermaster, Taiwan ROC).
[0053] The thermal cycler of the invention may further comprise a
thermosensor positioned to monitor the temperature of the first
surface of the TCE. Additional thermosensors can be added as
desired to achieve further improvement in sample temperature
control. The supplementary temperatures that can be monitored
include those on multiple regions on and within the substrate,
multiple regions on and within the heat sink, cooling air input and
output, sample input and output, and ambient.
[0054] Good thermal communication between the TCE and the heat sink
is desired. When the two mating surfaces are properly prepared,
intimate physical contact is sufficient to provide adequate thermal
transfer between the two components. Thermal interface materials
(TIMs) between the TCE and heat sink can be used to enhance thermal
coupling. Such TIMs include but are not limited to adhesives,
greases, phase-change materials (PCMs), metal thermal interface
materials, ceramic thermal interface materials, soft metal alloys,
indium, alumina nano-layer coatings, submicron films, glycol,
water, oils, antifreeze, epoxy compounds, and others. Specific
examples include Arctic Silver or Ceramique (Arctic Silver,
Visalia, Calif.; compounds that have thermal resistances of
<0.007.degree. C.-in.sup.2/W), compressible heat spring HSD4
(Indium Corp, Utica, N.Y.), HITHERM (GrafTech International
Holdings Inc., Lakewood, Ohio), or directly bonding of the TCE to
the surface of the heat sink. Thermal contact can be further
enhanced by physical clamping the components together with a
average force of more than 2 psi, or more than 5 psi, or more than
10 psi, or more than 30 psi, or more than 60 psi or more than 100
psi or more than 200 psi, or by direct bonding of the surfaces.
[0055] Thermal transfer between the TCE and a substrate in contact
therewith can be increased with respect to block thermal cyclers,
such as the Eppendorf Mastercycler.TM. ep gradient S thermal cycler
(which provide heat energy via a silver block with high thermal
conductivity and low specific heat capacity), by placing the
substrate directly on the TCE. Suitable TCEs include, but are not
limited to, a high heating and cooling capacity heat pump, and high
power output Peltier devices; examples of Peltier devices are
9500/131/150B (Ferrotec, Bedford N.H.), XLT2393 (Marlow, Dallas
Tex.). When utilized as a part of the TCE for thermal cyclers of
the invention, Peltier devices are advantageously powered by an
H-bridge. An example of an H-bridge device is the 5R7-001 (Oven
Industries).
[0056] When Peltier devices are used as a part of the TCE for
thermal cyclers of the invention, it is advantageous to power the
Peltier devices by an H-bridge with pulse width modulation for
heating and cooling. Temperature feedback from the thermosensor
which measures the sample temperature drives the TCE to set and
maintain the desired sample temperature. Closed-loop temperature
control algorithms for control of the TCE include, but are not
limited to, PID control and fuzzy logic control.
[0057] Said thermal controllers comprise a control algorithm that
provides the capacity for rapid transition from one target
temperature state to another target temperature state. This
transition can be divided into 3 distinct phases. In phase 1, there
is a large difference between the actual temperature and target
temperature (for example 1 to 20.degree. C. or higher). In this
phase, ramping takes place at or near the maximum rate of the TCE
device. In phase 2, the transition phase, the actual temperature
and target temperature are closer (less than approximately 1 to
20.degree. C.). In this case the controller must reduce the power
to the TCE in order to prevent overshoot of the solution
temperature and allow for rapid achievement of target temperature
with minimal deviations and oscillations. In phase 3, the target
temperature has been achieved and the controller moderates power to
the thermal cycler to maintain the solution within a narrow range
about the target temperature. Measurement of the temperature with
the sensor provides more accurate feedback of the actual
temperature and also allows the temperature of the TCE surface
temperature to be overdriven. Each of the above 3 phases may be
further subdivided into multiple sub-phases to provide for faster
response time, more accurate temperature control, increased
stability, and increased tolerance to external variability.
[0058] In one example, the temperature of the substrate can be
measured by placing a thin thermocouple into a channel on the
substrate surface. In another example, the second thermosensor can
be housed in an enclosure, formed from essentially the same
material as the substrate being utilized, that holds the second
thermosensor essentially the same distance from the TCE as a
reaction chamber on a substrate in contact with the TCE. Such a
second thermosensor can generally be separate from the substrate
(i.e., a stand-alone sensor), and can be placed next to the
substrate on the first surface of the TCE.
[0059] The heat sink may, optionally, further comprise a variable
speed cooling fan and/or a second heating element for controlling
the temperature of the heat sink, where each additional element of
the heat sink is in communication with the second control element.
This allows the cooling efficiency of the heat sink to be adjusted,
in particular to keep the heat sink temperature essentially
constant and independent of environmental temperature changes. The
heater can also precondition the heat sink to essentially the
operating temperature.
[0060] To facilitate thermal coupling of a reaction solution in a
substrate and the TCE, uniform thermal communication of a contact
surface of the substrate with the first surface of the TCE can be
provided by applying a force to the substrate to secure it thereto
while the thermal cycler is in operation. Such forces are
preferably applied by means that only temporarily hold the
substrate to the first surface of the TCE and can be readily
removed upon completion of theimal cycling. For example, a chip
compression element (CCE) can be situated above the first surface
of the TCE to allow the substrate to be placed between. The chip
compression element can then be engaged to hold the substrate in
place during operation of the thermal cycler, and released to allow
removal of the substrate. Proper integration of the CCE, TCE and
heat sink allows the CCE to improve thermal coupling between and
among all three of these components.
[0061] The portion of the CCE in contact with a substrate can be
formed from a low thermal mass insulating material, including, but
not limited to, a foam, for example WF71 Rohcell foam (Inspec
foams, Magnolia, Ariz.). For embodiments discussed herein the
Rohacell is preferred. It has a specific heat capacity of 1.4-1.6
(J/gK) [or less thermal mass] and a thermal conductivity of 0.0345
W/mK (or less).
[0062] Biochip compression elements include, but are not limited
to, one or more clamps, springs, compressible foam, or a
pressurized air bladder which can be inflated to provide force to
hold the substrate onto the first surface of the TCE. Preferably,
the chip compression element provides a substantially uniform force
of about 5 to about 250 psia to a surface of the substrate, and
more preferably, about 20 to about 50 psia to hold the substrate to
the first surface of the TCE. Notably, thermal communication
between the contact surface of the biochip substrate and the TCE
can be provided in the absence of a thermal coupling solutions such
as thermal grease or glycol, although such can be utilized as
necessary.
[0063] The biochip compression elements provide a force on the
biochip-thermoelectric cooler-heat sink. This force serves to
ensure good thermal contact and hence heat transfer between the
biochip and the top surface of the TCE.
[0064] In one embodiment, the low thermal mass insulator is an air
bladder and is utilized to provide the low thermal mass and
insulating properties. In another embodiment, the low thermal mass
insulator is a foam pad. The clamping force can be applied to the
foam pad by a pneumatic cylinder, or closed cell foam pads under
compression or air pressure from an air bladder. In the latter
case, the air bladder provides both the insulation and the
compressive force.
[0065] As described above, the thermal cycler can have a heating
and/or cooling rate at the first surface of the TCE surface about
4-150.degree. C. per second, and preferably about 8-150.degree.
C./sec, and more preferably about 10-150.degree. C./sec. The
thermal cycler can also have a heating or cooling rate at a
solution within a reaction chamber of a substrate in uniform
thermal communication with the first surface of the TCE (e.g., a
biochip) of about 4-150.degree. C. per second and preferably about
8-150.degree. C./sec, and more preferably about 10-150.degree.
C./sec. Further, the thermal cycler of the invention can have a
temperature stability of +/-1.0.degree. C., and preferably
+/-0.50.degree. C., and more preferably +/-0.25.degree. C.
[0066] Biochip
[0067] An embodiment of a biochip (i.e., a substrate for use with
the thermal cycler of the invention) according to another aspect of
the invention is shown for the sake of illustration in FIG. 1B as
having 16 microfluidic systems, each comprising an inlet and an
outlet in fluid communication with each of the reaction chambers
formed within the biochip. However, such disclosure is not intended
to be limiting, rather, one skilled in the art will readily
recognize that the biochip can contain alternate numbers of
microfluidic systems (infra) including biochips with one system and
biochips with two or more systems. The term "plurality" as used
herein, means two or more, four or more, eight or more, 16 or more,
32 or more, 48 or more, 64 or more, 96 or more, 128 or more, or
2-16, 2-32, 2-48, 2-64, 2-96, 2-128, 8-128, 8 - 64, or 8-32
microfluidic channels.
[0068] The biochip can comprise a substrate layer and a cover
layer, where a portion of one or a plurality of microfluidic
systems, comprising grooves and/or shaped depressions, are
patterned into the substrate layer. A series of vias (i.e., through
holes and/or inlets or outlets) can be formed in the cover layer to
provide fluidic access to the microfluidic channels and reaction
chambers, and can be located at any location about the biochip.
Alternatively, vias can be formed in the substrate layer instead of
the cover layer to achieve the same functionality. The top surface
of the substrate layer can be bonded with the bottom surface of the
cover layer to complete the microfluidic systems. Techniques for
fabricating polymer-based microfluidic systems are reviewed
extensively by Becker and Gartner (Becker, 2000, Electrophoresis
21, 12-26 and Becker, 2008, Electrophoresis 390, 89), which are
hereby incorporated by reference in its entirety. Biochips can be
fabricated using materials such as unsaturated, partially
unsaturated or saturated cyclic olefin copolymers "COC",
unsaturated, partially unsaturated, or saturated cyclic olefin
polymers "COP", poly(methyl) methacrylate "PMMA", polycarbonate
"PC", polypropylene "PP", polyethylene "PE", polyetheretherketone
"PEEK", poly(dimethylsiloxane) "PDMA", polyimide "PI". It is
important to select a plastic with a glass transition temperature
greater than that of the maximal temperature to be utilized in the
amplification reaction. Any number of these processes and materials
can be used to fabricate the biochips described herein. In
particular, the biochips can be prepared by injection molding of a
plastic substrate, for example, a COC or COP based polymers
(currently sold under the tradenames Topas.TM., Zeonex.TM.,
Zeonor.TM., and Apel.TM.. In this fabrication methodology, an
injection mold and mold insert consisting of the negative of the
features to be formed is fabricated by machining and subsequent
surface polishing. Together, the mold and insert allow the
substrate layers to be fabricated and the formed substrate to
comprise the channels, reaction chamber features and vias. The
substrate and cover layers can be diffusion bonded by the
application of heat and pressure.
[0069] Alternatively, the biochips can be prepared by hot embossing
of thin thermoplastic films with a master die of the negative of
the structure to be produced. The master die can be prepared by
using electroforming to replicate the device prepared in a solid
substrate. The solid substrate can be glass sheets that are
patterned by standard photolithographic and chemical etching
methods known to those skilled in the art. The substrate and cover
layers are diffusion bonded by the application of heat and
pressure.
[0070] The substrate and cover layers of the biochip can be
constructed from a variety of plastic substrates including, but not
limited to, polyethylene, poly(acrylates) (e.g., poly(methyl
methacrylate)), poly(carbonate)s, and unsaturated, partially
unsaturated or saturated cyclic olefin polymers (COP), or an
unsaturated, partially unsaturated, or saturated cyclic olefin
copolymers (COC). The thickness of plastic substrate and cover
layers utilized in the present process is kept thin to minimize the
mass thereof to thereby maximize thennal transfer between the
thermal cycler and the reaction solution contained in each reaction
chamber during their use. The plastic substrate and cover layers
can each, independently, have a thickness of less than 2 mm, less
than 1 mm, less than 750 .mu.m, less than 650 .mu.m, less than 500
.mu.m, less than 400 .mu.m, less than 300 .mu.m, less than 200
.mu.m, or less than 100 .mu.m; or plastic substrate and cover
layers can each, independently, comprise a plastic having a
thickness ranging from 25-2000 .mu.m, 25-1000, 25-750 .mu.m, 25-650
mm, 25-500 .mu.m, 25-400 .mu.m, 25-300 .mu.m, 25-200 .mu.m, or
25-100 .mu.m. Preferably, at least one of the substrate and cover
layers has a thickness of less than about 200 .mu.m to maximize
thermal transfer to the reaction solution contained in the reaction
chambers of the biochip. More preferably, a contact surface of the
biochip which is in contact with the first surface of the TCE has a
thickness of less than about 200 .mu.m.
[0071] Each reaction chamber can be foimed to have a volume of, for
example, less than 100 .mu.L. Preferably, each reaction chamber has
a volume of less than about 50 .mu.L, or less than about 40 .mu.L,
or less than about 30 .mu.L, or less than about 25 .mu.L, or less
than about 20 .mu.L, or less than about 15 .mu.L, or less than
about 10 .mu.L, or less than about 5 .mu.L or less than about 1
.mu.L, or less than about 0.1 .mu.L. Alternatively, each reaction
chamber can be formed to have a volume ranging from about 0.1 .mu.L
to about 100 L. Preferably, each reaction chamber has a volume
ranging from about 0.1 .mu.L to about 10 .mu.L or about 10 .mu.L to
about 50 .mu.L. The reaction chambers are generally not coated with
a polymer or silane coating. Reaction chambers may be designed to
have an inlet and an outlet channel. Alternatively, a single
channel may be used for inlet and outlet.
[0072] The biochip design of the invention leverages the benefits
of microfluidics including having a high surface to volume ratio
and reduced diffusion times to maximize heat transfer, and uniforni
heating and cooling. The use of microfluidic technology also
provides benefits with respect to a fully-integrated forensic
analysis instrument. Further, biochips fabricated by diffusion
bonding, and without the use of adhesives to bond the various
layers (e.g. COC layers), were tested and demonstrated to be
capable of withstanding from 100 to 1500 psi of pressure before
failure based on the requirements of the desired application. For
example, the biochips of the present invention withstand 450 psi,
sufficient for the desired thermal cycling applications.
[0073] It is noted that the specific embodiments of the biochips of
the invention set forth herein substantially lack any heating
elements integrated into the biochip for heating and/or cooling the
reaction chambers. Thermal cycling of the reaction chambers on the
biochip is provided externally, for example, by the thermal cycler
of the invention. Heating elements can be integrated into the
biochips of the present invention, however.
[0074] In operation, one portion of the biochip can receive one or
more reaction solutions, each independently comprising one or more
reagents (e.g., for PCR) and or nucleic acid samples, through one
or more inlets in fluid communication with one or more reaction
chambers formed within the biochip. Simultaneous amplification of a
plurality of samples can be performed by injecting each of the
nucleic acid samples in a separate separation reaction chamber. An
injector for simultaneously injecting a plurality samples into the
plurality of sample or buffer wells can be provided with the
biochip to enable simultaneous multiple sample amplification. Such
injectors provide, for example, one sample of the plurality of
samples to one reaction chamber of the plurality of reaction
chambers. Injectors can introduce the samples to the channels
according to any methods known to those skilled in the art, for
example, by electrophoretic transport, pneumatic actuation or
liquid actuation through a needle or tube or channel that connects
the sample to the reaction chamber.
[0075] Following amplification (and optionally, nucleic acid
extraction and quantification) the amplified nucleic acid product
can be passed (e.g., to a Genebench-FX.TM. 100) through one or more
outlets in fluid communication with the reaction chambers for
fragment separation and generation of STR profiles.
[0076] The relatively low cost of plastic manufacture allows the
biochips of the invention to be disposable, eliminating the labor
required to reuse the biochip and essentially eliminating the
possibility of contamination. A single-use disposable would be
particularly advantageous for low copy number analyses in that no
possibility of contamination (other than initial sample collection)
would exist. In settings where neither contamination nor labor are
major considerations, reusable plastic and glass biochips may be
utilized.
[0077] Integration Methods
[0078] Using microfluidics allows fabrication of features to
perform more than one function on a single biochip. These functions
can include nucleic acid extraction, nucleic acid purification,
pre-PCR nucleic acid cleanup, post-PCR cleanup, pre-sequencing
cleanup, sequencing, post-sequencing cleanup, nucleic acid
separation, nucleic acid detection, reverse transcription,
pre-reverse transcription cleanup, post-reverse transcription
cleanup, nucleic acid ligation, nucleic acid hybridization and
quantification. Two or more of these functions can be connected
microfluidically to enable sequential processing of a sample; this
coupling is termed integration.
[0079] One form of microfluidic DNA extraction can be achieved by
inserting a purification medium between an input and output
channel. This purification medium can be silica fiber based and use
chaotropic-salt reagents to lyse the biological sample, expose the
DNA and bind the DNA to the purification media. The lysate is then
transported via the input channel through the purification medium
to bind the DNA. Bound DNA is washed by an ethanol based buffer to
remove contaminants. This can be accomplished by flowing wash
reagents via the input channel through the purification membrane.
Bound DNA is then eluted from the membrane by flowing an
appropriate low salt buffer (see, e.g., Boom, U.S. Pat. No.
5,234,809) via the input channel through the purification membrane
and out the output channel.
[0080] One approach to DNA quantification in a microfluidic foimat
is based upon real-time PCR. In this method of quantification, a
reaction chamber is fabricated between an input and output channel.
The reaction chamber is coupled to a thermal cycler and an optical
excitation and detection system is coupled to the reaction chamber
to allow fluorescence from the reaction solution to be measured.
The amount of DNA in the sample is correlated to the intensity of
the fluorescence from the reaction chamber per cycle (see, e.g.,
Heid et al., Genome Research 1996, 6, 986-994).
[0081] For further infoiivation about integration in microfluidic
formats, see the U.S. Patent application entitled "INTEGRATED
NUCLEIC ACID ANALYSIS" filed on even day herewith (Attorney Docket
No. 07-801-US), which is hereby incorporated by reference in its
entirety. For further information about separation and detection in
microfluidic formats see the U.S. Patent application entitled
"Plastic Microfluidic Separation and Detection Platfoinis" filed on
even day herewith (Attorney Docket No. 07-865-US which is hereby
incorporated by reference in its entirety.
[0082] Microfluidic drives of the invention are means for
transporting fluids within the reaction chambers of the integrated
biochips. One type of microfluidic drive is effected by
incorporated a membrane pump which transports the fluid by
sequential application of positive and negative pressure to the
membrane. Alternatively, a positive displacement pump can be
connected to the input of the microfluidic chamber. A displacement
of the pump forces the fluid through the microfluidic channel.
[0083] Integration can make use of microfluidic valves to gate
fluid flow within the biochip. Valving can be accomplished with
passive or active structures. Passive valving structures include
capillary valves that stop fluid flow by utilizing capillary
pressure. Fluids can flow through the capillary valving structure
by the application of a pressure that is sufficiently large enough
to overcome the capillary forces. Active valving structures include
membrane valves which use flexible or semi-rigid structures at a
point between two channels. The application of pressure on the
membrane causes it to close the channel. The application of a
vacuum to the membrane lifts it from the channel, allowing passage
of fluids.
[0084] Amplification Methods
[0085] In yet another aspect, the invention provides methods for
simultaneously amplifying a plurality of nucleic acid loci in one
or more target nucleic acids via rapid polymerase chain reaction
(PCR). Such methods comprise providing one or a plurality of
reaction solutions to one or a plurality of reaction chambers,
wherein each reaction solution comprises (i) at least one copy of
at least one target nucleic acid, wherein each target nucleic acid
is the same or different and each target nucleic acid independently
comprises a plurality loci to be amplified; (ii) one or more
buffers; (iii) one or more salts; (iv) a primer set corresponding
to the plurality of loci to be amplified; (v) a nucleic acid
polymerase; and (vi) nucleotides. Each of the reaction solutions,
for example, each of the target nucleic acids, can be the same or
different as necessary, for example, to run multiple simultaneous
analyses on the same nucleic acid sample, or to simultaneously run
multiple nucleic acid samples.
[0086] Each reaction chamber may be contained within a biochip of
the invention as described above or thin-walled reaction tubes.
Thin-walled reaction tubes preferably have a wall thickness of less
than about 200 .mu.m. Preferably, thin-walled reaction tubes
preferably have a wall thickness of less than about 100 .mu.m.
[0087] Primers for PCR amplification are oligonucleotide sequences
that are specifically designed to hybridize to loci of the target
DNA. These primers serve as starting points for polymerase
extensions. To facilitate analysis of amplified fragments, labeled
primers can also be used in PCR reactions. Labeled primers are
oligonucleotide sequences that are coupled to a detectable moiety;
a non-limiting example thereof is a fluorescent dye. When PCR is
carried out with fluorescently labeled primers, amplicons with a
fluorescent label are generated. The methods for performing fast
PCR are compatible with both labeled and unlabeled primers, and
fast multiplexed PCR have been demonstrated.
[0088] Primer sets can be any known to those skilled in the art for
the amplification of a plurality of loci with a target nucleic
acid, as described above. For example, primers useful in
amplification of one or more loci in a human nucleic acid sample
are described in U.S. Pat. No. 5,582,989; U.S. Pat. No. 5,843,660;
U.S. Pat. No. 6,221,598; U.S. Pat. No. 6,479,235; U.S. Pat. No.
6,531,282; and U.S. Pat. No. 7,008,771; and US Patent Application
Publication Nos. 2003/0180724; 2003/0186272; and 2004/0137504, each
of which are hereby incorporated by reference.
[0089] Further, primers useful in amplification of one or more loci
in a viral nucleic acid sample are described in, for example, U.S.
Pat. No. 7,312,036; U.S. Pat. No. 6,958,210; U.S. Pat. No.
6,849,407; U.S. Pat. No. 6,790,952, and U.S. Pat. No. 6,472,155,
each of which are hereby incorporated by reference.
[0090] Examples of primers useful in amplification of one or more
loci in a bacterial nucleic acid sample are described in U.S. Pat.
No. 7,326,779; U.S. Pat. No. 7,205,111; U.S. Pat. No. 7,074,599;
U.S. Pat. No. 7,074,598; U.S. Pat. No. 6,664,080; and U.S. Pat. No.
5,994,066, each of which are hereby incorporated by reference.
[0091] Salts and buffers include those familiar to those skilled in
the art, including those comprising MgCl.sub.2, and Tris-HCl and
KCl, respectfully. Buffers may contain additives such as
surfactants (e.g., Tweens), dimethyl sulfoxide (DMSO), glycerol,
bovine serum albumin (BSA) and polyethylene glycol (PEG), as well
as others familiar to those skilled in the art. Nucleotides are
generally deoxyribonucleoside triphosphates, such as deoxyadenosine
triphosphate (dATP), deoxycytidine triphophate (dCTP),
deoxyguanosine triphosphate (dGTP) and deoxythymidine triphosphate
(dTTP) are also added to the synthesis mixture in adequate amount
for amplification of the target nucleic acid.
[0092] The solutions can be optionally heated to and held at a
first temperature for a first period of time suitable for hot-start
activation of the nucleic acid polymerases. Generally, the first
period of time is less than about 90 seconds. The first temperature
can be about 95 to about 99.degree. C. Polymerases with hot start
mechanisms that can be activated in 60 seconds or less include
those utilizing antibody mediated hot-start and aptmer mediated hot
start mechanisms. Alternatively, hot-start polymerases need not be
utilized in the present invention.
[0093] Subsequently, the temperature of the reaction solutions are
sequentially cycled between a denaturing state, an annealing state,
and an extension state for a predetermined number of cycles.
Generally, the one or a plurality of reaction solutions are cooled
from the denaturing state to the annealing state at a first cooling
rate of about 1 to about 150.degree. C./sec, or about 1 to about
100.degree. C./sec; or about 1 to about 80.degree. C./sec; or about
1 to about 60.degree. C./sec; or about 1 to about 40.degree.
C./sec; or about 1 to about 30.degree. C./sec; or about 1 to about
20.degree. C./sec; about 4 to about 150.degree. C./sec, or about 4
to about 100.degree. C./sec; or about 4 to about 80.degree. C./sec;
or about 4 to about 60.degree. C./sec; or about 4 to about
40.degree. C./sec; or about 4 to about 30.degree. C./sec; or about
4 to about 20.degree. C./sec; or about 10 to about 150.degree.
C./sec; or about 10 to about 100.degree. C./sec; or about 10 to
about 80.degree. C./sec; or about 10 to about 60.degree. C./sec; of
about 10 to about 40.degree. C./sec; or about 10 to about
30.degree. C./sec; or about 10 to about 20.degree. C./sec. The one
or a plurality of reaction solutions can be heated from the
annealing state to the extension state at a first heating rate of
about 1 to about 150.degree. C./sec, or about 1 to about
100.degree. C./sec; or about 1 to about 80.degree. C./sec; or about
1 to about 60.degree. C./sec; or about 1 to about 40.degree.
C./sec; about 1 to about 30.degree. C./sec; about 1 to about
20.degree. C./sec; 4 to about 150.degree. C./sec, or about 4 to
about 100.degree. C./sec; or about 4 to about 80.degree. C./sec; or
about 4 to about 60.degree. C./sec; or about 4 to about 40.degree.
C./sec; about 4 to about 30.degree. C./sec; about 4 to about
20.degree. C./sec; or about 10 to about 150.degree. C./sec; or
about 10 to about 100.degree. C./sec; or about 10 to about
80.degree. C./sec; or about 10 to about 60.degree. C./sec; of about
10 to about 40.degree. C./sec; or about 10 to about 30.degree.
C./sec; or about 10 to about 20.degree. C./sec; and/or the one or a
plurality of reaction solutions are heated from the extension state
to the denaturing state at a second heating rate of about 1 to
about 150.degree. C./sec, or about 1 to about 100.degree. C./sec;
or about 1 to about 80.degree. C./sec; or about 1 to about
60.degree. C./sec; or about 1 to about 40.degree. C./sec; about 1
to about 30.degree. C./sec; about 1 to about 20.degree. C./sec;
about 4 to about 150.degree. C./sec, or about 4 to about
100.degree. C./sec; or about 4 to about 80.degree. C./sec; or about
4 to about 60.degree. C./sec; or about 4 to about 40.degree.
C./sec; about 4 to about 30.degree. C./sec; about 4 to about
20.degree. C./sec; or about 10 to about 150.degree. C./sec; or
about 10 to about 100.degree. C./sec; or about 10 to about
80.degree. C./sec; or about 10 to about 60.degree. C./sec; of about
10 to about 40.degree. C./sec; or about 10 to about 30.degree.
C./sec; or about 10 to about 20.degree. C./sec. Finally, the
reaction solutions are held at a final state to provide one or a
plurality of ampli tied nucleic acid products.
[0094] Denaturing states can range generally include from about 90
to 99.degree. C. for times ranging from about 1 to 30 seconds. The
actual times and temperatures are enzyme, primer and target
dependent. For the Applied Biosystems (AB) multiplexed STR kit for
amplifying human genomic DNA, about 95.degree. C. for about 5 sec.
being preferred.
[0095] The annealing temperature and time influence the specificity
and efficiency of primer binding to a particular locus within a
target nucleic acid and are particularly important for multiplexed
PCR reactions. The correct binding of a complete set of primer
pairs during the annealing step can allow production of multiplexed
amplification of a plurality of loci, for example, one or a
plurality of full STR profiles with acceptable PHR and inter-locus
signal strength balance. For a given primer pair, annealing states
can range from about 50.degree. C. to 70.degree. C. and times from
about 1 to 30 seconds. The actual times and temperatures are
enzyme, primer, and target dependent. For the AB multiplexed STR
kit for amplifying human genomic DNA, about 59.degree. C. for 15
seconds is preferred.
[0096] Extension temperature and time primarily impact the allele
product yield and are an inherent property of the enzyme under
study. It should be noted that the extension rates reported by the
manufacturer are often provided for singleplex reactions; extension
rates for multiplex reactions can be much slower. For a given
enzyme, extension states can range from about 60 to 75.degree. C.
and times from about 1 to 30 seconds. The actual times and
temperatures are enzyme, primer, and target dependent. For the AB
multiplexed STR kit for amplifying human genomic DNA, about
72.degree. C. for about 5 seconds is preferred. Preferably, for
continuing a predetermined number of cycles, the reaction solution
is heated from the extension state to the denaturing state at a
third rate of about 1 to about 150.degree. C./sec, or about 1 to
about 100.degree. C./sec; or about 1 to about 80.degree. C./sec; or
about 1 to about 60.degree. Clsec; or about 1 to about 40.degree.
C./sec; or about 1 to about 30.degree. C./sec; or about 1 to about
20.degree. C./sec; 4 to about 150.degree. C./sec, or about 4 to
about 100.degree. C./sec; or about 4 to about 80.degree. C./sec; or
about 4 to about 60.degree. C./sec; or about 4 to about 40.degree.
C./sec; or about 4 to about 30.degree. C./sec; or about 4 to about
20.degree. C./sec; or about 10 to about 150.degree. C./sec; or
about 10 to about 100.degree. C./sec; or about 10 to about
80.degree. C./sec; or about 10 to about 60.degree. C./sec; of about
10 to about 40.degree. Clsec; or about 10 to about 30.degree.
C./sec; or about 10 to about 20.degree. C./sec. Generally, the
predetermined number of cycles is chosen to be about 10 to about 50
cycles, although fewer or more cycles may be used as necessary.
[0097] Final extension times can be reduced significantly until
incomplete NTA begins to increase. For a given enzyme, final
extension temperatures can range from about 60 to 75.degree. C. and
times from about 0 to 300 seconds. The actual times and
temperatures are enzyme, primer, and target dependent. For the AB
multiplexed STR kit for amplifying human genomic DNA, about
72.degree. C. for about 90 seconds is preferred.
[0098] In addition to the 3-step thermal cycling approach set forth
above, this process is also amenable to 2-step thermal cycling
approaches. In this approach, the reaction solutions are
sequentially cycled between a denaturing state, and an
annealing/extension state for a predetermined number of cycles.
This approach utilizes primers designed to anneal at the extension
temperature, allowing the annealing and extension steps to share
the same temperature. The reduced number of temperature transition
results in a further reduction in the cycle time.
[0099] In certain embodiments, a plurality of amplified nucleic
acid products can be obtained in about 5 to about 20 minutes. In
certain other embodiments, a plurality of amplified nucleic acid
products can be obtained in about 5 to 10 minutes, about 1 to 5
minutes, or less than 5 minutes. Each amplified nucleic acid
product can be generated starting from less than about 10 ng of a
target nucleic acid. Preferably, amplified nucleic acid products
can be generated starting from less than about 5 ng or less than
about 2 ng of nucleic acid, or less than about 1 ng of nucleic
acid, or less than about 0.5 ng of nucleic acid, or less than about
0.2 ng of nucleic acid, or less than about 0.1 ng of nucleic acid,
or less than about 0.05 ng of nucleic acid, or less than about
0.006 ng of nucleic acid.
[0100] In other embodiments, such as the identification of
biological weapons agents in clinical or environmental samples or
the diagnosis of bacterial, viral, or fungal infections in humans,
plants, and animals, amplified nucleic acid products can be
generated starting from at least one copy of a target nucleic acid.
For example, a sample to be analyzed can comprise less than 1000
copies (e.g., 1-1000 copies), less than 400 copies, less than 200
copies, less than 100 copies, less than 50 copies, less than 30
copies, less than 10 copies or 1 copy of a target nucleic acid
prior to the multiplexed amplification reaction.
[0101] In addition, less than a single genome equivalent of DNA can
be utilized for amplification if the target nucleic acid locus is
present in more than one copy in the genome.
[0102] In any of the preceding methods, the theiinal cycling can be
perfoimed for a predetermined number of cycles to achieve
sufficient amplification of the loci in the target nucleic acid as
can be readily deteiiuined by one skilled in the art. For example,
the predetermined number of cycles can range between about 10 and
about 50 cycles, and preferably between about 20 and 50 cycles.
Further, in any of the preceding methods, at least 2 loci of one or
a plurality of nucleic acids can be simultaneously amplified.
Depending on the desired application, greater than four, 5 to 10,
10 to 20, 20 to 30 or about 10 to 250 loci are simultaneously
amplified For example, for amplification of STR loci, 10-20 loci
may be preferred.
[0103] Preferably, the temperature of the reaction solutions is
cycled by a thermal cycler of the invention (supra). While it can
be possible to utilize commercial block thermal cyclers for fast
thermal cycling by the compensating for lagging response of the PCR
solution by setting the block temperature higher than the desired
solution temperature on heating steps and setting the block
temperature lower than the desired solution temperature on cooling
steps, this mode of operation is cumbersome to implement as the
temperature setpoints required to compensate for the slow ramping
response must be determined empirically. Furtheiniore, as feedback
and control are still performed by the block and no monitoring of
the solution temperature takes place, the repeatability and
reproducibility of the profile can be influenced by external
factors including the changes in the room temperature. Hence, the
temperature profile of the solution is not reproducible.
[0104] Many commercially available polymerases can be adapted for
use in fast PCR applications using the approaches described here.
Typically, the nucleic acid polymerase has an extension rate of at
least 100 bases/sec. A large number of polymerases available for
PCR amplification including Therms aquaticus (Taq), Pyrococcus
furiosus (Pfu), Pyrococcus woesei (Pwo), Thermas flavus (Tfl),
Themus thermophilus (Tth), Therms litoris (Tli) and Thermotoga
maritime (Tma). These enzymes, modified version of these enzymes,
and combination of enzymes, are commercially available from vendors
including Roche, Invitrogen, Qiagen, Strategene, and Applied
Biosystems. Representative enzymes include PHUSION (New England
Biolabs, Ipswich , Mass.), Hot MasterTae.TM. (Eppendorf), PHUSION
Mpx (Finnzymes), PyroStart (Fermentas), KOD (EMD Biosciences),
Z-Taq (TAKARA), and CS3AC/LA (KlenTaq, University City , Mo.). A
widely used enzyme for PCR amplification for STR typing is the Taq
polymerase, and the TaqGold variant is supplied with the
Identifiler.TM., Profiler.TM., and COfiler.TM. kits.
[0105] In certain embodiments, the PCR conditions presented here
can generate full STR profiles from a human target nucleic acid
with high efficiency, although production of a full profile is not
required. A full profile for autosomal STR can comprise loci such
as amelogenin, D8S1179, D21S11, D7S820, CFSIPO, D3S1358, TH01,
D13S317, D16S539, D2S1338, D19S433, vWA, TPDX, D18S51, D5S818, FGA,
or a plurality thereof. Other STR loci including mini-STRs, and
Y-STR analysis. The criteria for optimization of the protocols
include the generation of full profiles, signal strength, dynamic
range, inter-locus signal strength balance, PHR, incomplete NTA,
stutter, and total cycle time.
[0106] According one embodiment, protocols using the SpeedSTAR
enzyme and the thermal cycler of the invention can reduce the total
cycling time for biochip and tube reactions to 17.3 and 19.1 min
respectively, to generate full STR profiles. In the protocol, the
denaturing state is about 98.degree. C. for about 4 seconds, the
annealing state is about 59.degree. C. for about 15 seconds, the
extension state is about 72.degree. C. for about 7 seconds, and the
final state is about 70.degree. C. for about 90 seconds.
[0107] In certain embodiments, the total cycling time for at least
10, 20, or 30 multiplexed PCR cycles can range from about 1 minute
to about 90 minutes. Preferably, total cycling time for at least
10, 20, or 30 multiplexed PCR cycles ranges from about 1 minute to
about 90 minutes; or from about 1 minute to about 85 minutes; or
from about 1 minute to about 80 minutes; or from about 1 minute to
about 75 minutes; or from about 1 minute to about 70 minutes; or
from about 1 minute to about 65 minutes; or from about 1 minute to
about 60 minutes; or from about 1 minute to about 55 minutes; or
from about 1 minute to about 50 minutes; or from about 1 minute to
about 45 minutes; or from about 1 minute to about 40 minutes; or
from about 1 minute to about 35 minutes; or from about 1 minute to
about 30 minutes; or from about 1 minute to about 25 minutes; or
from about 1 minute to about 20 minutes; or from about 1 minute to
about 15 minutes; or from about 1 minute to about 10 minutes or
from about 1 minute to about 5 minutes. In other embodiments, the
total cycling time for at least 10, 20, or 30 multiplexed PCR
cycles is less than about 90 minutes. Preferably, the total cycling
time for at least 10, 20, or 30 multiplexed PCR cycles is less than
about 89, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 25, 20,
15, 10, 5, 4, 3, 2, or 1 minute.
[0108] The invention contemplates an integrated biochip comprising
one or a plurality of microfluidic systems, for performing the
multiplexed PCR amplification of a plurality of loci within a
nucleic acid sample as well as at least one other sample
preparation and/or analysis method within the same biochip
platform. For example, within each microfluidic system on a
biochip, each having a flow direction from an inlet port to an
outlet port, the system can comprise a plurality of reaction
chambers, wherein a first reaction chamber of the plurality of
reaction chambers is in fluid communication with the inlet port,
and an ultimate reaction chamber of the plurality of reaction
chambers is in fluid communication with the outlet port, and at
least one microchannel fluidly connecting each consecutive pair of
reaction chambers along the flow direction. At least one reaction
chamber in each microfluidic system can be less than 200 .mu.m from
a contact surface of the biochip substrate to facilitate thermal
communication with a thermal cycler of the invention for performing
multiplexed PCR within said reaction chamber.
[0109] Each of the remaining reaction chambers within each of the
microfluidic systems of the biochip can be adapted for nucleic acid
extraction, nucleic acid purification, nucleic acid hybridization,
nucleic acid ligation, pre-PCR nucleic acid cleanup, post-PCR
cleanup, pre-sequencing cleanup, sequencing, post-sequencing
cleanup, separation and detection, reverse transcription,
pre-reverse transcription cleanup, and/or post-reverse
transcription cleanup, electrophoretic separation, nucleic acid
detection. The term "cleanup" as used herein means the removal of
reaction components (including anions, cations, oligonucleotides,
nucleotides, preservatives, enzymes, or inhibitors) that may
interfere with any of the reaction chamber processes listed
above.
[0110] The Examples which follow are illustrative of specific
embodiments of the invention, and various uses thereof. They set
forth for explanatory purposes only, and are not to be taken as
limiting the invention.
EXAMPLES
Example 1
Custom Thermal Cycler and Microfluidic Biochip
[0111] A thermal cycler of the invention, as shown in FIG. 1A, was
used to perform fast cycling by allowing the PCR reaction solution
temperatures to be heated and cooled rapidly, controllably, and
reproducibly. This instrument accepts a 16-chamber microfluidic
biochip and consists of a high output thermoelectric cooler/heater
mounted to a high efficiency heat sink. Each of 16 PCR reaction
solutions was placed into an individual chamber of the microfluidic
biochip, coupled to the heat pump by applying a 0.2 MPa of
compressive pressure with a clamping mechanism. FIG. 1B shows a
photograph of the 16-sample disposable plastic microfluidic
biochip. Each PCR chamber is 500 .mu.m deep and approximately 1 mm
wide and holds 7 .mu.l of PCR reaction solution.
[0112] Instrumentation and Temperature Profiles
[0113] In the following examples, all amplification reactions in
tubes were performed with an Eppendorf Mastercyler.TM. ep gradient
S (Eppendorf North America, Westbury, N.Y.). Block temperature
profiles of the above instrument were obtained using a 127 .mu.m
diameter type K thermocouple sensor which was attached directly to
the block. For reaction solution profiles a 127 .mu.m diameter type
K thermocouple sensor was placed in the 20 .mu.L reaction solution,
within a thin-walled PCR tube. Data acquisition was performed with
an Omega HH506RA Multilogger thermometer set to acquire data at a
rate of 100 Hz.
[0114] Amplification reactions in biochips were perfoimed using the
thermal cycler of Example 1 with 16-sample plastic biochips as the
reaction vessels. The solution temperature within the microfluidic
biochip was monitored by inserting a thermocouple into a sensing
chamber within the biochip.
[0115] PCR --Reaction Mix Components and Cycling Conditions
[0116] Multiplex PCR reactions were performed with the
AmpFCSTR.RTM. Profiler Plus.RTM. ID PCR Amplification Kit (Profiler
Plus ID kit) (Applied Biosystems, Foster City, Calif.) using 9947A
genomic DNA (Promega, Madison, Wis.) as a template. Polymerases
used for amplification were either AmpliTaq Gold.RTM. DNA
Polymerase (TaqGold.TM.) supplied with the Profiler Plus ID kit or
other polymerases: SpeedSTAR HS DNA Polymerase (SpeedSTAR) (Takara
BIO USA Inc., Madison, Wis.), KOD Hot Start DNA Polymerase (KOD)
(EMD Biosciences Inc., Gibbstown, N.J.), or PyroStartmi Fast PCR
Master Mix (PyroStart) (Fermentas Inc., Glen Burnie, Md.).
Multiplex PCRs with other polymerases were carried out using the
labeled multiplex primer set from the Profiler Plus ID kit.TM. in
combination with the polymerase specific buffers and dNTPs. All
tube PCRs were carried out in 0.2 mL thin-walled PCR tubes
(Eppendorf North America, Westbury; NY) using the Eppendorf
Mastercyler.TM. ep gradient S. All biochip reactions were amplified
in the thermal cycler of FIG. 1A using 16-sample biochips.
[0117] The following PCR reaction mixtures were prepared and used
for thermal cycling:
[0118] Standard TaqGold.TM. reactions:
[0119] Standard TaqGold.TM. multiplex reactions consisted of 9.55
.mu.L Profiler Plus ID reaction mix, 1 ng 9947A genomic DNA, 5
.mu.L Profiler. Plus ID Primer set and 2.25 U TaqGold.TM. in a 25
.mu.L reaction volume. Cycling conditions (block temperatures and
times) were chosen following the manufacturers recommendations and
set to an initial 95.degree. C. for 11 min (hot start) followed by
28 cycles of 1 min at 94.degree. C. (denaturing), 1 min at
59.degree. C. (annealing), 1 min at 72.degree. C. (extension) and a
final extension of 45 min at 60.degree. C. Optimized TaqGold.TM.
reactions:
[0120] TaqGold.TM. reactions optimized for fast cycling were
carried out in a 10 .mu.L reaction volume containing 3.82 .mu.L
Profiler Plus ID reaction mix, 1 ng 9947A genomic DNA, 2 .mu.L
Profiler Plus ID Primer set and 0.9 U TaqGold.TM.. Reactions were
cycled at 95.degree. C. for 11 min, 28 cycles 10 s, 98.degree. C.;
45 s, 59.degree. C.; 30 s, 72.degree. C. and a final extension of
15 min at 72.degree. C.
SpeedSTAR Tube Reactions:
[0121] SpeedSTAR PCR mix components for tube PCR were: 2 .mu.L
Profiler Plus ID primer set, 9947A genomic DNA, lx Fast Buffer I
(Takara BIO USA Inc., Madison, Wis.), 200 .mu.M dNTPs and 0.315 U
SpeedSTAR in a 10 .mu.L reaction volume. Cycling conditions for
fast performance were set to: 1 min at 95.degree. C. (enzyme
activation) followed by 28 cycles of 4 s at 98.degree. C., 15 s at
59.degree. C., 5 s at 72.degree. C. and a 1 min at 72.degree. C.
final extension.
SpeedSTAR Biochip Reactions:
[0122] For biochip PCR the 7 .mu.L reaction mix contained 1.4 .mu.L
Profiler Plus ID primer set, 9947A genomic DNA, 1.times. Fast
Buffer I buffer, 200 .mu.M dNTPs and 0.42 U SpeedSTAR. Cycling
parameters were set to 70 s at 95.degree. C., 28 cycles of 4 s,
98.degree. C.; 15 s, 59.degree. C.; 7 s, 72.degree. C. and a final
extension of 1:30 min at 70.degree. C.
KOD Reactions:
[0123] Amplification with KOD were perfoiiiied with 2 .mu.L
Profiler Plus ID primer set, lx KOD buffer (EMD Biosciences Inc.,
Gibbstown, N.J.), 200 .mu.M dNTPs, 1 ng 9947A genomic DNA, 1.5 mM
MgSO.sub.4, 0.2 U KOD in a 10 .mu.L reaction volume. Cycling
conditions were: 2 min, 95.degree. C. followed by 28 cycles of 4 s,
98.degree. C.; 30 s, 59.degree. C.; 10 s, 72.degree. C. with a
final extension of 1 min, 72.degree. C.
PyroStart Reactions:
[0124] Reaction mixtures with PyroStart in a lx final concentration
also contained 2 .mu.L Profiler Plus ID primer set and 1 ng 9947A
genomic DNA in a 10 .mu.L reaction and were cycled at: 1 min,
95.degree. C. and 28 cycles of 4 s, 98.degree. C.; 20 s, 59.degree.
C.; 30 s, 72.degree. C. followed by a final extension of 1 min at
72.degree. C.
Multiplex PCR with Other STR Typing Kits:
[0125] The suitability of SpeedSTAR to generate full. STR profiles
with other STR typing kits (AmpFCSTR.RTM. Identifier.RTM.
(Identifiler), AmpFlSTR.RTM. COfiler.RTM. PCR Amplification Kit
(COfiler), (Applied Biosystems) was tested in tube and biochip with
the reaction conditions as described above for SpeedSTAR with the
Profiler Plus ID kit. In these reactions, the Profiler Plus ID
primer sets were replaced with the primer set from each of the
kits.
[0126] Reproducibility
[0127] Reproducibility studies in tube and biochip were performed
with TaqGold.TM. and SpeedSTAR using ing 9947A genomic DNA as a
template. For tube reproducibility 5 individual reactions were
prepared. Biochip reproducibility was determined in 3 biochip PCR
runs with 8 reactions each.
[0128] Sensitivity
[0129] Sensitivity studies for SpeedSTAR amplification in tube and
biochip were performed using the following amounts of 9947A
template DNA: In tube: 4 ng, 2 ng, 1.5 ng, 1 ng, 0.5 ng, 0.25 ng,
0.125 ng, 0.1 ng, 0.05 ng, 0.03 ng, 0.02 ng, 0.01 ng, 0.006 ng; in
biochip: 4 ng, 2 ng, 1.5 ng, 1 ng, 0.5 ng, 0.25 ng, 0.1 ng, 0.05
ng, 0.025 ng, 0.02 ng, 0.015 ng, 0.01 ng, 0.006 ng. The reactions
at each template level were performed in duplicate.
[0130] STR Separation and Detection Instrumentation
[0131] Amplified products were separated and detected using the
Network Biosystem Genebench-FX.TM. Series 100 (Pyzowski and Tan,
Advances in Biochip-Based Analysis: A Rapid Field-Based Approach
59th Annual Meeting of the American Academy of Forensic Sciences
San Antonio, Tex., Feb. 19-24, 2007). This instrument was developed
and optimized specifically for STR analysis. To 2.7 .mu.L of each
amplified product 10.2 .mu.L formamide and 0.1 .mu.L of Genescan
500 LIZ internal lane standard (both Applied Biosystems, Foster
City, Calif.) were added. After denaturation at 95.degree. C. for 3
min and snap cooling on ice, samples were loaded into the
separation chip and electrophoretically moved into the separation
channels by applying a 350 V/cm electric field for 90 seconds. This
was followed by the application of a 150 V/cm electric field along
the separation channel to separate the DNA fragments. All
separations were carried out at 50.degree. C.
[0132] Data Analysis
[0133] Data was analyzed with the GeneMarker.RTM. HID STR Human
Identification Software, Version 1.51 (SoftGenetics LLC, State
College, PA). Signal strengths were noimalized to the internal lane
standard and the percentages of stutter, incomplete NTA as well as
PHR were determined. PHR is calculated by dividing the lower signal
strength allele by the higher signal strength allele within the
locus. The level of incomplete NTA is calculated by dividing the
signal strength of the template fragment (-A) by the signal
strength of the adenylated fragment (+A).
Example 2
Temperature Profiles of Thermal Cycling Instruments and Reaction
Solutions in Conventional PCR Tubes and Microfluidic Biochips
[0134] Amplification reactions were performed in thin-walled PCR
tubes using a commercial thermal cycler and in microfluidic
biochips using the theiival cycler of Example 1. For tube
reactions, the Eppendorf Mastercyler.TM. was utilized. FIG. 2A
shows the temperature of the block and the reaction solution within
a tube for one of the 28 thermal cycles using a conventional STR
cycling protocol. The Mastercycler.TM. heating and cooling system
is based on a heat pump with an integrated block for tube
insertion. The time and temperature setpoints are 1 minute at
98.degree. C. for denaturation, 1 minute at 59.degree. C. for
annealing, and 1 minute at 72.degree. C. for extension. A
comparison of the temperature profiles for the heat block and the
reaction solution shows a lag in the response of the solution
temperature relative to the block temperature. The measured heating
and cooling rates of the block are 5.6.degree. C./sec and
4.9.degree. C./sec and of the solution are 4.8.degree. C./sec and
3.3.degree. C./sec. The block makes the temperature transition from
extension (72.degree. C.) to denaturation (98.degree. C.) in 14
seconds, but the solution does not achieve the setpoint temperature
for 39 seconds. Transitions between the denaturation and annealing
steps (59.degree. C.) take 10 and 27 seconds and between the
annealing and extension steps take 7 and 24 seconds for the block
and solution respectively.
[0135] The temperature profiles of the Eppendorf Mastercyler.TM.
block and the reaction solution for one of the 28 thermal cycles
under fast cycling conditions are shown in FIG. 2B. The time and
temperature setpoints are 5 seconds at 98.degree. C. for
denaturation, 15 seconds at 59.degree. C. for annealing, and 5
seconds at 72.degree. C. for extension. However, the delayed and
dampened response of the solution prevents it from achieving the
desired setpoint temperatures.
[0136] The temperature profiles of the heat pump and the reaction
solution for one of the 28 themial cycles for the thermal cycler of
the invention using fast cycling conditions were also determined
(FIG. 3). For the determination of the reaction solution
temperature, a sensing chamber within the biochip was used. The
time and temperature setpoints are 4 seconds at 95.degree. C. for
denaturation, 15 seconds at 59.degree. C. for annealing, and 7
seconds at 72.degree. C. for extension. The measured heating and
cooling rates of the heat pump are 21.5.degree. C./sec and
21.7.degree. C./sec, and the measured heating and cooling rates of
the reaction solution are 14.8.degree. C./sec and 15.4.degree.
C./sec.
[0137] Accordingly, the thermal cycler of the invention is capable
of heating and cooling the reaction solution at a rate that is 3 to
5 times faster than the commercial block-based cycler. The
transition times between extension, denaturation, and annealing
steps for the heat pump are 1.7, 2.1, and 0.7 seconds and for the
solution 2.7, 4.5, and 2.2 seconds. The thermal cycler of the
invention allows the reaction solution to reach the required
temperatures approximately 7-fold faster than the block-based
cycler, resulting in defined and controlled incubation temperatures
and times under fast cycling conditions.
Example 3
Evaluation of PCR Enzymes in Tubes
[0138] A large number of polymerases were evaluated for potential
use for fast, multiplexed. STR analysis, and candidates were
selected based in part on hot-start activation time and extension
rate. The reported properties of the four polymerases selected for
experimental evaluation compared with recommended conditions for
TaqGold.TM. are presented in Table 1(A).
TABLE-US-00001 TABLE 1 A - Reported Polymerase characteristics
Polymerase ATG SpeedSTAR PyroStart KOD 3'-5' Exonuclease activity
No Yes, <20% No Yes Generation of 3'-dA Yes Yes, >80% Yes No
overhangs Hot Start mechanism Chemical Antibody Chemical Antibody
modified modified Initial activation 95.degree. C./ 95.degree. C./
95.degree. C./ 95.degree. C./ 11 min 1 min 1 min 2 min Elongation
rate 16.67 100-200 40 100 [nucleotides/sec] B - Optimized
performance of polymerases in tube reactions Standard ATG Optimized
ATG SpeedSTAR Cycling 95.degree. C./11 min 95.degree. C./11 min
95.degree. C./1 min conditions 94.degree. C./1 min 98.degree. C./10
sec 98.degree. C./4 sec 59.degree. C./1 min {close oversize
bracket} .times.28 59.degree. C./45 sec {close oversize bracket}
.times.28 59.degree. C./15 sec {close oversize bracket} .times.28
72.degree. C./1 min 72.degree. C./30 sec 72.degree. C./5 sec
60.degree. C./45 min 72.degree. C./15 min 72.degree. C./1 min
Amplification 145.1 min 71.67 min 19.13 min time Signal Strength
561-1655 600-3876 945-3669 range [RFU] Stutter range 4.18-11.16%
3.91-13.77% 6.49-13.56% NTA range 1.54-7.67% 1.93-20.13%
3.07-19.68% PHR 0.88-0.93% 0.74-0.96% 0.83-0.93% B - Optimized
performance of polymerases in tube reactions PyroStart KOD Cycling
95.degree. C./1 min 95.degree. C./2 min conditions 98.degree. C./4
sec 98.degree. C./4 sec 59.degree. C./20 sec {close oversize
bracket} .times.28 59.degree. C./30 sec {close oversize bracket}
.times.28 72.degree. C./30 sec 72.degree. C./10 sec 72.degree. C./1
min 72.degree. C./1 min Amplification 33.12 min 29.47 min time
Signal Strength 751-3197 1091-3494 range [RFU] Stutter range
6.21-16.91% 4.46-23.61% NTA range 3.01-23.09% PHR 0.71-0.94%
0.61-0.94%
[0139] The evaluated enzymes have reported extension rates ranging
from approximately 15-200 nucleotides/second; in general, the
reported extension rates are based on singleplex amplifications and
may be somewhat lower for multiplex applications.
[0140] PCR conditions in tubes were initially investigated for
these four enzymes with the goal of achieving full STR profiles in
the least amount of time. For all reactions, 1 ng of human genomic
DNA was amplified using primer pairs from the Profiler Plus ID kit
and vendor recommended buffers and enzyme concentrations, and
resulting profiles were separated, detected, sized, and quantified
using Genebench-FX.TM. Series 100. Various times and temperatures
for the denaturation, annealing, and extension steps were
deteimined to give total times for PCR amplification with signal
strengths suitable for STR interpretation ranging from 19.13
minutes for SpeedSTAR to 71.7 minutes for TaqGold.TM. [Table 1(B)].
Method conditions of the invention allow amplification to be
performed 2-10 fold more rapidly than recommended conditions for
TaqGold.TM..
[0141] Further evaluation of the enzymes for forensically relevant
performance includes signal strength, levels of stutter and
incomplete NTA and PHR [Table 1(B)]. All enzymes are capable of
performing highly multiplexed amplification using the Profiler Plus
ID primers. Signal strengths for SpeedSTAR, Pyrostart, KOD, and
optimized TaqGold.TM. reactions are all either approximately the
same or higher than those generated using standard TaqGold.TM. PCR
conditions.
[0142] With respect to incomplete NTA, both SpeedSTAR and PyroStart
as well as optimized TaqGold.TM. reactions exhibited levels that
are up to three times higher than that of standard TaqGold.TM.
reactions. For most alleles, levels fall below the 15%
interpretation threshold. Those alleles having higher levels of
incomplete NTA can be decreased to below the 15% interpretation
threshold as discussed below. The KOD polymerase possesses 3'-5'
exonuclease activity and does not generate fragments with
A-overhangs; accordingly, all alleles were 1 nucleotide shorter
than their allelic ladder counterpart.
[0143] The relative levels of stutter observed for optimized
TaqGold.TM., SpeedSTAR and PyroStart reactions are similar to the
range of stutter produced with standard TaqGold.TM. reactions; the
range of stutter generated with KOD is slightly higher than the
stutter for standard TaqGold.TM..
Example 4a
Fast PCR Protocol Using SpeedSTAR Polymerase in Tubes and
Biochips
[0144] Based on the results presented above, the SpeedSTAR
polymerase was selected for further evaluation in biochips with the
goal of minimizing the total cycling time and achieving full STR
profiles that satisfy signal strength, PHR, incomplete NTA and
stutter interpretation requirements.
[0145] The time and temperature setpoints for amplification using
SpeedSTAR in the microfluidic 16-sample biochip on the thermal
cycler of the invention are 70 seconds 95.degree. C. for hot-start
activation followed by 28 cycles of 4 seconds at 95.degree. C. for
denaturation, 15 seconds at 59.degree. C. for annealing, and 7
seconds at 72.degree. C. for extension. A final extension of 90
seconds at 72.degree. C. is performed for a total protocol time of
17.3 minutes. Tube reactions in the Eppendorf Mastercycler were
performed in 19.13 minutes comprising of block times and
temperatures set to an initial activation time of 1 minute at
95.degree. C., 28 cycles of 4 seconds at 98.degree. C., 15 seconds
at 59.degree. C. and 5 seconds at 72.degree. C. followed by a final
extension of 1 minute at 72.degree. C.
[0146] FIGS. 4A and 4B show STR profiles generated with the
preceding SpeedSTAR cycling conditions in (FIG. 4A) 7 .mu.L biochip
and (FIG. 4B) 10 .mu.L tube reactions using 0.5 ng of DNA and Table
2 presents signal strengths for all Profiler Plus ID alleles from
the SpeedSTAR biochip and tube reactions as well as TaqGold.sup.rm
in tubes using the standard protocol. Signal strengths of the 0.5
ng SpeedSTAR biochip reactions are on average approximately 2 times
higher than those of the Ing standard TaqGold.TM. reactions, while
the signal strengths of the 0.5 ng SpeedSTAR tube reactions are on
average approximately the same as those of the TaqGold.TM.
reactions.
TABLE-US-00002 TABLE 2 Comparison of signal strength, PHR, NTA and
stutter for SpeedSTAR biochip and tube reactions and ATG standard
reactions SpeedSTAR biochip reaction SpeedSTAR tube reaction Signal
Stutter Signal Stutter Locus Allele strength PHR NTA (%) (%)
strength PHR NTA (%) (%) D3S1358 14 1404.218 0.79 9.08 727.11 0.81
9.74 D3S1358 15 1110.915 8.05 10.35 895.12 10.50 8.14 vWA 17
2338.633 0.95 6.14 1346.81 0.65 6.62 vWA 18 2216.64 6.83 12.87
875.84 6.78 11.96 FGA 23 747.5319 0.87 4.21 877.22 0.96 2.54 FGA 24
648.8992 3.34 9.72 840.03 2.30 8.32 Amelogenin X 5645.423 4.04
1324.78 2.02 D8S1179 13 3784.38 5.62 10.70 1012.17 5.47 11.56
D21S11 30 2008.992 3.15 13.05 787.70 3.45 13.29 D18S51 15 1655.991
0.70 6.90 11.44 924.04 0.72 5.48 9.09 D18S51 19 1157.636 9.53 14.13
663.76 8.92 13.90 D5S818 11 2904.473 7.56 9.65 1608.46 3.97 8.73
D13S317 11 3906.373 3.32 6.78 1867.36 3.21 7.74 D7S820 10 1232.908
0.93 7.23 647.24 0.73 8.01 D7S820 11 1149.849 10.16 7.37 469.59
10.00 5.96 Standard ATG reactions Signal strength PHR NTA (%)
Stutter Locus Allele Average STDEV Average STDEV Average STDEV
Average STDEV D3S1358 14 831.69 167.25 0.92 0.04 1.88 0.52 D3S1358
15 802.99 141.78 1.54 0.34 5.31 0.23 vWA 17 765.61 83.69 0.90 0.08
4.22 0.44 vWA 18 736.85 88.40 4.23 0.19 7.38 0.48 FGA 23 735.41
130.32 0.93 0.05 2.14 0.45 FGA 24 727.02 122.82 1.98 0.44 7.19 0.43
Amelogenin X 1655.65 343.77 3.35 0.49 D8S1179 13 1405.57 105.18
4.52 0.58 6.51 0.62 D21S11 30 1280.31 81.30 3.00 0.66 7.33 0.60
D18S51 15 879.42 137.76 0.88 0.05 4.68 0.74 7.89 0.80 D18S51 19
814.14 125.75 5.95 0.68 11.16 0.52 D5S818 11 1599.08 223.78 3.71
0.17 4.94 0.44 D13S317 11 1486.50 196.47 2.33 0.28 4.18 0.47 D7S820
10 634.96 113.82 0.89 0.08 4.69 0.99 D7S820 11 561.37 92.47 7.67
0.72 4.57 0.62
Example 4b
Allele Characterization of Fast PCR Using SpeedSTAR Polymerase in
Tubes and Biochips
[0147] In order to characterize the products of fast PCR reactions
from Example 4a, quantification of PHR, incomplete NTA and stutter
was performed. Biochip and tube reactions using the SpeedSTAR
polymerase show more inter-locus peak height imbalance compared to
that for the TagGold.TM. reactions. The PHR for alleles generated
in biochip reactions is between 0.70 and 0.95 and is approximately
the same in tubes; all fall within acceptable interpretation
guidelines. Reactions using SpeedSTAR have PHR that are
approximately 10% lower than those determined for standard
TaqGold.TM. reactions. Similarly, the level of incomplete NTA for
most alleles in both biochip and tube reactions using SpeedSTAR are
approximately the same (2.0 and 10.6%); both are approximately 2
times higher than for TaqGold.TM. control reactions. The exception
is incomplete NTA for the D3S1358 alleles, which is 4.8 to 7 times
higher with SpeedSTAR than with TaqGold.TM.; even in this case, the
level of incomplete NTA is below 12% for the SpeedSTAR enzyme.
Finally, the level of stutter in both biochip and tube based
reactions using SpeedSTAR is between approximately 6.0 and 14.1%,
on average approximately 1.6-fold higher than that for standard
TagGold.TM. tube reactions.
[0148] The microfluidic biochip reactions using 0.5 ng template DNA
generate signal strengths that are approximately 2 times higher
than those for standard TaqGold.TM. reactions using 1 ng template.
This result suggests that the SpeedSTAR enzyme in the biochip and
the TaqGold.TM. enzyme in the conventional reaction act with
similar efficiencies; the DNA concentration in the biochip is
approximately 1.8-fold that in the tube, which corresponds to the 2
fold greater in signal strength. In contrast, the fast tube based
reactions are less efficient than the control TaqGold.TM.
reactions; the approximately 40% reduction in product yield is
likely the consequence of the poor cycling profile that results
when commercial thermal cyclers are used for fast thermal cycling.
Even in this circumstance, signal strengths are well over the
levels required for interpretation and can be raised significantly
by increasing the extension time by a few seconds per cycle (data
not shown). Repeatability and reproducibility of the signal
strength for fast PCR reactions in biochips and tubes are similar
to those in conventional reactions.
[0149] The inter-locus allele signal strength for the fast biochip
and tube reactions shows a higher level of imbalance as compared to
the TaqGold.TM. reaction. The inter-loci signal strength balance is
influenced by numerous factors including primer concentration,
annealing temperature and time, and molecular weight of the loci.
The STR amplification kit used for these experiments has a set of
primer concentrations that are optimized for the TaqGold.TM. enzyme
and the recommended cycling protocols. The signal strengths of the
loci can be modified by adjusting the primer concentrations
utilized in the amplification reactions (Henegariu et al.,
Biotechniques 1997, 23, 504-11).
[0150] The relationship between signal strength and template level
for fast biochip and tube reactions is as expected with signal
strength generally increasing with template. Good peak morphology
is observed for all alleles at high template levels of 4 ng (which
generate alleles with simal strengths of greater than 12000 RFU).
At template levels of 0.03 ng and below some allele drop-out
occurs. This effect is observed when amplification reactions are
carried out with limited number of template DNA strands in the
solution leading to stochastic amplification (Walsh et al., PCR
Methods Appl. 1992, 1, 241-250). The presence of readily detectable
signal for both the high-signal strength alleles and low-signal
strength alleles at a template level of 0.006 ng, demonstrates the
high sensitivity of the fast biochip and tube reaction coupled with
Genebench-FX.TM. Series 100 separation and detection, demonstrating
the utility of this system for low copy number analysis. Taken
together, this data also suggests that the fast PCR approach and
the thermal cycler of the invention and Genebench instrumentation
have a high template dynamic range.
Example 4c
DNA Template Levels and Allele Characteristics in Fast PCR
Reactions
[0151] The effects of template DNA on signal strength for fast PCR
reactions using SpeedSTAR polymerase in (FIG. 5A) biochip and (FIG.
5B) tube reactions are presented in FIGS. 5A and 5B. The alleles
selected for analysis were Amelogenin, the allele with the highest
signal level in the STR profile and FGA 23 and 24 and D7S820 10 and
11, the alleles with the lowest signal levels in the profile.
Signal strengths for all alleles increase as the DNA template level
increases from 0.006 ng to 4 ng in both SpeedSTAR biochip and tube
reactions. At a template level of 0.006 ng, signal strengths for
the amelogenin peak of 111 RFU for biochip and 58 RFU for tube
reactions were observed. At a template level of 4 ng, signal
strengths of 12680 RFU were seen for biochip and 5570 RFU for tube
reactions. All alleles observed in both reaction types showed good
peak morphology.
[0152] For fast biochip reactions (FIG. 6A), PHR is between 0.6 and
1.0 for template levels ranging from 0.05 to 4.0 ng. For template
levels below 0.05 ng, PHR decreases until 0.025 ng, when instances
of allelic dropouts occur and PHR of zero are observed. Similar
results are observed for fast tube reactions, although they
generally exhibit somewhat lower PHR than biochips reactions (FIG.
6B). For biochip reactions, the level of incomplete NTA is 15% or
less for template levels of 2.0 ng and below. For tube reactions,
the incomplete NTA levels surpass 15% at template levels of 1 ng
and increase dramatically by 4 ng.
[0153] Two major differences between biochip and tube reactions are
the temperature profiles of the reaction solutions and the relative
concentration of template and polymerase. The level of incomplete
NTA decreases as more polymerase is available. For biochip
reactions experimental data show that over a DNA template range
from 0.5-4.0 ng the level of incomplete NTA decreases by
approximately 50% as the amount of SpeedSTAR polymerase increases
from 0.3U to 1.2U (FIGS. 7A and 7B). The level of stutter for fast
biochip and tube reactions was relatively constant and generally
less than 15% for all alleles over a template level range of
0.25-4.0 ng (FIGS. 8A and 8B).
[0154] The speed of an STR amplification reaction is only relevant
if the reaction itself generates actionable data that meets
forensic interpretation guidelines. The FBI has general guidelines
that are used for STR interpretation, and individual laboratories
set thresholds that must be met before a profile can be considered
acceptable based on their validation work (Holt et al., J. Forensic
Sci. 2002, 47(1), p. 66-96; LaFountain et al., J. Forensic Sci.,
2001, 46(5), 1191-8).
[0155] The conditions presented herein can generate fast STR
profiles that meet these guidelines. PHR for 0.5 ng template in
biochip and tube reactions meet with the interpretation guidelines
that state a level of 0.6 or greater is required and are consistent
with previously reported results (Leclair et al., J. Forensic Sci.
2004, 49, 968-80). For higher DNA template amounts, PHR remain
relatively constant but are lower than those for the ing
TaqGold.TM. reactions. For low copy numbers, the PHR is dominated
by amplification due to stochastic fluctuations.
[0156] The level of incomplete NTA is based on the ability of the
polymerase to fully adenylate all STR amplicons. For conventional
amplification, this is accomplished by attaching a "pigtail" to the
primer and increasing the final extension time. The level of
incomplete NTA for 0.5 ng biochips and tube reactions described
herein are within interpretation guidelines.
[0157] Levels of incomplete NTA increase with increasing DNA
template (a consequence of the increasing ratio of DNA to
polymerase) and can be reduced by increasing the amount of
polymerase, extension time per cycle, and final extension time. The
later two approaches are not well-suited to fast multiplexed
amplification, as they increase the reaction time. Increasing
polymerase concentration is effective and compatible with fast PCR.
Stutter is a result of DNA strand slippage during extension (Walsh
et al., Nucleic Acids Res. 1996, 24(14), 2807-12). The level of
stutter described here for the 0.5 ng biochip and tube reactions
fall within the interpretational guidelines and are also consistent
with previously cited reports. As expected, the level of stutter
appears to be independent of the DNA template level.
Example 4d
Repeatability and Reproducibility Studies
[0158] The repeatability and reproducibility of the fast biochip
(Table 3A) and tube (Table 3B) reactions using the SpeedSTAR
polymerase were evaluated by performing 24 identical PCR reactions
in 3 PCR biochips and by performing 5 identical tube reactions. For
biochip reactions, the confidence value (CV) for signal strength
ranges from 17 to 24% and for tube reactions from 15 to 34%. The CV
for standard TaqGold.TM. reactions is between 6 and 21%.
TABLE-US-00003 TABLE 3 Reproducibility of SpeedSTAR biochip (3A)
and tube (3B) reactions PHR Signal Strength (RFU) Aver- NTA (%)
Stutter (%) Allele Average STDEV Max Min age STDEV Max Min Average
STDEV Max Min Average STDEV Max Min A: SpeedSTAR biochip reactions
D3S1358.14 1235.40 271.43 1963.95 781.79 0.85 0.11 1.00 0.63 9.11
1.77 11.86 6.64 D3S1358.15 1066.55 251.75 1793.70 689.23 8.97 1.80
12.08 6.53 8.78 0.63 9.84 7.67 vWA.17 2765.49 551.47 3818.46
1732.31 0.81 0.12 0.96 0.56 6.19 1.27 8.25 4.76 vWA.18 2274.33
398.37 3197.88 1379.49 6.22 1.34 8.29 4.71 12.95 0.66 14.35 11.78
FGA.23 884.74 153.51 1276.87 620.51 0.84 0.11 0.99 0.61 2.51 0.58
3.51 1.03 FGA.24 794.52 176.07 1109 30 376.41 2.68 0.48 3.52 1.71
10.10 0.95 12.18 8.63 AMEL 5085.29 1138.51 7276.15 3271.82 3.70
0.40 4.54 3.01 D8S1179.13 3787.27 778.68 5700.08 2420.29 7.35 0.74
8.82 6.17 10.96 0.53 12.08 10.01 D21S11.30 1914.04 424.28 2725.91
1005.45 2.91 0.61 4.14 2.04 12.74 0.85 14.44 10.73 D18S51.15
2248.76 429.94 3056.15 1475.43 5.80 2.08 7.99 0.00 10.61 0.64 11.54
9.04 D18S51.19 1843.92 358.13 2549.69 1271.08 0.83 0.10 0.99 0.59
5.90 2.23 8.19 0.00 14.52 0.85 16.64 12.96 D5S818.11 2734.70 500.56
3646.65 1629.74 9.04 1.88 12.07 6.34 8.90 0.33 9.89 8.35 D13S317.11
4097.95 701.10 5279.96 2724.10 3.02 0.85 6.39 2.25 6.87 0.42 7.95
6.09 D7S820.10 1877.24 384.59 3262.80 1397.95 0.84 0.09 1.00 0.69
6.68 0.60 7.67 5.67 D7S820.11 1594.27 309.99 2336.39 1124.30 10.60
0.68 11.81 9.19 7.26 0.47 7.99 6.42 CV Min: 17% CV Min: 11% CV Min:
6% CV Min: 4% CV Max: 24% CV Max: 14% CV Max: 28% CV Max: 9% B.
SpeedSTAR tube reactions D3S1358.14 1718.86 464.62 2321.62 1249.71
0.86 0.08 0.94 0.74 19.51 0.44 20.04 18.84 D3S1358.15 1455.28
285.03 1719.04 1110.96 19.68 0.78 20.71 18.56 8.34 0.49 8.88 7.65
vWA.17 1934.44 299.00 2150.18 1483.24 0.83 0.11 0.98 0.71 12.12
0.22 12.32 11.75 vWA.18 1722.47 450.99 2439.38 1257.89 12.04 0.27
12.29 11.65 12.72 0.50 13.37 12.18 FGA.23 1625.37 289.29 2020.33
1275.75 0.91 0.08 0.99 0.80 3.57 0.21 3.84 3.28 FGA.24 1561.32
346.77 2003.50 1185.22 3.07 0.21 3.30 2.75 9.57 0.53 10.22 8.90
AMEL 3669.80 844.56 4967.47 2799.39 5.02 0.27 5.41 4.68 D8S1179.13
2447.48 658.60 3268.31 1820.49 8.20 0.40 8.61 7.58 10.47 0.45 10.86
9.72 D21S11.30 1628.98 436.18 2147.27 1222.17 4.85 0.33 5.26 4.45
11.78 0.28 12.14 11.54 D18S51.15 1603.23 545.46 2261.97 1066.52
0.79 0.17 0.95 0.61 8.30 0.34 8.67 7.91 9.67 0.31 10.09 9.30
D18S51.19 1296.20 434.98 2043.27 963.18 8.79 0.99 10.49 7.91 13.56
0.88 14.69 12.28 D5S818.11 3412.19 894.75 4629.47 2506.84 6.27 0.17
6.47 6.02 8.38 0.31 8.86 8.03 D13S317.11 3093.19 749.20 3987.13
2204.34 3.94 0.14 4.16 3.81 6.49 0.25 6.86 6.25 D7S820.10 1009.46
228.75 1297.92 780.76 0.93 0.03 0.98 0.90 7.86 0.65 8.55 6.86
D7S820.11 945.50 208.75 1228.39 705.49 12.13 1.53 14.38 10.56 6.52
0.34 7.02 6.15 CV Min: 15% CV Min: 3% CV Min: 2% CV Min: 2% CV Max:
34% CV Max: 21% CV Max: 13% CV Max: 6%
[0159] The CV for PHR is up to 14% for biochips and 21% for tube
reactions, compared to the 5% to 10% range observed for standard
TaqGold.TM. reactions. CVs for incomplete NTA in biochip reactions
vary between 6% and 28%, and for tube reactions between 2 to 13%.
Again, these variations are similar to the 4 to 28% range observed
for standard TaqGold.TM. reactions. The CVs for stutter in biochips
are 4 to 9%, in tubes 2 to 6%, and are also similar to the range of
4-13% observed for standard TaqGold.TM. reactions.
Example 4e
[0160] Compatibility with Other Commercially Available STR Kits
[0161] Using the same fast biochip and tube conditions described
above, a series of samples were evaluated using primer sets from
the COfiler.TM. and Identifiler.TM. kits. FIGS. 9A and 9B show the
achievement of full profiles using these primer sets using the
thermal cycler of the invention, the SpeedSTAR enzyme, and the
protocols described herein. Each is suitable for these commercially
available kits as well. Although full profiles were achieved,
imbalance in the signal strengths across the loci was observed.
Example 5
[0162] Fast Sequencing with the Thermal Cycler
[0163] The thermal cycling instrument and methodology can also be
applied to fast DNA sequencing reactions. In this implementation of
the fast thermal cycler, the instrumentation and biochip are the
same as that used for PCR. Different reaction solutions, polymerase
and cycling temperatures are applied for the sequencing reaction.
The currently commercially available sequencing reactions take 49
min (for GE Amersham DYEnamic.TM. ET Terminato Cycle Sequencing
Kit) and 2.25 hr (for AB Big Dye V3.1. Utilizing the NetBio thermal
cycler, with conventional reagents, allowed the sequencing reaction
time to be reduced to 21 minutes.
[0164] Fast sequencing has been achieved using the thermocycler
disclosed herein and biochip comprising 16 lanes. The final
reaction volume in the chips was 7 .mu.L. Half strength sequencing
reactions were set up with the DYEnamic.TM. ET Terminator Cycle
Sequencing Kit from GE Healthcare following the manufacturer's
protocol. All volumes were scaled down accordingly to accommodate
the 7 .mu.L final volume. Template for the reaction was 0.1 .mu.mol
B. subtilus with a fragment size of 343 bp.
[0165] Three cycling protocols were demonstrated with the first
protocol consisting of 30 cycles of (20 s at 95.degree. C., 15 s at
50.degree. C. and 60 s at 60.degree. C.) (total cycling time is
51.7 min), the second protocol consisting of 30 cycles of 5 s at
95.degree. C., 15 s at 50.degree. C. and 30 sat 60.degree. C.
(total cycling time is 29 min) and a third protocol consisting of
30 cycles of 5 sat 95.degree. C., 10 sat 50.degree. C. and 20 s at
60.degree. C. (total cycling time of 21.6 min). Each sequencing
reaction was cleaned-up with ethanol precipitated, and separated on
Genebench FX Series 100. The average PHRED scores for sequencing a
343 bp PCR product for the 3 cycling protocols were 282, 287, and
279 respectively; demonstrating that sequencing of a 343 bp product
can be achieved in chip in less than 22 min. FIG. 10 shows the DNA
sequence of the fast DNA sequencing protocol.
[0166] In general, biochip based multiplexed amplification of one
or more nucleic acids utilizing the systems and methods described
herein have the advantage of providing amplified nucleic acid
products in significantly shorter overall reaction times with
respect to reactions run in thin-walled tubes and utilizing
presently commercialized thermal cycling units.
* * * * *