US20090105081A1 - Methods and systems for solution based sequence enrichment - Google Patents

Methods and systems for solution based sequence enrichment Download PDF

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Publication number
US20090105081A1
US20090105081A1 US12/194,574 US19457408A US2009105081A1 US 20090105081 A1 US20090105081 A1 US 20090105081A1 US 19457408 A US19457408 A US 19457408A US 2009105081 A1 US2009105081 A1 US 2009105081A1
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nucleic acid
probes
sequences
hybridization
target nucleic
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Matthew Rodesch
Thomas Albert
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Roche Sequencing Solutions Inc
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Roche Nimblegen Inc
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Application filed by Roche Nimblegen Inc filed Critical Roche Nimblegen Inc
Priority to EP12184423.7A priority Critical patent/EP2535429B1/en
Priority to PCT/EP2008/008920 priority patent/WO2009053039A1/en
Priority to ES12184423.7T priority patent/ES2633567T3/es
Priority to ES08842936.0T priority patent/ES2522912T3/es
Priority to EP08842936.0A priority patent/EP2209913B1/en
Priority to JP2010530331A priority patent/JP2011500069A/ja
Priority to CN200880113397.8A priority patent/CN101835907B/zh
Priority to CA2699835A priority patent/CA2699835C/en
Publication of US20090105081A1 publication Critical patent/US20090105081A1/en
Assigned to ROCHE NIMBLEGEN, INC. reassignment ROCHE NIMBLEGEN, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: ALBERT, THOMAS, RODESCH, MATTHEW
Priority to US13/239,585 priority patent/US9790543B2/en
Priority to JP2013104784A priority patent/JP2013150637A/ja
Priority to US15/706,133 priority patent/US10900068B2/en
Abandoned legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers

Definitions

  • the present invention provides methods and systems for the capture and enrichment of target nucleic acids and analysis of the enriched target nucleic acids.
  • the present invention provides for the enrichment of targeted sequences in a solution based format.
  • nucleic acid microarray technology makes it possible to build an array of millions of nucleic acid sequences in a very small area, for example on a microscope slide (e.g., U.S. Pat. Nos. 6,375,903 and 5,143,854). Initially, such arrays were created by spotting pre-synthesized DNA sequences onto slides. However, the construction of maskless array synthesizers (MAS) as described in U.S. Pat. No. 6,375,903 now allows for the in situ synthesis of oligonucleotide sequences directly on the slide itself.
  • MAS maskless array synthesizers
  • MAS-based oligonucleotide microarray synthesis technology allows for the parallel synthesis of millions of unique oligonucleotide features in a very small area of a standard microscope slide.
  • Nucleic acid microarray technology has been applied to many areas of research and diagnostics, such as gene expression and discovery, mutation detection, allelic and evolutionary sequence comparison, genome mapping, drug discovery, and more. Many applications require searching for genetic variants and mutations across the entire human genome that underlies human diseases. In the case of complex diseases, these searches generally result in a single nucleotide polymorphism (SNP) or set of SNPs associated with diseases and/or disease risk. Identifying such SNPs has proved to be an arduous and frequently fruitless task because resequencing large regions of genomic DNA, usually greater than 100 kilobases (Kb), from affected individuals or tissue samples is required to find a single base change or to identify all sequence variants.
  • Kb kilobases
  • Prior art microarray technology is typically a substrate associated technology with inherent variability, such as microarray slides, chips, and the like. Variability can take on many forms, for example variability in background, probe/hybridization kinetics, glass source, and the like. Variability plays a big part in experimental interpretation and can make or break an experiment.
  • the present invention provides methods and systems for the capture and enrichment of target nucleic acids and analysis of the enriched target nucleic acids.
  • the present invention provides for the enrichment of targeted sequences in a solution based format.
  • Methods and systems of the present invention are useful in aiding investigators and clinicians in identifying, studying and following treatment regimens associated with disease and disease states.
  • the present invention is summarized as a novel method for reducing the complexity of a large nucleic acid sample, such as a genomic sample, cDNA library or mRNA to facilitate further processing and genetic analysis.
  • Embodiments of the present invention comprise (pre-selected) immobilized nucleic acid probes to capture target nucleic acid sequences from, for example, a genomic sample by hybridizing the sample to probes, or probe derived amplicons, on a solid support or in solution.
  • the captured target nucleic acids are preferably washed and eluted off of the probes.
  • the eluted genomic sequences are more amenable to detailed genetic analysis than a sample that has not been subjected to the methods described herein.
  • the present invention provides methods and systems for the capture and enrichment of target nucleic acids and analysis of the enriched target nucleic acids. In some embodiments, the present invention provides for the enrichment of targeted sequences in a solution based format. In some embodiments, the present invention provides methods and systems for solution based capture and enrichment of target nucleic acids (e.g., genomic DNA, RNA, cDNA, mRNA, etc.).
  • target nucleic acids e.g., genomic DNA, RNA, cDNA, mRNA, etc.
  • Genomic samples are used herein for descriptive purposes, but it is understood that other non-genomic samples could be subjected to the same procedures.
  • the methods and systems described herein provide for enrichment of target sequences in a solution based approach thereby providing an alternative to microarray substrate based methods for use in research and therapeutics associated with disease and disease states such as cancers (Durkin et al., 2008, Proc. Natl. Acad. Sci. 105:246-251; Natrajan et al., 2007, Genes, Chr.
  • solution based capture methods comprise probe derived amplicons wherein said probes for amplification are affixed to a solid support.
  • the solid support comprises support-immobilized nucleic acid probes to capture specific nucleic acid sequences (e.g., target nucleic acids) from, for example, a genomic sample.
  • Probe amplification provides probe amplicons in solution which are hybridized to target sequences.
  • target nucleic acid sequences present in the sample are enriched by capturing (e.g., via linker chemistry such as biotin, digoxigenin, etc.) and washing the probes and eluting the hybridized target nucleic acids from the captured probes ( FIG. 1 ).
  • the target nucleic acid sequence(s) may be further amplified using, for example, non-specific ligation-mediated PCR (LM-PCR), resulting in an amplified pool of PCR products of reduced complexity compared to the original target sample.
  • LM-PCR non-specific ligation-mediated PCR
  • hybridization between the probes and target nucleic acids is performed under preferably stringent conditions sufficient to support hybridization between the solution based probe amplicons, wherein said probes comprise linker chemistry and complementary regions of the target nucleic acid sample to provide probe/target hybridization complexes.
  • the complexes are subsequently captured via the linker chemistry and washed under conditions sufficient to remove non-specifically bound nucleic acids and the hybridized target nucleic acid sequences are eluted from the captured probe/target complexes.
  • the present invention provides methods of isolating and reducing the genetic complexity of a plurality of nucleic acid molecules, the method comprising the steps of exposing fragmented, denatured nucleic acid molecules of said population to multiple, different oligonucleotide probes that are bound on a solid support under hybridizing conditions to capture nucleic acid molecules that specifically hybridize to said probes, or exposing fragmented, denatured nucleic acid molecules of said population to multiple, different oligonucleotide probes under hybridizing conditions followed by binding the complexes of hybridized molecules to a solid support to capture nucleic acid molecules that specifically hybridize to said probes, wherein in both cases said fragmented, denatured nucleic acid molecules have an average size of about 100 to about 1000 nucleotide residues, preferably about 250 to about 800 nucleotide residues and most preferably about 400 to about 600 nucleotide residues, separating unbound and non-specifically hybridized nucleic acids from the captured molecules, eluting the
  • the multiple, different oligonucleotide probes comprise a chemical group or linker chemistry, for example a binding moiety such as biotin, digoxigenin, etc., which is able to bind to a solid support.
  • the solid support for binding comprises the corresponding capture chemistry, for example steptavidin for biotin and anti-digoxigenin antibody for digoxigenin.
  • the population or plurality of target nucleic acid molecules preferably contains the whole genome or at least one chromosome of an organism or at least one nucleic acid molecule with at least about 100 kb.
  • the size(s) of the nucleic acid molecule(s) is/are at least about 200 kb, at least about 500 kb, at least about 1 Mb, at least about 2 Mb or at least about 5 Mb, especially a size between about 100 kb and about 5 Mb, between about 200 kb and about 5 Mb, between about 500 kb and about 5 Mb, between about 1 Mb and about 2 Mb or between about 2 Mb and about 5 Mb.
  • the target nucleic acid molecules are selected from an animal, a plant or a microorganism, in preferred embodiments the organism is a human. If only limited samples of nucleic acids (e.g. of the human genome) are available, the nucleic acids may be amplified, for example by whole genome amplification, prior to practicing the methods of the present invention. Prior amplification may be necessary for performing the inventive method(s), for example, for forensic purposes (e.g. in forensic medicine for genetic identity purposes).
  • the population of target nucleic acid molecules is a population of genomic DNA molecules.
  • probes are selected from a plurality of sequences that, for example, define a plurality of exons, introns or regulatory sequences from a plurality of genetic loci, a plurality of probes that define the complete sequence of at least one single genetic locus, said locus having a size of at least 100 kb, preferably at least 1 Mb, or at least one of the sizes as specified above, a plurality of probes that define single nucleotide polymorphisms (SNPs), or a plurality of probes that define an array, for example a tiling array designed to capture the complete sequence of at least one complete chromosome.
  • SNPs single nucleotide polymorphisms
  • the present invention comprises the step of ligating adaptor molecules to one or both, preferably both ends of the nucleic acid molecules prior to or after exposing fragmented nucleic samples to the probes for hybridization.
  • methods of the present invention further comprise the amplifying of the target nucleic acid molecules with at least one primer, said primer comprising a sequence which specifically hybridizes to the sequence of said adaptor molecule(s).
  • the amplified target nucleic acid sequences may be sequenced, hybridized to a resequencing or SNP-calling array and the sequence or genotypes may be further analyzed.
  • the present invention provides an enrichment method for target nucleic acid sequences in a genomic sample, such as exons or variants, preferably SNP sites. This can be accomplished by synthesizing genomic probes specific for a region of the genome to capture complementary target nucleic acid sequences contained in a complex genomic sample.
  • the present invention further comprises determining the nucleic acid sequence of the captured and eluted target molecules, in particular by means of performing sequencing by synthesis reactions.
  • the present invention is directed to a method for detecting coding region variation relative to a reference genome, in particular relative to a reference genome that comprises fragmented, denatured genomic nucleic acid molecules, the method as previously described further comprising determining the nucleic acid sequence of the captured and eluted target molecules, in particular by means of performing sequencing by synthesis reactions and comparing the determined sequence to a sequence in a database, in particular to a sequence in a database of polymorphisms in the reference genome to identify variants from the reference genome.
  • the present invention is directed to a kit comprising compositions and reagents for performing a method according to the present invention.
  • a kit may comprise, but is not limited to, a double stranded adaptor molecule, multiple, different oligonucleotide probes, a solid support for capturing said probes, wherein the probes are selected from a plurality of sequences that define a plurality of exons, introns or regulatory sequences from a plurality of genetic loci, a plurality of probes that define the complete sequence of at least one single genetic locus, said locus having a size of at least 100 kb, preferably at least 1 Mb, or at least one of the sizes as specified above, a plurality of probes that define sites known to contain SNPs, or a plurality of probes that define a tiling array designed to capture the complete sequence of at least one complete chromosome.
  • a kit comprises a plurality of beads or a microarray substrate (e.g., slide, chip, etc.). In some embodiments, a kit comprises two different double stranded adaptor molecules.
  • a kit may further comprise at least one or more other components selected from DNA polymerase, T4 polynucleotide kinase, T4 DNA ligase, hybridization solution(s), wash solution(s), and/or elution solution(s).
  • nucleic acid (pre-selected) capture probes are immobilized onto a solid support (e.g., slide, chip, bead, etc.) using any number of recognized methods (e.g., spotting, photolithography, in situ synthesis, etc.).
  • the probes are synthesized in situ by maskless array synthesis on a substrate and subsequently amplified by, for example, PCR resulting in probe derived amplicons in solution.
  • the probe sequences as synthesized comprise primer binding sites for amplification at one or both the 3′ and 5′ termini (e.g., at or near the ends) of the probes.
  • the sequence of the primer binding sites on the probes are the same at both the 3′ and 5′ prime ends or the probes, whereas in other embodiments the sequence of the primer binding sites is different at the 3′ prime end then the sequence at the 5′ prime end.
  • amplification primers for probe amplification further comprise a restriction endonuclease site, for example an MlyI site for easy removal of primer sequences from the final captured target, wherein one of the primers (e.g., forward or reverse primer) further comprises linker chemistry such as a binding moiety or sequence (e.g., biotin, digoxigenin, HIS tag, etc.) and are deposited onto the support with the immobilized probes along with reagents necessary for exponential PCR amplification (e.g., PCR procedures for exponential amplification of targets as known to a skilled artisan).
  • linker chemistry such as a binding moiety or sequence (e.g., biotin, digoxigenin, HIS tag, etc.) and are deposited onto the support with the immobilized probes along with reagents necessary for exponential PCR amplification (e.g., PCR procedures for exponential amplification of targets as known to a skilled artisan).
  • PCR is performed thereby creating amplicons of probe capture sequences such that one of the strands comprises linker chemistry, such as a binding moiety or sequence.
  • the amplicon containing solution is transferred to a vessel (e.g., tube, well of a 96 well plate, etc.) and, in some embodiments, purified from reaction components.
  • An additional round of amplification is preferentially performed on the probe derived amplicons using asymmetric PCR, wherein the linker chemistry labeled primer is in abundance compared to the non-labeled primer to preferentially synthesize single stranded binding moiety/sequence labeled amplicons.
  • the amplicons are purified away from reaction components and transferred to a vessel, denatured nucleic acid sample is added, and hybridization is allowed to occur.
  • labeled amplicon/target nucleic acid complexes are captured.
  • a streptavidin (SA) coated substrate such as SA coated beads (e.g., paramagnetic beads/particles) are used to capture the biotin labeled amplicon/target complex.
  • SA coated beads e.g., paramagnetic beads/particles
  • the SA bound complex is washed and the hybridized target nucleic acids are eluted from the complex and utilized in downstream applications, such as sequencing applications.
  • the present invention provides methods for isolating and reducing the complexity of a plurality of nucleic acid sequences comprising providing a solid support wherein said solid support comprises hybridization probes hybridizable to target nucleic acid sequences and providing a fragmented nucleic acid sample comprising target nucleic acid sequences, amplifying the hybridization probes wherein the amplification products comprise a binding moiety and wherein the amplification products are in solution, hybridizing the nucleic acid sample to the amplification products in solution under conditions such that hybridization between the amplification products and target nucleic acid sequences is allowed to occur, separating the hybridized target nucleic acid sequences/amplification product complexes from non-specifically hybridized nucleic acids by said binding moiety, and eluting the hybridized target nucleic acid sequences from the complex thereby isolation and reducing the complexity of a plurality of nucleic acid sequences.
  • the solid support is a microarray slide.
  • the target nucleic acid sample is fragmented genomic DNA with or without adaptor molecules at one or both ends of the fragments.
  • the hybridization probes comprise a restriction endonuclease site, for example a MlyI site.
  • probe amplification comprises exponential polymerase chain reaction, and may further comprise asymmetric non-exponential amplification.
  • the binding moiety is biotin and the capture substrate, such as a bead for example a paramagnetic particle, is coated with streptavidin for separation of the target nucleic acid/amplification product complex from non-specifically hybridized target nucleic acids.
  • the captured target nucleic acid/amplification product complexes are washed prior to elution of the bound target nucleic acids.
  • the eluted target nucleic acids are sequenced.
  • the present invention provides methods for isolating and reducing the complexity of a plurality of nucleic acid sequences comprising providing a solid support wherein said solid support comprises hybridization probes hybridizable to target nucleic acid sequences and providing a fragmented nucleic acid sample comprising target nucleic acid sequences, amplifying the hybridization probes wherein the amplification products comprise a binding moiety and wherein the amplification products are in solution, hybridizing the nucleic acid sample to the amplification products in solution under conditions such that hybridization between the amplification products and target nucleic acid sequences is allowed to occur, separating the hybridized target nucleic acid sequences/amplification product complexes from non-specifically hybridized nucleic acids by said binding moiety, eluting the hybridized target nucleic acid sequences from the complex thereby isolation and reducing the complexity of a plurality of nucleic acid sequences, and sequencing the eluted target nucleic acid sequences.
  • the solid support is a microarray slide.
  • the target nucleic acid sample is fragmented genomic DNA with or without adaptor molecules at one or both ends of the fragments.
  • the hybridization probes comprise a restriction endonuclease site, for example a MlyI site.
  • probe amplification comprises exponential polymerase chain reaction, and may further comprise asymmetric non-exponential amplification.
  • the binding moiety is biotin and the capture substrate, such as a bead for example a paramagnetic particle, is coated with streptavidin for separation of the target nucleic acid/amplification product complex from non-specifically hybridized target nucleic acids.
  • the captured target nucleic acid/amplification product complexes are washed prior to elution of the bound target nucleic acids.
  • the present invention provides a kit comprising hybridization probe sequences comprising a binding moiety and a restriction enzyme site wherein said probe sequences are designed to hybridize to one or more target nucleic acid sequences and wherein said probe sequences are in solution, a substrate comprising a binding partner for binding said binding moiety, and instruction for performing methods of the present invention.
  • a kit further comprises one or more solutions such as hybridization, washing, and elution solution(s).
  • a kit comprises a magnet.
  • a kit comprises one or more enzymes and corresponding reagents, buffers, and the like, for example a restriction enzyme such as MlyI and buffers/reagents for performing restriction enzyme reactions using MlyI.
  • sample is used in its broadest sense. In one sense, it is meant to include a specimen or culture obtained from any source, preferentially a biological source. Biological samples may be obtained from animals (including humans) and encompass fluids, solids, tissues, and gases. Biological samples include blood products, such as plasma, serum and the like. As such, a “sample of nucleic acids” or a “nucleic acid sample”, a “target sample” comprises nucleic acids (e.g., DNA, RNA, cDNA, mRNA, tRNA, miRNA, etc.) from any source.
  • nucleic acids e.g., DNA, RNA, cDNA, mRNA, tRNA, miRNA, etc.
  • a nucleic acid sample preferably derives from a biological source, such as a human or non-human cell, tissue, and the like.
  • a biological source such as a human or non-human cell, tissue, and the like.
  • non-human refers to all non-human animals and entities including, but are not limited to, vertebrates such as rodents, non-human primates, ovines, bovines, ruminants, lagomorphs, porcines, caprines, equines, canines, felines, aves, etc.
  • Non-human also includes invertebrates and prokaryotic organisms such as bacteria, plants, yeast, viruses, and the like.
  • a nucleic acid sample used in methods and systems of the present invention is a nucleic acid sample derived from any organism, either eukaryotic or prokaryotic.
  • hybridization is used in reference to the pairing of complementary nucleic acids. Hybridization and the strength of hybridization (e.g., the strength of the association between the nucleic acids) is affected by such factors as the degree of complementary between the nucleic acids, stringency of the conditions involved, the melting temperature (T m ) of the formed hybrid, and the G:C ratio of the nucleic acids. While the invention is not limited to a particular set of hybridization conditions, stringent hybridization conditions are preferably employed. Stringent hybridization conditions are sequence dependent and differ with varying environmental parameters (e.g., salt concentrations, presence of organics, etc.). Generally, “stringent” conditions are selected to be about 50° C. to about 20° C.
  • T m is the temperature (under defined ionic strength and pH) at which 50% of a nucleic acid (e.g., target nucleic acid) hybridizes to a perfectly matched probe.
  • “Stringent conditions” or “high stringency conditions,” for example, can be hybridization in 50% formamide, 5 ⁇ SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 ⁇ Denhardt's solution, sonicated salmon sperm DNA (50 mg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2% SSC (sodium chloride/sodium citrate) and 50% formamide at 55° C., followed by a wash with 0.1 ⁇ SSC containing EDTA at 55° C.
  • SSC sodium chloride/sodium citrate
  • buffers containing 35% formamide, 5 ⁇ SSC, and 0.1% (w/v) sodium dodecyl sulfate (SDS) are suitable for hybridizing under moderately non-stringent conditions at 45° C. for 16-72 hours.
  • the formamide concentration may be suitably adjusted between a range of 20-45% depending on the probe length and the level of stringency desired. Additional examples of hybridization conditions are provided in several sources, including Molecular Cloning: A Laboratory Manual, Eds. Sambrook et al., Cold Spring Harbour Press (incorporated herein by reference in its entirety).
  • “stringent” wash conditions are ordinarily determined empirically for hybridization of a target to a probe, or in the present invention, a probe derived amplicon.
  • the amplicon/target are hybridized (for example, under stringent hybridization conditions) and then washed with buffers containing successively lower concentrations of salts, or higher concentrations of detergents, or at increasing temperatures until the signal-to-noise ratio for specific to non-specific hybridization is high enough to facilitate detection of specific hybridization.
  • Stringent temperature conditions will usually include temperatures in excess of about 30° C., more usually in excess of about 37° C., and occasionally in excess of about 45° C.
  • Stringent salt conditions will ordinarily be less than about 1000 mM, usually less than about 500 mM, more usually less than about 150 mM (Wetmur et al., 1966, J. Mol. Biol., 31:349-370; Wetmur, 1991, Critical Reviews in Biochemistry and Molecular Biology, 26:227-259, incorporated by reference herein in their entireties).
  • the term “primer” refers to an oligonucleotide, whether occurring naturally as in a purified restriction digest or produced synthetically, that is capable of acting as a point of initiation of synthesis when placed under conditions in which synthesis of a primer extension product that is complementary to a nucleic acid strand is induced, (e.g., in the presence of nucleotides and an inducing agent such as DNA polymerase and at a suitable temperature and pH).
  • the primer is preferably single stranded for maximum efficiency in amplification.
  • the primer is an oligodeoxyribonucleotide.
  • the primer must be sufficiently long to prime the synthesis of extension products in the presence of the inducing agent. The exact lengths of the primers will depend on many factors, including temperature, source of primer and the use of the method.
  • probe refers to an oligonucleotide (e.g., a sequence of nucleotides), whether occurring naturally as in a purified restriction digest or produced synthetically, recombinantly or by PCR amplification, that is capable of hybridizing to at least a portion of another oligonucleotide of interest, for example target nucleic acid sequences.
  • a probe may be single-stranded or double-stranded. Probes are useful in the detection, identification and isolation of particular gene sequences.
  • target nucleic acid molecules and “target nucleic acid sequences” are used interchangeably and refer to molecules or sequences from a target genomic region to be studied.
  • the pre-selected probes determine the range of targeted nucleic acid molecules.
  • the “target” is sought to be sorted out from other nucleic acid sequences.
  • a “segment” is defined as a region of nucleic acid within the target sequence, as is a “fragment” or a “portion” of a nucleic acid sequence.
  • the term “isolate” when used in relation to a nucleic acid, as in “isolating a nucleic acid” refers to a nucleic acid sequence that is identified and separated from at least one component or contaminant with which it is ordinarily associated in its natural source. Isolated nucleic acid is in a form or setting that is different from that in which it is found in nature. In contrast, non-isolated nucleic acids as nucleic acids such as DNA and RNA found in the state they exist in nature.
  • the isolated nucleic acid, oligonucleotide, or polynucleotide may be present in single-stranded or double-stranded form.
  • FIG. 1 exemplifies an embodiment of the present invention
  • a generalized flow diagram of an enrichment process wherein said enrichment methods are used to isolate and enrich for a plurality of nucleic acid sequences in an aqueous solution.
  • Hybridization probes affixed to a microarray substrate, are amplified in situ to produce probe derived amplicons in solution the amplicons of which comprise a binding moiety.
  • Fragmented nucleic acids e.g. labeled with a detection moiety
  • the complexes being subsequently captured (e.g., by paramagnetic capture particles).
  • the captured and immobilized hybridized complexes are washed and the specifically bound targets are eluted from the bound immobilized probe amplicons.
  • the eluted (e.g., isolated and enriched) target sequences are applied to downstream applications, such as sequencing.
  • FIG. 2 demonstrates resequencing conformance using the solution capture methods of the present invention.
  • the resequencing assay is comprised of a subset of the targeted captured regions.
  • the x-axis represents an arbitrary set of regions from the larger target region, which serves as a representation of the targeted capture region as a whole.
  • the y-axis represents the percent sequence conformance with known target sequences.
  • the present invention broadly relates to cost-effective, flexible and rapid solution based methods and systems for isolating a plurality of nucleic acid sequences and reducing nucleic acid sample complexity to enrich for target nucleic acids of interest and to facilitate further processing and analysis, such as sequencing, resequencing and SNP calling.
  • the captured target nucleic acid sequences which are of a more defined, less complex genomic population are more amenable to detailed genetic analysis, for example genetic analysis of disease and disease states (e.g., cancers, genetic mutations, genetic diseases, etc).
  • the present invention provides methods and systems useful, for example, in searching for genetic variants and mutations such a single nucleotide polymorphisms (SNPs), sets of SNPs, genomic insertions, deletions, etc. that underlie human diseases.
  • SNPs single nucleotide polymorphisms
  • a sample containing denatured (e.g., single-stranded) nucleic acid molecules, preferably genomic nucleic acid molecules, which can be fragmented molecules is exposed under hybridizing conditions to a plurality of oligonucleotide probes, wherein the plurality of oligonucleotide probes or amplicons derived from said probes are in solution, to capture from the sample nucleic acid molecules target nucleic acid sequences and separating non-hybridizing regions of the genome or any other sample nucleic acids from the hybridized target sequences, wherein said separating comprises capturing via a binding moiety (e.g., associated with the probe or probe derived amplicon) the hybridization complexes that are in solution and washing the bound complexes thereby separating the hybridized target sequences from the non-specific non-target hybridized sequences ( FIG. 1 ).
  • a binding moiety e.g., associated with the probe or probe derived amplicon
  • the present invention provides methods and systems for isolating a plurality of nucleic acid sequences and reducing the complexity of a large nucleic acid sample, such as a genomic DNA or RNA sample, cDNA library or mRNA library to facilitate further processing and genetic analysis.
  • methods and systems comprise in situ amplification of (pre-selected) immobilized nucleic acid probes wherein the probe derived amplicons comprise a binding moiety.
  • the labeled amplicons capture, in solution, target nucleic acid sequences from a sample by hybridizing the sample to the amplicons in solution based methods.
  • the labeled amplicon/target nucleic acid hybrid complex is captured via the binding moiety, preferably washed and the target nucleic acid eluted.
  • the eluted genomic sequences are more amenable to detailed genetic analysis than a genomic sample that has not been subjected to this enrichment procedure. Accordingly, the disclosed methods provide a cost-effective, flexible and efficient approach for reducing the complexity of a genomic sample. Throughout the remainder of the description, genomic samples are used for descriptive purposes, but it is understood that other non-genomic samples could be subjected to the same procedures.
  • the invention provides a method of isolating a plurality of nucleic acid sequences and reducing the complexity of a nucleic acid sample by hybridizing the sample against nucleic acid probe amplicons in solution under preferably stringent conditions sufficient to support hybridization between the probe amplicons and complementary regions of the nucleic acid sample.
  • the probe amplicon/target nucleic acid complexes are washed under conditions sufficient to remove non-specifically bound nucleic acids.
  • the hybridized target nucleic acid sequences are eluted from the probe derived amplicons and may optionally be further amplified (e.g., by LM-PCR), for example for downstream applications such as resequencing.
  • the present invention provides a method for isolating a plurality of nucleic acid sequences and reducing the genetic complexity of a population of nucleic acid molecules, the method comprising the steps of exposing fragmented, denatured nucleic acid molecules of a target population to multiple, different oligonucleotide probe derived amplicons wherein the amplicons are in solution and wherein the amplicons further comprise a binding moiety, under hybridizing conditions to capture nucleic acid molecules that specifically hybridize to the probe amplicons, binding or capturing the complexes of hybridized molecules by binding the binding moiety found on the probe amplicon to its binding partner (e.g., biotin/SA, digoxigenin/anti-digoxigenin, 6HIS/nickel, etc.), wherein the fragmented, denatured nucleic acid molecules have an average size of about 100 to about 1000 nucleotide residues, preferably about 250 to about 800 nucleotide residues and most preferably about 400 to about 600 nucleotide
  • embodiments of the present invention provide solution based methods and systems for isolating a plurality of nucleic acid sequences and reducing the genetic complexity of a population of nucleic acid molecules.
  • Methods and systems of the present invention comprise exposing fragmented, denatured nucleic acid sample sequences, which may or may not comprise one or more ligation adaptors at one or both ends of the fragmented nucleic acid sample prior to denaturation, to multiple, different hybridization probe amplicons in solution wherein said amplicons are derived from pre-designed multiple, different hybridization probes wherein said amplicons comprise a binding moiety or sequence and optionally a restriction endonuclease (RE) site, under hybridization conditions sufficient to hybridize the denatured nucleic acid target sequences to the probe derived amplicons (e.g., in solution), wherein the fragmented, denatured nucleic acid sequences have an average size of about 100 to about 1000 nucleotide residues, preferably about 250 to about 800 nucleo
  • probes for capture of target nucleic acids are immobilized on a substrate by a variety of methods.
  • probes can be spotted onto slides (e.g., U.S. Pat. Nos. 6,375,903 and 5,143,854).
  • probes are synthesized in situ on a substrate by using maskless array synthesizers (MAS) as described in U.S. Pat. Nos. 6,375,903, 7,037,659, 7,083,975, 7,157,229 that allows for the in situ synthesis of oligonucleotide sequences directly on the slide for subsequent in situ polymerase chain reaction (PCR) amplification.
  • MAS maskless array synthesizers
  • a solid support is a population of beads or particles.
  • the capture probes are initially synthesized on a microarray slide using a maskless array synthesizer, amplified, released or cleaved off according to standard methods, optionally amplified and immobilized on said population of beads.
  • the beads may be packed, for example, into a column so that a target sample is loaded and passed through the column and hybridization of probe/target sample takes place in the column, followed by washing and elution of target sample sequences for reducing genetic complexity.
  • a column has fluid inlet and outlet ports.
  • hybridization takes place in an aqueous solution comprising the beads with the immobilized multiple probes in suspension in an aqueous environment.
  • nucleic acid probes for target molecules are synthesized on a solid support, released from the solid support as a pool of probes and amplified.
  • the amplified pool of released probed are covalently or non-covalently immobilized onto a support (e.g., glass, metal, ceramic, polymeric beads, paramagnetic particles, etc.).
  • the probes are designed for convenient release from the solid support by, for example, providing at or near the support-proximal probe termini an acid or alkali-labile nucleic acid sequence that releases the probes under conditions of low or high pH, respectively.
  • the art is familiar with methods for immobilizing nucleic acids onto supports, for example by incorporating a biotinylated nucleotide into the probes and coating a support with streptavidin such that the coated support attracts and immobilizes the probes in the pool.
  • the sample or samples pass across the probe containing support (e.g., slide, column, etc.) under hybridizing conditions such that target nucleic acid molecules that hybridize to the immobilized support can be eluted for subsequent analysis or other use.
  • the initial hybridization probes designed for subsequent amplification for use in solution based capture methods as described herein are printed or deposited on a solid support such as a microarray slide, chip, microwell, column, tube, beads or particles.
  • the substrates may be, for example, glass, metal, ceramic, polymeric beads, etc.
  • the solid support is a microarray (e.g., glass slide), wherein the probes are synthesized on the microarray using a maskless array synthesizer.
  • the lengths of the multiple oligonucleotide probes may vary and are dependent on the experimental design and limited only by the possibility to synthesize such probes.
  • the average length of the population of multiple probes prior to in situ amplification is about 20 to about 100 nucleotides, preferably about 40 to about 85 nucleotides, in particular about 45 to about 75 nucleotides.
  • the immobilized hybridization probes are subsequently utilized as the templates for in situ PCR amplification and optionally asymmetric PCR amplification thereby providing probe derived amplicons for solution based hybridization and enrichment of target nucleic acid molecules from a complex sample.
  • hybridization probes correspond in sequence to at least one region of a genome and can be provided on a solid support in parallel using, for example, maskless array synthesis (MAS) technology.
  • probes can be obtained serially using a standard DNA synthesizer and then applied to the solid support or can be obtained from an organism and then immobilized on the solid support.
  • hybridization probes regardless of the method of synthesis, comprise amplification primer sequences for use in amplification techniques.
  • amplification primer sequences incorporated into hybridization probe sequences further comprise restriction endonuclease (RE) sequences.
  • RE restriction endonuclease
  • hybridization probes as found on a microarray substrate are amplified in situ using primers complementary to the primer sequences wherein one or both of the primers further comprise linker chemistry, such as a binding moiety (e.g., biotin, digoxigenin, etc.) and such that the hybridization probe derived PCR amplicons are in solution.
  • linker chemistry such as a binding moiety (e.g., biotin, digoxigenin, etc.) and such that the hybridization probe derived PCR amplicons are in solution.
  • the solution comprising the probe derived amplicons is transferred to, for example, a tube, well, or other vessel and maintained in solution. It is contemplated that one or more additional rounds of amplification to boost the production of the amplicon strand that comprises the binding moiety, for example by asymmetric PCR, is additionally performed.
  • a nucleic acid sample preferably fragmented and denatured to yield fragmented single stranded target sequences, is added to the amplicons in solution and hybridization is allowed to occur between the probe derived amplicons and the fragmented single stranded target nucleic acid sample.
  • nucleic acids that do not hybridize, or that hybridize non-specifically are separated from the amplicon/target complex by capturing the amplicon/target complex via the binding moiety and washing the amplicon/target complex.
  • the binding moiety is biotin
  • a streptavidin coated substrate is used to capture the complex.
  • the bound complex is washed, for example with one or more washing solutions.
  • the remaining nucleic acids are eluted from the complex, for example, by using water or an elution buffer (e.g., comprising TRIS buffer and/or EDTA) to yield an eluate enriched for the target nucleic acid sequences.
  • Microarray based oligonucleotides provided for amplification in solution based capture methods and systems as described herein are designed to target a region or regions of a genome.
  • the length of individual probes is typically between 50 and 200 bases.
  • These probes may be either designed to be overlapping probes, meaning that the starting nucleotides of adjacent probes are separated in the genome by less than the length of a probe, or non-overlapping probes, where the distance between adjacent probes are greater than the length of a probe.
  • the distance between adjacent probes is generally overlapping, with spacing between the starting nucleotide of two probes varying between 1 and 100 bases. The distance is varied to cause some genomic regions to be targeted by a larger number of probes than others.
  • This variation is used, for example, to modulate the capture efficiency of individual genomic regions, normalizing capture.
  • Probes can be tested for uniqueness in the genome.
  • highly repetitive elements of the genome are excluded from selection probe designs using a method that utilizes a strategy similar to the WindowMasker program developed by, for example, Morgolis (2006, Bioinformatics 15:134-141, incorporated herein by reference in its entirety) to identify these regions and exclude them from probe design.
  • the nature and performance of the designed probes for amplification for solution based capture methods of the present invention can be varied to advantageously normalize or adjust the distribution of the target molecules captured and enriched in accord with the methods of the present invention.
  • a goal of such normalization is to deliver one expressed gene per read (e.g., Soares, et al., 1994, Proc. Natl. Acad. Sci. 91:9228-9232). Normalization is applied, for example, to populations of cDNA molecules before library construction since generally the distribution of molecules in the population reflects the different expression levels of expressed genes from which the cDNA molecule populations are produced.
  • the number of sequencing reactions required to effectively analyze each target region is reduced by normalizing the number of copies of each target sequence in the enriched population such that across the set of probes the capture performance of distinct probes is normalized, on the basis of a combination of fitness and other probe attributes.
  • oligonucleotide probes as described in U.S. Patent Publication No. 2005/10282209, that enable uniform probe performance, eliminate hybridization artifacts and/or bias and provide higher quality output.
  • Probe lengths are adjusted (typically, about 20 to about 100 nucleotides, preferably about 40 to about 85 nucleotides, in particular about 45 to about 75 nucleotides, but optionally also more than 100 nucleotides until about 250 nucleotides) to equalize the melting temperature (e.g.
  • probes are optimized to perform equivalently at a given stringency in the genomic regions of interest, including AT- and GC-rich regions.
  • probe length, melting temperature and sequence can be coordinately adjusted for any given probe derived amplicon to arrive at a desired hybridization performance for the probe amplicon.
  • Capture performance can also be normalized by ascertaining the capture fitness of probe amplicons in the probe set, and then adjusting the quantity of individual probes on the solid support for amplification purposes accordingly. For example, if probe amplicons derived from a first probe is anticipated to capture twenty times as much nucleic acid as a second set of probe derived amplicons, then the capture performance of both probe amplicon sets can be equalized by providing twenty times as many copies of the second probe from amplification purposes, for example by increasing by twenty-fold the number of microarray probes displaying the second probe prior to amplification.
  • an additional strategy for normalizing capture of target nucleic acids is to subject the eluted target molecules to a second round of solution based hybridization against the probe derived amplicons under less stringent conditions than were used for the first hybridization round.
  • the second hybridization can be conducted under hybridization conditions that saturate all capture probes. Presuming that substantially equal amounts of the probe derived amplicons are provided in solution, saturation of the amplicons will ensure that substantially equal amounts of each target are eluted after the second hybridization and washing.
  • amplification primers utilized for in situ amplification of the hybridization probes for subsequent solution based capture and enrichment methods and systems described herein comprise linker chemistry such as binding moieties.
  • Binding moieties comprise any moiety that is attached or incorporated into the 5′ end of an amplification primer useful in subsequent capture of the probe amplicon/target nucleic acid hybridization complex.
  • a binding moiety is any sequence that is engineered into 5′ of a primer sequence, such as a 6 histidine (6HIS) sequence that is capturable.
  • a primer that comprises a 6HIS sequence is captureable by nickel, for example in a tube, microwell, or purification column that is coated with nickel or contains nickel coated beads, particles, etc.
  • Digoxigenin is capturable by use of an antibody to digoxigenin, for example a substrate that is coated or contains an anti-digoxigenin antibody.
  • an amplification primer used in methods and systems of the present invention contains a biotin moiety attached to the 5′ end of the primer and subsequent probe derived amplicons.
  • Biotin is capturable by streptavidin (SA), as such the biotin labeled amplicon can be captured on a substrate or column that is coated or contains SA.
  • streptavidin is coated onto paramagnetic particles that can be in turn captured magnetically for easy washing and elution of the target enriched nucleic acids.
  • the present invention is not limited by the kind of linker chemistry used, and a skilled artisan will know of other options that are equally amendable to methods and systems of the present invention.
  • the methods and systems comprise determining nucleic acid sequence information about at least one region of nucleic acid(s), in particular genomic nucleic acid(s), (the whole genome or at least one whole or partial chromosome) in a sample, the method comprising the steps of performing the methods as previously described followed by determining the nucleic acid sequence of the captured molecules, in particular by performing sequencing by synthesis reactions.
  • target nucleic acids are typically deoxyribonucleic acids or ribonucleic acids, and include products synthesized in vitro by converting one nucleic acid molecule type (e.g., DNA, RNA and cDNA) to another as well as synthetic molecules containing nucleotide analogues.
  • Denatured genomic DNA molecules are in particular molecules that are shorter than naturally occurring genomic nucleic acid molecules.
  • a skilled person can produce molecules of random- or non-random size from larger molecules by chemical, physical or enzymatic fragmentation or cleavage using well known protocols.
  • chemical fragmentation can employ ferrous metals (e.g., Fe-EDTA)
  • physical methods can include sonication, hydrodynamic force or nebulization (e.g., see European patent application EP 0 552 290)
  • enzymatic protocols can employ nucleases such as micrococcal nuclease (Mnase) or exo-nucleases (such as Exo1 or Bal31) or restriction endonucleases.
  • nucleases such as micrococcal nuclease (Mnase) or exo-nucleases (such as Exo1 or Bal31) or restriction endonucleases.
  • the present invention is not limited to the method in which fragments are generated and any method useful in fragmenting nucleic acids is contemplated.
  • embodiments of the present invention contemplate nucleic acid fragment sizes in the range of between about 100 and about 1000 nucleotide residues or base pairs, or between about 250 and about 800 nucleotide residues or base pairs, or about 400 to about 600 nucleotide residues or base pairs, in particular about 500 nucleotide residues or base pairs.
  • the population of nucleic acid molecules which may comprise the target nucleic acid sequences preferably contains the whole genome or at least one chromosome of an organism or at least one nucleic acid molecule with at least about 100 kb.
  • the size(s) of the nucleic acid molecule(s) is/are at least about 200 kb, at least about 500 kb, at least about 1 Mb, at least about 2 Mb or at least about 5 Mb, especially a size between about 100 kb and about 5 Mb, between about 200 kb and about 5 Mb, between about 500 kb and about 5 Mb, between about 1 Mb and about 2 Mb or between about 2 Mb and about 5 Mb.
  • the nucleic acid molecules are genomic DNA, while in other embodiments the nucleic acid molecules are cDNA, or RNA species (e.g., tRNA, mRNA, miRNA).
  • the nucleic acid molecules which may or may not comprise the target nucleic acid sequences may be selected from an animal, a plant or a microorganism, in particular embodiments the nucleic acid molecules are from a primate, preferably a human.
  • the nucleic acids are amplified (e.g., by whole genome amplification) prior to practicing the method of the present invention. For example, prior amplification may be necessary for performing embodiments of the present invention for forensic purposes (e.g., in forensic medicine, etc.).
  • the population of nucleic acid molecules is a population of genomic DNA molecules.
  • the hybridization probes and subsequent amplicons may comprise one or more sequences that target a plurality of exons, introns or regulatory sequences from a plurality of genetic loci, the complete sequence of at least one single genetic locus, said locus having a size of at least 100 kb, preferably at least 1 Mb, or at least one of the sizes as specified above, sites known to contain SNPs, or sequences that define an array, in particular a tiling array, designed to capture the complete sequence of at least one complete chromosome.
  • target nucleic acid sequences are enriched from one or more samples that include nucleic acids from any source, in purified or unpurified form.
  • the source need not contain a complete complement of genomic nucleic acid molecules from an organism.
  • the sample preferably from a biological source, includes, but is not limited to, pooled isolates from individual patients, tissue samples, or cell culture.
  • the target region can be one or more continuous blocks of several megabases, or several smaller contiguous or discontiguous regions, such as all of the exons from one or more chromosomes, or sites known to contain SNPs.
  • the hybridization probes and subsequent probe derived amplicons can support a tiling array designed to capture one or more complete chromosomes, parts of one or more chromosomes, all exons, all exons from one or more chromosomes, selected exons, introns and exons for one or more genes, gene regulatory regions, and so on.
  • the probes can be directed to sequences associated with (e.g., on the same fragment as, but separate from) the actual target sequence, in which case genomic fragments containing both the desired target and associated sequences will be captured and enriched.
  • the associated sequences can be adjacent or spaced apart from the target sequences, but a skilled person will appreciate that the closer the two portions are to one another, the more likely it will be that genomic fragments will contain both portions.
  • sequential rounds of capture using distinct but related capture probe sets, and thus probe derived amplicons, directed to the target region is performed.
  • Related probes are probes corresponding to regions in close proximity to one another in the genome that hybridize to the same genomic DNA fragment.
  • the methods comprise the step of ligating adaptor or linker molecules to one or both ends of the nucleic acid molecules prior to denaturation and hybridization to the probe amplicons in solution.
  • the methods further comprise amplifying said adaptor modified nucleic acid molecules with at least one primer, said primer comprising a sequence which specifically hybridizes to the sequence of said adaptor molecule(s).
  • double-stranded linkers are provided at one or both ends of the fragmented nucleic acid molecules before sample denaturation and hybridization to the probe derived amplicons in solution.
  • target nucleic acid molecules are amplified after elution to produce a pool of amplified products having further reduced complexity relative to the original sample.
  • the target nucleic acid molecules can be amplified using, for example, non-specific Ligation Mediated-PCR (LM-PCR) through multiple rounds of amplification and the products can be further enriched, if required, by one or more rounds of selection against the amplicon derived probes.
  • LM-PCR non-specific Ligation Mediated-PCR
  • the linkers or adaptors are provided, for example, in an arbitrary size and with an arbitrary nucleic acid sequence according to what is desired for downstream analytical applications subsequent to the complexity reduction step.
  • the linkers can range between about 12 and about 100 base pairs, including a range between about 18 and 100 base pairs, and preferably between about 20 and 24 base pairs.
  • Adaptor molecules in the context of the present invention are preferably defined as blunt-ended double-stranded oligonucleotides.
  • the double stranded target molecules are subjected to, for example, a fill-in reaction with a DNA Polymerase such as T4 DNA polymerase or Klenow polymerase in the presence of dNTPs, which results in blunt ended target molecules.
  • a DNA Polymerase such as T4 DNA polymerase or Klenow polymerase
  • ends of the fragments are phosphorylated using T4 Polynucleotide kinase and methods known to skilled artisans (for example, see Molecular Cloning: A Laboratory Manual, Eds.
  • phosphate groups to the 5′ termini of the fragments prior to the ligation of the adaptors.
  • Subsequent ligation of the adaptors (e.g., short double stranded blunt end DNA oligonucleotides with about 3-20 base pairs) onto the polished, phosphorylated target DNA may be performed according to any method which is known in the art, for example by T4 DNA ligase reaction.
  • the ligation of the adaptors to the fragmented target nucleic acid molecules may be performed prior to, or after, exposing a sample that comprises fragmented, denatured genomic nucleic acid molecules to multiple oligonucleotide probes amplicons in solution under hybridizing conditions to capture target nucleic acid molecules.
  • a sample that comprises fragmented, denatured genomic nucleic acid molecules to multiple oligonucleotide probes amplicons in solution under hybridizing conditions to capture target nucleic acid molecules.
  • the enriched nucleic acids which are released from the amplicons in single stranded form are initially re-annealed followed by a primer extension reaction and a fill-in reaction according to standard methods known in the art.
  • adaptor molecules allows for a step of subsequent amplification of the captured molecules. Independent from whether ligation takes place prior to or after the capturing step, there exist several alternative embodiments.
  • one type of adaptor molecule e.g., adaptor molecule A
  • two types of adaptor molecules A and B are used.
  • enriched molecules composed of three different types: (i) fragments having one adaptor (A) at one end and another adaptor (B) at the other end, (ii) fragments having adaptors A at both ends, and (iii) fragments having adaptors B at both ends.
  • the generation of enriched molecules with adaptors is of outstanding advantage, if amplification and sequencing is to be performed, for example using the 454 Life Sciences Corporation GS20 and GSFLX instrument (e.g., see GS20 Library Prep Manual, December 2006, WO 2004/070007; incorporated herein by reference in their entireties).
  • the present invention is directed to a method for detecting coding region variation(s) of a test genome sample relative to a reference genome sample, in particular relative to a reference genome that comprises fragmented, denatured genomic nucleic acid molecules, the method comprising the steps as previously described on both a test and reference genome, further comparing the sequences to a sequence in a database, in particular to a sequence in a database of polymorphisms in a reference genome sample to identify variants from a test genome sample.
  • the invention is, therefore, useful in searching for genetic variants and mutations, such as single nucleotide polymorphisms (SNP), or set of SNPs, genomic insertions and/or deletions, translocations, etc. that may underlie human diseases. It is contemplated that capture and enrichment using solution based hybridization technology as described herein is more flexible than other methods currently available in the field of genomic enrichment.
  • the eluted target nucleic acid sequences may be sequenced, hybridized to a resequencing or SNP-calling array and the sequence or genotypes may be further analyzed.
  • Solution based enrichment as provided by embodiments of the present invention enables targeted array-based-, shotgun-, capillary-, or other sequencing methods known in the art.
  • strategies for shotgun sequencing of randomly generated fragments are cost-effective and readily integrated into a pipeline.
  • the present invention enhances the efficiency of the shotgun approach by presenting only fragments from one or more genomic regions of interest for sequencing.
  • the invention provides an ability to focus the sequencing strategies on specific genomic regions, such as individual chromosomes or exons for medical sequencing purposes. As such, a more focused approach to disease discovery is realized.
  • the eluted target nucleic acid sequences resulting from solution based enrichment methods as described herein are subsequently sequenced.
  • Sequencing can be performed by a number of different methods, such as by employing sequencing by synthesis technology.
  • Sequencing by synthesis according to the prior art is defined as any sequencing method which monitors the generation of side products upon incorporation of a specific deoxynucleoside-triphosphate during the sequencing reaction (Hyman, 1988, Anal. Biochem. 174:423-436; Rhonaghi et al., 1998, Science 281:363-365).
  • One prominent embodiment of the sequencing by synthesis reaction is the pyrophosphate sequencing method.
  • the 454 Genome Sequencer System (Roche Applied Science cat. No. 04 760 085 001), an example of sequence by synthesis, is based on the pyrophosphate sequencing technology.
  • the average genomic DNA fragment size is in the range of 200 or 600 bp, respectively, as described in the product literature.
  • a sequencing by synthesis reaction can alternatively be based on a terminator dye type of sequencing reaction.
  • the incorporated dye deoxynucleotriphosphates (ddNTPs) building blocks comprise a detectable label, which is preferably a fluorescent label that prevents further extension of the nascent DNA strand.
  • the label is then removed and detected upon incorporation of the ddNTP building block into the template/primer extension hybrid for example by using a DNA polymerase comprising a 3′-5′ exonuclease or proofreading activity.
  • amplification is performed by emulsion PCR.
  • the step of amplification is performed by emulsion PCR methods.
  • the beads carrying the clonally amplified target nucleic acids may then become arbitrarily transferred into a picotiter plate according to the manufacturer's protocol and subjected to a pyrophosphate sequencing reaction for sequence determination.
  • the present invention comprises a kit comprising reagents and materials for performing methods according to the present invention.
  • a kit may include one or more of a microarray substrate upon which is immobilized a plurality of hybridization probes specific to one or more target nucleic acid sequences from one or more target genetic loci (e.g., specific to exons, introns, SNP sequences, etc.), a plurality of probes that define a tiling array designed to capture the complete sequence of at least one complete chromosome, amplification primers, reagents for performing polymerase chain reaction methods (e.g., salt solutions, polymerases, dNTPs, amplification buffers, etc.), reagents for performing ligation reactions (e.g., ligation adaptors, T4 polynucleotide kinase, ligase, buffers, etc.), substrates comprising a binding partner moiety, tubes, hybridization solutions, wash solutions, el
  • the present invention provides a system (e.g., kit) for performing a method or part of a method according to the present invention as disclosed herein.
  • the present invention is a kit comprising a (first) double stranded adaptor molecule and multiple probe derived amplicons in solution, wherein the probe derived amplicons are amplified from a plurality of probes that defines a plurality of exons, introns and/or regulatory sequences from a plurality of genetic loci, and/or a plurality of probe derived amplicons in solution that defines the complete sequence of at least one single genetic locus, said locus having a size of at least 100 kb, preferably at least 1 Mb or a size as specified herein, and/or a plurality of probe derived amplicons that defines sites known to contain SNPs, and/or a plurality of probe derived amplicons that defines an array, in particular a tiling array especially designed to capture the complete sequence of at least one complete chro
  • a kit comprises one or more capture molecules or compounds.
  • at least one oligonucleotide probe comprises a modification which allows for immobilization onto a solid support.
  • a probe comprises a biotin moiety for immobilization onto a streptavidin coated paramagnetic particle.
  • a hapten such as digoxigenin
  • a hapten recognizing antibody e.g., anti-digoxigenin
  • kits of the present invention further comprises at least one or more compounds from a group consisting of DNA polymerase, T4 polynucleotide kinase, T4 DNA ligase, one or more array hybridization solutions, and/or one or more array wash solutions.
  • three wash solutions are included in a kit of the present invention, the wash solutions comprising SSC, DTT and optionally SDS.
  • kits of the present invention comprise Wash Buffer I (0.2% SSC, 0.2% (v/v) SDS, 0.1 mM DTT), Wash Buffer II (0.2% SSC, 0.1 mM, DTT) and/or Wash Buffer III (0.05% SSC, 0.1 mM DTT).
  • systems of the present invention further comprise an elution solution, for example water or a solution containing TRIS buffer and/or EDTA.
  • Microarrays having immobilized probes are used in one- or multiple rounds of hybridization selection with a target of total genomic DNA, and the selected sequences are amplified by LM-PCR
  • DNA is fragmented using sonication to an average size of 500 base pairs.
  • a reaction to polish the ends of the sonicated DNA fragments is set up:
  • the reaction is incubated at 11° C. for 30 min.
  • the reaction is then subjected to phenol/chloroform extraction procedures and the DNA is recovered by ethanol precipitation.
  • the precipitated pellet is dissolved in 10 ⁇ l water (to give a final concentration of 2 ⁇ g/ ⁇ l).
  • Two complementary oligonucleotides are annealed to create a double-stranded linker, by mixing the following:
  • Oligonucleotide 1 (1 ⁇ g/ ⁇ l) 22.5 ⁇ l (5′-CTCGAGAATTCTGGATCCTC-3′) (SEQ ID NO: 1)
  • Oligonucleotide 2 (1 ⁇ g/ ⁇ l) 22.5 ⁇ l (5′-GAGGATCCAGAATTCTCGAGTT-3′) (SEQ ID NO: 2) 10x annealing buffer 5 ⁇ l Water to 50 ⁇ l
  • the reaction is heated at 65° C. for 10 min; then allowed to cool at 15-25° C. for 2 hours.
  • the length of the 2 complementary oligonucleotides 1 and 2 is between 12 and 24 nucleotides, and the sequence is selected depending upon the functionality desired by the user.
  • the double-stranded linker is then purified by column chromatography through a Sephadex G-50 spin column. The purified linker solution is then concentrated by lyophilization to a concentration of 2 ⁇ g/ ⁇ l.
  • the following reaction to ligate the linkers to genomic DNA fragments is set up.
  • the reaction is incubated at 14° C. overnight.
  • Annealed linkers from Step a) (20 ⁇ g) 10 ⁇ l Genomic DNA from Step a) (10 ⁇ l) 5 ⁇ l T4 DNA ligase 10 U 10x ligation buffer 2 ⁇ l Water to 20 ⁇ l
  • the reaction volume is adjusted to 500 ⁇ l with water and the ligated genomic DNA is purified using a QIAquick PCR purification kit.
  • the purified DNA is stored at a concentration of 1 ⁇ g/ ⁇ l.
  • linker modified genomic DNA (10 ⁇ g) is resuspended in 3.5 ⁇ l of nuclease-free water and combined with 31.5 ⁇ l NimbleGen Hybridization Buffer (Roche NimbleGen, Inc., Madison, Wis.), 9 ⁇ l Hybridization Additive (Roche NimbleGen, Inc), in a final volume of 45 ⁇ l.
  • the samples are heat-denatured at 95° C. for 5 minutes and transferred to a 42° C. heat block.
  • NimbleGen CGH arrays manufactured as described in U.S. Pat. No. 6,375,903 (Roche NimbleGen, Inc.).
  • Maskless fabrication of capture oligonucleotides on the microarrays is performed by light-directed oligonucleotide synthesis using a digital micromirror as described in Singh-Gasson et al. (1999, Nat. Biotech. 17:974-978, incorporated herein by reference in its entirety) as performed by a maskless array synthesizer.
  • Gene expression analysis using oligonucleotide arrays produced by maskless photolithography is described in Nuwaysir et al. (2002, Genome Res.
  • Hybridization is performed in a MAUI Hybridization System (BioMicro Systems, Inc., Salt Lake City, Utah) according to manufacturer instructions for 16 hours at 42° C. using mix mode B. Following hybridization, arrays are washed twice with Wash Buffer I (0.2 ⁇ SSC, 0.2% (v/v) SDS, 0.1 mM DTT, NimbleGen Systems) for a total of 2.5 minutes. Arrays are then washed for 1 minute in Wash Buffer II (0.2 ⁇ SSC, 0.1 mM DTT, NimbleGen Systems) followed by a 15 second wash in Wash Buffer III (0.05 ⁇ SSC, 0.1 mM DTT, Roche NimbleGen, Inc.).
  • Wash Buffer II 0.2 ⁇ SSC, 0.1 mM DTT, NimbleGen Systems
  • the arrays are incubated twice for 5 minutes in 95° C. water.
  • the eluted DNA is dried down using vacuum centrifugation.
  • the primary selected genomic DNA is amplified as described below. Ten separate replicate amplification reactions are set up in 200 ⁇ l PCR tubes. Only one oligonucleotide primer is required because each fragment has the same linker ligated to each end:
  • Cycle number Denaturation Annealing Polymerization 1 2 min at 95° C. 2-31 30 s at 95° C. 30 s at 55° C. 1 min at 72° C.
  • the reaction products are analyzed by agarose gel electrophoresis.
  • the amplification products are purified using a QIAquick PCR purification kit.
  • the eluted samples are pooled and the concentration of amplified primary selected DNA is determined by spectrophotometry. A volume of DNA in the pool equivalent to 1 ⁇ g is reduced to 5 ⁇ l in a speed vacuum concentrator.
  • One ⁇ l (at least 200 ng) of the primary selected material is set aside for comparison with the secondary selection products. As necessary, subsequent rounds of enrichment are performed by further rounds of array hybridization and amplification of the eluted sample.
  • Probes are synthesized on a microarray, then are released using a base-labile Fmoc (9-fluorenylmethyloxycarbonyl) group.
  • the probes are labelled with biotin and are then immobilized onto the surface of a streptavidin solid support using known methods for covalent or non-covalent attachment.
  • the synthesized probes are amplified using LM-PCR, Phi29 or other amplification strategy to increase the amount of the synthesized probes by virtue of inserting sequences upon them that facilitate their amplification.
  • This material can now be used for direct sequencing, array based resequencing, genotyping, or any other genetic analysis targeting the enriched region of the genome by employing solution phase hybridization and SA mediated capture of the hybridization products.
  • a series of high-density oligonucleotide microarrays that capture short segments that correspond to 6,726 individual gene exon regions of at least 500 base pairs were chosen from 660 genes distributed about the human genome (sequence build HG17) (approximately 5 Mb of total sequence) were synthesized according to standard Roche NimbleGen, Inc. microarray manufacturing protocols. Overlapping microarray probes of more than 60 bases each on the array spanned each target genome region, with a probe positioned each 10 bases for the forward strand of the genome.
  • Highly-repetitive genomic regions were excluded by design from the capture microarrays, to reduce the likelihood of non-specific binding between the microarrays and genomic nucleic acid molecules.
  • the strategy for identifying and excluding highly-repetitive genomic regions was similar to that of the WindowMasker program (Morgulis et al.).
  • the average 15-mer frequency of each probe was calculated by comparing the frequencies of all 15-mers present in the probe against a pre-computed frequency histogram of all possible 15-mer probes in the human genome. The likelihood that the probe represents a repetitive region of the genome increases as the average 15-mer frequency increases. Only probes having an average 15-mer frequency below 100 were included on the capture microarrays.
  • genomic DNA (20 ⁇ g) was subjected to whole genome amplification (WGA; using Qiagen service (Hilden, Germany)). Twenty ⁇ g of the WGA product was treated with Klenow fragment of DNA polymerase I (NEB, Beverly Mass.) to generate blunt-ends. The blunt-ended fragments were sonicated to generate fragments of about 500 base pairs and then 5′ phosphorylated with polynucleotide kinase (NEB).
  • WGA whole genome amplification
  • NEB DNA polymerase I
  • Oligonucleotide linkers 5′-Pi-GAGGATCCAGAATTCTCGAGTT-3′ (SEQ ID NO:2) and 5′-CTCGAGAATTCTGGATCCTC-3′ (SEQ ID NO: 1) were annealed and ligated to the ends of the 5′ phosphorylated fragments:
  • linker-terminated fragments were denatured to produce single stranded products that were exposed to the capture microarrays under hybridization conditions in the presence of 1 ⁇ hybridization buffer (Roche NimbleGen, Inc.) for approximately 65 hours at 42° C. with active mixing using a MAUI hybridization station (Roche NimbleGen, Inc.). Single-stranded molecules that did not hybridize were washed from the microarrays under stringent washing conditions, 3 ⁇ 5 minutes with Stringent Wash Buffer (Roche NimbleGen, Inc.) and rinsed with Wash Buffers I, II, and III (Roche NimbleGen, Inc.).
  • Fragments captured on the microarrays were immediately eluted with 2 ⁇ 250 ⁇ l of water at 95° C., dried and resuspended for amplification by LM-PCR using a primer complementary to the previously ligated linkers oligonucleotides.
  • Region 1 F 5′-CTACCACGGCCCTTTCATAAAG-3′ (SEQ ID NO: 3) R: 5′-AGGGAGCATTCCAGGAGAGAA-3′ (SEQ ID NO: 4) Region 2 F: 5′-GGCCAGGGCTGTGTACAGTT-3′ (SEQ ID NO: 5) R: 5′-CCGTATAGAAGAGAAGACTCAATGGA-3′ (SEQ ID NO: 6) Region 3 F: 5′-TGCCCCACGGTAACAGATG-3′ (SEQ ID NO: 7) R: 5′-CCACGCTGGTGATGAAGATG-3′ (SEQ ID NO: 8) Region 4 F: 5′-TGCAGGGCCTGGGTTCT-3′ (SEQ ID NO: 9) R: 5′-GCGGAGGGAGAGCTCCTT-3′ (SEQ ID NO: 10) Region 5 F: 5′-GTCTCTTTCTCTCTCTTGTCCAGTTTT-3′ (SEQ ID NO: 11) R: 5′-CACTGTCTTCTCCCGGACATG-3
  • the enriched, amplified samples and control genomic DNA, that was fragmented, linker-ligated and LM-PCR amplified, but not hybridized to a capture array were compared using an ABI 7300 real time PCR system (Applied Biosystems, Foster City, Calif.) measuring SYBR green fluorescence according to manufacturer's protocols. An average of 378-fold enrichment was achieved for three replicate exonic capture products. The theoretical maximum enrichment level was 600 fold (3,000 Mb in the genome and 5 Mb of total sequence).
  • BLAST analysis showed that 91%, 89%, and 91% of reads, respectively, mapped back uniquely to the genome; 75%, 65%, and 77% were from targeted regions and 96%, 93%, and 95% of target sequences contained at least one sequence read (Table 1, upper three rows) representing an average enrichment of about 400 fold.
  • the median per-base coverage for each sample was 5-, 7- and 7-fold coverage respectively.
  • genomic DNA samples from four cell types in the human HapMap collection were captured on the exon arrays of the prior examples, eluted and sequenced, as disclosed herein, except that the genomic DNAs were not whole genome amplified before capture.
  • the capture results (shown in Table 1, rows 4-7) were similar to those above, except that sequence coverage was consistently more uniform than before, suggesting a bias introduced during WGA.
  • the sequence from the four HapMap samples was assembled and mutations were identified and compared to the HapMap SNP data for each sample (Tables 1 and 2).
  • the total number of positions in the target regions that were genotyped in the HapMap project was 8103 (CEU), 8134 (CHB), 8134 (JPT), 8071 (YR1) for each of the four genomes. Of these, most ( ⁇ 6000) sites were homozygous for the reference genome allele.
  • the number of known variant alleles is listed in the second row of Table 2. These positions were analyzed for coverage and to determine whether the allele(s) were found in the captured DNA.
  • Table 4 shows that all capture targets performed well, with up to 140 Mb of raw sequence generated in a single sequencing machine run, generating 18 fold coverage, from a 5 Mb capture region. It was demonstrated that the percentage of reads that map to the target sequence increased with the size of the target region.
  • Example 2 and 3 The sample of Examples 2 and 3 was tested using capture probes synthesized upon, then liberated from, a solid support such that the enrichment was advantageously executed in solution phase.
  • Standard microarray designs e.g. the BRCA1 200K Tiling array and human exon capture arrays of the prior examples
  • terminal 15mer primer sequences containing an MlyI recognition site were modified by adding terminal 15mer primer sequences containing an MlyI recognition site, which facilitates enzymatic primer removal while leaving the capture oligonucleotide sequence intact.
  • Arrays were synthesized by adding chemical phosphorylating reagent (Glen Research) after the initial T 5 linker and before the 3′ primer sequence. Three individual couplings were performed to maximize subsequent cleavage of capture probes from the arrays.
  • the array-immobilized capture probes were treated with 30% ammonium hydroxide (NH 4 OH, Aldrich). After synthesis, arrays were placed in a humid chamber and approximately 700 ⁇ l of NH 4 OH was applied to the synthesis area at ambient room temperature for 20 minutes to cleave the probes from the array. The NH 4 OH remained largely within the confines of the synthesis area because of hydrophobicity differences between the reaction area and the surrounding glass. The solution was removed using a pipette and was retained. An additional 700 ⁇ l of fresh NH 4 OH was applied to the surface. The process was repeated for a total of 3 ⁇ (60 min and 2.1 ml total). Cleaved oligonucleotide capture probes were then dried by centrifugation under vacuum under standard conditions known in the art
  • the cleaved capture probes were amplified under standard conditions. Dried probes were resuspended in 30 ⁇ l deionized water (diH 2 O) and aliquoted into 30 individual PCR runs as follows:
  • Primer 1a 5′-TGCCGGAGTCAGCGT-3′ (SEQ ID NO: 19)
  • Primer 1b 5′-Biotin-AGTCAGAGTCGCCAC-3′ (SEQ ID NO: 20) The reactions are amplified according to the following program:
  • PCR products were purified away from reaction components using the QiaQuick Nucleotide Removal Kit (Qiagen), dried down, and resuspended in 20 ⁇ l diH 2 O. Typical yield after purification was approximately 400-700 ng/rxn by Nanodrop. Amplicons may be checked on a 3% agarose gel. Depending on quantity requirements of capture probes, additional PCR rounds were performed as above yielding approximately 200 ng of sample per reaction. Amplicons were purified and characterized as above.
  • the final round of amplification of the capture probes was performed using asymmetric PCR.
  • the protocol was as above, except that while the biotinylated primer concentration remained the same, the non-biotinylated primer concentration was reduced to 0.001 ⁇ of the original concentration.
  • the protocol was extended to 35 cycles to allow for non-exponential amplification. Amplicons were dried, resuspended in 20 ⁇ l DIH 2 O, and characterized.
  • the genomic DNA sample was prepared per standard protocol; 20 ⁇ g of WGA Tinkered sample was dried with 100 ⁇ g Cot-1 DNA and resuspended in 7.5 ⁇ l hybridization buffer and 3 ⁇ l formamide. A 2 ⁇ g aliquot of capture probes was dried and resuspended in 4.5 ⁇ l diH 2 O. The sample solution was mixed with the capture probe solution and incubated at 95° C. for 10 minutes. The mixture was then transferred to a PCR tube and placed in a thermal cycler for 3 days at 42° C. for hybridization to form duplexes.
  • the duplexes were bound to paramagnetic beads (Dynal). 25 ⁇ l of beads were washed three times in 2 ⁇ BW buffer (10 mM Tris HCl, 1 mM EDTA, 2M NaCl), and the beads were resuspended in the hybridization mixture. Binding occurred over 45 minutes at 42° C. with occasional gentle mixing.
  • Bound beads were isolated using a magnet and washed briefly with 40 ⁇ l Wash Buffer I, incubated for 2 ⁇ 5 minutes in 47° C. stringent wash buffer, washed with Wash Buffer I for approximately 2 minutes at ambient room temperature, with Wash Buffer II for approximately 1 minute, and with Wash Buffer III for approximately 30 seconds.
  • the solution containing beads in Wash Buffer III was transferred to a 1.5 ml Eppendorf tube.
  • the beads were isolated with a magnet.
  • the wash buffer was removed and ⁇ 100 ul of 95° C. diH 2 O is added.
  • the solution was incubated at 95° C. for 5 minutes, after which the beads were bound with a magnet and gently washed with 95° C. diH 2 O.
  • the wash liquid was then removed and retained, and replaced with fresh 95° C. diH 2 O. Incubation and washing was repeated for a total of 3 times (15 minutes, approximately 300 ⁇ l eluate).
  • the Eppendorf tube containing eluate is placed on a magnetic stand for approximately 5 minutes to isolate any beads aspirated during elution.
  • the solution was dried at high heat in a fresh Eppendorf tube.
  • the eluted captured fragments were resuspended in 263 ⁇ l diH 2 O prior to standard LM-PCR.
  • LM-PCR Following LM-PCR, the captured fragments were subjected to standard ultra-deep sequencing using the 454 FLX platform, as above.
  • LM-PCR can be avoided by ligating 454 sequencing adapter sequences to the pre-enrichment sample. In that case, the eluted enriched sequences can be piped directly into the emulsion PCR for ultra-deep sequencing.
  • a standard microarray design was modified by addition of a terminal 15 mer primer sequence containing a MlyI (GAGTC(5/5)) recognition site. Incorporation of a MlyI site into the primer sequence facilitates enzymatic primer removal while leaving the capture oligonucleotide sequences intact.
  • Arrays were synthesized via standard maskless array synthesis methods known to those skilled in the art.
  • Capture probes were amplified using in situ polymerase chain reaction (PCR) on an array in a thermal cycler using a sealing hybridization chamber (Grace Bio-Labs, Inc., Bend, Oreg.) and Slide Griddle Adaptor (Bio-Rad Laboratories, Hercules, Calif.).
  • PCR in situ polymerase chain reaction
  • PCR reaction constituents 25 ul of 10 ⁇ polymerase buffer, 1.25 ul of 25 mM dNTPs, 12.5 ul each of 20 uM primer 1a and 1b, 2.5 ul of Hotstart Taq polymerase, 10 ul 25 mM MgCl 2 and 176.5 ul diH 2 O, total reaction volume of 250 ul
  • PCR reaction constituents 25 ul of 10 ⁇ polymerase buffer, 1.25 ul of 25 mM dNTPs, 12.5 ul each of 20 uM primer 1a and 1b, 2.5 ul of Hotstart Taq polymerase, 10 ul 25 mM MgCl 2 and 176.5 ul diH 2 O, total reaction volume of 250 ul
  • PCR reaction constituents 25 ul of 10 ⁇ polymerase buffer, 1.25 ul of 25 mM dNTPs, 12.5 ul each of 20 uM primer 1a and 1b, 2.5 ul of Hotstart Taq polymerase, 10 ul 25 mM MgCl 2
  • Primer sequences were primer 1a 5′-TGCCGGAGTCAGCGT-3′ (SEQ ID NO: 19) and primer 1b 5′-Biotin-AGTCAGAGTCGCCAC-3′ (SEQ ID NO: 20), reflecting primer binding sites that were incorporated into the probe sequences.
  • Polymerase chain reaction capture probe amplicons were purified from the reaction components using the QIAquick® Nucleotide Removal Kit (Qiagen, Inc., Valencia, Calif.), dried down and resuspended in 20 ul diH 2 O. Amplification yield was roughly 5 ug total as measured by NanoDrop® spectrophotometry (Thermo Fisher Scientific). Additional amplification rounds, following the protocol above, can be performed if additional amplicon quantity is needed (e.g., using the above protocol and 100 ng sample per reaction).
  • the final round of amplification of the capture probes was performed using asymmetric PCR; 2.5 ul 10 ⁇ polymerase buffer, 0.125 ul 25 mM dNTPs, 0.0125 ul of 20 uM primer 1a, 1.25 ul of 20 uM primer 1b, 0.25 ul Hotstart Taq, 1 ul 25 mM MgCl 2 and 18.86 ul diH 2 O (total reaction volume of 25 ul). Amplicons were purified away from reaction components using the Qiagen MinEluteTM columns and quantitated as previously described.
  • a genomic DNA sample was prepared per standard protocol. Twenty ug of the sample with linkers attached was dried with 100 ug Cot-1 DNA and resuspended in 7.5 ul hybridization buffer (Roche NimbleGen, Madison, Wis.) and 3 ul formamide. A 1 ug aliquot of capture probes was dried and resuspended in 4.5 ul diH 2 O. The sample solution was incubated at 95° C. for 10 min. to denature the DNA and added to the capture probe solution. The mixture was transferred to a PCR tube and placed in a thermal cycler at 42° C. for 3 days to allow duplex formation to occur.
  • duplexes were bound to streptavidin coated paramagnetic beads (Dynal®, Invitrogen, Carlsbad, Calif.). One hundred microliters of beads were washed three times with 2 ⁇ BW buffer (10 mM Tris HCl, 1 mM EDTA, 2M NaCl) and resuspended in the hybridization duplex mixture. Binding between the beads and duplexes was allowed to occur over 45 min. at 42° C. with occasional gentle mixing. Bound beads were isolated using a magnet and briefly washed in Wash Buffer I (0.2 ⁇ SSC, 0.2% (v/v) SDS, 0.1 mM DTT) at room temperature, followed by two washes (each wash for 5 min.
  • Wash Buffer I 0.2 ⁇ SSC, 0.2% (v/v) SDS, 0.1 mM DTT
  • Captured fragments were eluted from the beads.
  • the washed bead solution in Wash Buffer III was transferred to a 1.5 ml Eppendorf tube, the beads were isolated with a magnet, the wash buffer removed and replaced with 100 ul 95° C. diH 2 O and the beads released from the magnet.
  • the suspended beads were incubated at 95° C. for 5 min. after which the beads were captured and gently washed with 95° C. diH 2 O to elute the captured fragments.
  • the eluate was removed and the beads were washed again, for a total of three water washes; total of 10 min. with final volume of pooled eluate approximately 300 ul.
  • LM-PCR Following LM-PCR, the captured fragments were subjected to ultradeep sequencing using the 454 FLX platform (454 Life Sciences, Branford, Conn.). Alternatively, LM-PCR can be avoided by ligating 454 sequencing adaptor sequences to the pre-enrichment sample. In the latter case, the eluted enriched sequences can be added directly in the emulsion PCR of the 454 FLX platform workflow.
  • FIG. 2 illustrates a resequencing experiment from fragments captured in solution using the methods as described above.
  • the qPCR controls utilizing PCR control primer sequences indicate an average of 2600 fold enrichment across the four control loci.

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EP2535429A1 (en) 2012-12-19
EP2209913A1 (en) 2010-07-28
ES2633567T3 (es) 2017-09-22
CA2699835A1 (en) 2009-04-30
EP2209913B1 (en) 2014-09-10
ES2522912T3 (es) 2014-11-19
CN101835907A (zh) 2010-09-15
US9790543B2 (en) 2017-10-17
US20180030521A1 (en) 2018-02-01
WO2009053039A1 (en) 2009-04-30
EP2053132A1 (en) 2009-04-29
CN101835907B (zh) 2014-06-11
CA2699835C (en) 2015-12-15
EP2535429B1 (en) 2017-04-19
JP2013150637A (ja) 2013-08-08
JP2011500069A (ja) 2011-01-06
US10900068B2 (en) 2021-01-26
US20120046175A1 (en) 2012-02-23

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