Screening For Structural Variants

  *US10066259B2*
  US010066259B2                                 
(12)United States Patent(10)Patent No.: US 10,066,259 B2
  et al. (45) Date of Patent:Sep.  4, 2018

(54)Screening for structural variants 
    
(75)Inventor: Good Start Genetics, Inc.,  Cambridge, MA (US) 
(73)Assignee:Good Start Genetics, Inc.,  Cambridge, MA (US), Type: US Company 
(*)Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 U.S.C. 154(b) by 34 days. 
(21)Appl. No.: 14/989,073 
(22)Filed: Jan.  6, 2016 
(65)Prior Publication Data 
 US 2016/0194692 A1 Jul.  7, 2016 
 Related U.S. Patent Documents 
(60)Provisional application No. 62/100,254, filed on Jan.  6, 2015.
 
Jan.  1, 2013 C 12 Q 1 6827 F I Sep.  4, 2018 US B H C Jan.  1, 2013 C 12 Q 1 686 L I Sep.  4, 2018 US B H C Jan.  1, 2013 C 12 Q 1 6809 L I Sep.  4, 2018 US B H C Jan.  1, 2013 C 12 Q 1 6869 L I Sep.  4, 2018 US B H C 1 1 Jan.  1, 2013 C 12 Q 1 6827 L I Sep.  4, 2018 US B H C 2 Jan.  1, 2013 C 12 Q 2521 501 L A Sep.  4, 2018 US B H C 3 Jan.  1, 2013 C 12 Q 2525 161 L A Sep.  4, 2018 US B H C 4 Jan.  1, 2013 C 12 Q 2525 301 L A Sep.  4, 2018 US B H C 2 1 Jan.  1, 2013 C 12 Q 1 686 L I Sep.  4, 2018 US B H C 2 Jan.  1, 2013 C 12 Q 2531 125 L A Sep.  4, 2018 US B H C
(51)Int. Cl. C12Q 001/68 (20180101); C07H 021/00 (20060101); C12P 019/34 (20060101); C12Q 001/6827 (20180101); C12Q 001/6869 (20180101); C12Q 001/6809 (20180101); C12Q 001/686 (20180101)

 
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     * cited by examiner
 
     Primary Examiner —Ethan C Whisenant
     Art Unit — 1634
     Exemplary claim number — 1
 
(74)Attorney, Agent, or Firm — Brown Rudnick LLP; Thomas C. Meyers

(57)

Abstract

The invention relates to carrier screening and methods for describing a structural variant, such as a large rearrangement or chromosomal abnormality, in a person's genome using probes that are designed to determine the person's genetic sequence and reveal substitution mutations and small structural variants. Identifying a structural variant may include exposing a nucleic acid to a plurality of probes. Each probe has a linked pair of targeting arms designed to hybridize upstream and downstream of a target in a genome. The method includes hybridizing two of the probes to the nucleic acid and attaching the two probes together to create an inter-probe product as well as detecting the inter-probe product and reporting a structural variant of the genome in the nucleic acid.
21 Claims, 5 Drawing Sheets, and 5 Figures


CROSS-REFERENCE TO RELATED APPLICATION

[0001] This application claims priority to, and the benefit of, U.S. Provisional Patent Application No. 62/100,254, filed Jan. 6, 2015, the contents of which are incorporated by reference.

FIELD OF THE INVENTION

[0002] The invention relates to carrier screening and methods of detecting structural variant breakpoints using molecular inversion probes.

BACKGROUND

[0003] Molecular inversion probes (MIPs) can be used to capture targeted regions of a person's genetic material and to assay for disease-associated mutations. Each MIP has two linked oligonucleotide targeting arms that are designed to hybridize to a strand of nucleic acid in positions that flank a region of interest. In a typical assay, a set of MIPs is used to cover a gene segment of interest. Most of the MIPs hybridize to their intended target. Upon successful hybridization, the two targeting arms of one MIP are connected together in a ligation step into a covalently closed circle. Such assays are useful in interrogating the genome for mutations such as single-nucleotide polymorphisms.
[0004] Unfortunately, some mutations such as unexpected deletions, insertions, translocations, or inversions may be associated with an absent or incomplete targeting arm hybridization site and thus interfere with the ability of the MIPs to hybridize and be circularized. Unbound DNA and un-circularized MIPs are typically digested away by an exonuclease after which the circularized MIPs are used in amplification or sequencing reactions.

SUMMARY

[0005] Methods of the invention use MIPs to detect structural variants such as insertions, inversions, translocations, and deletions in a nucleic acid. Where a nucleic acid contains a structural variant, that nucleic acid may either lack one of the two hybridization sites for the two targeting arms of a MIP or one of the two arm targeting sites may be sufficiently separated such that the two arms of the probe will not connect as efficiently. Accordingly, that MIP effectively hybridizes to the genome with a single targeting arm. If a second MIP hybridizes in proximity to that first MIP, also by only one targeting arm, those two MIPs may be ligated together without being circularized. The second probe may hybridize by only one arm because the nucleic acid lacks one of its intended hybridization sites, or it could simply be the case this second arm has temporarily melted off the template molecule, thereby allowing the connection of the arm of probe 1 and probe. Since structural variants in the nucleic acid causes the two MIPs to be ligated together without circularization, detecting the two MIPs ligated together can reveal the presence of the insertion or deletion in the nucleic acid. If the un-circularized MIPs are discarded, as is common in MIP reactions, then information about structural variants gets thrown away. Instead, methods of the invention use the detection of un-circularized MIPs that have been ligated together to report the presence of an insertion, inversion, translocation, or deletion (structural variants) in the nucleic acid.
[0006] Reporting of structural variants via detection of MIPs ligated together may be performed as part of the same amplification and/or sequencing reactions that are also used to analyze the circularized MIPs. Thus, reporting of substitutions and structural variants through sequencing of circularized and non-circularized MIPs, respectively, may be provided in an assay that uses a single multiplex capture reaction.
[0007] Preferably, genomic DNA is captured using a set of MIPs designed to cover portions of genes of interest. Genomic DNA that is captured by the circularized MIPs can be sequenced to show substitutions or small structural variants in the genome while MIPs ligated together, or ‘inter-probe products,” are detected and used to describe a location of structural variants. While conventional MIP capture reactions digest the inter-probe product with exonuclease, methods of the invention may include protecting inter-probe product from exonuclease digestion, for example, by including a phosphorothioate base in the MIP backbone. Methods include detecting or sequencing the captured inter-probe product and reporting on a patient's genotype using information from sequencing both circularized probes and inter-probe product. Thus, methods of the invention provide genotyping assays that robustly and reliably detect and report mutations of different categories, such as small structural variants and substitutions as well as large chromosomal abnormalities. Methods of the invention have particular application in carrier screening, for reporting whether a patient is a carrier of a mutation that is associated with a Mendelian recessive genetic disease.
[0008] In certain aspects, the invention provides a method of identifying a mutation. The method includes exposing a nucleic acid to a plurality MIPs, each MIP having two targeting arms designed to hybridize upstream and downstream of a target in a genome. Two of the MIPs that each hybridizes to the nucleic acid by only one of their two targeting arms are connected together to create an inter-probe product. The method includes detecting the inter-probe product and detecting, identifying, or reporting a structural variant of the genome in the nucleic acid. The attaching may include filling in a gap between the two MIPs along the strand of nucleic acid using a polymerase, making a covalent attachment with a ligase, or both. Preferably, the method includes sequencing the inter-probe product to produce sequence reads, comparing the sequence reads to a reference genome, and describing a location of the structural variant within a gene associated with a Mendelian recessive hereditary disorder. A breakpoint in the nucleic acid based on the two MIPs that each hybridizes to the nucleic acid by a single targeting arm may be described. The structural variant may be identified as lying within an exon of a gene associated with the hereditary disorder. In some embodiments, the method includes producing a report that describes whether a person is a carrier of a hereditary disorder.
[0009] The method may include enzymatically converting at least some MIPs that hybridize to the nucleic acid by both targeting arms into covalently closed circles and sequencing at least a portion of the covalently closed MIPs to produce the sequence reads. Based on analysis of the sequence reads, one or more mutations in the nucleic acid from a person may be described in comparison to the reference genome. Methods of the invention may include multiplex sequencing and/or capture reactions. For example, MIPs may be exposed to the nucleic acid all free in solution and in one reaction volume. The method may include circularizing some of the MIPs (e.g., using ligase) and sequencing the circularized MIPs and the inter-probe product. The method may include digesting single-stranded nucleic acid material with an exonuclease prior to detecting the inter-probe product. In some embodiments, one or more MIPs include some moiety or feature to resist exonuclease digestion of that probe such as a phosphorothioate base or bases.
[0010] Aspects of the invention provide a method of identifying a structural variant that includes exposing a nucleic acid from a patient to a plurality of probes. Each probe has a linked pair of targeting arms designed to hybridize upstream and downstream of a target in a genome. Preferably, the plurality of probes is designed to cover at least a portion of a gene associated with a Mendelian recessive hereditary disorder. Two of the probes that hybridize to the nucleic acid are ligated together to create an inter-probe product, and some probes that hybridize to the nucleic acid by both targeting arms may be circularized. The method includes sequencing the inter-probe product and at least a portion of the circularized probes to produce sequence reads, which may be analyzed, e.g., by assembly or comparison to a reference genome. One or more substitution mutations and a structural variant within the gene are described as found in the nucleic acid from the patient.
[0011] In a preferred embodiment, the probes are molecular inversion probes that each include two linked targeting arms. For each probe, the arms include oligonucleotide portions that are designed to hybridize to portions of the nucleic acid that flank a target of interest. The hybridized probes are circularized, which may include extending one targeting arm with a polymerase and ligating the extended targeting arm to the other targeting arm to close the probe into a circle. Additionally, inter-probe products may be made by ligating pairs of probes together that are hybridized adjacent to one another along the nucleic acid. Making the inter-probe product may include filling in a gap between the two probes along the strand of nucleic acid using a polymerase and using a DNA ligase.
[0012] Methods may include a digestion step for the capture reaction. Single-stranded nucleic acid material may be digested with a nuclease prior to the sequencing. With the probes exposed to the nucleic acid, an exonuclease or a cocktail of exonucleases digests non-circularized product. Additionally, the probes may be designed to resist nuclease digestion when in inter-probe product form by, for example, inclusion of phosphorothioate base in the backbone.
[0013] The circularized probes and the inter-probe product may optionally be amplified and then preferably are sequenced to produce sequence reads. The sequence reads are assembled, compared to a reference, or both, to describe a genotype (e.g., of the patient from whom the nucleic acid was obtained). Where sequence reads vary from a reference, a mutation can be called and reported. For example, if a base of the person's DNA is different than the corresponding base in the reference, a substitution mutation may be reported. Where inter-probe product is present, a structural variant is reported. By using information about the target to which the pair of probes in the inter-probe product is designed to hybridize, a location of the structural variant in the patient's genome may be described. Thus methods of the invention may include producing a report that describes, within the patient's genome, both mutations such as substitutions or small indels as well as information on structural variants such as a location of a breakpoint. By these means, the methods may be used to produce a report that identifies that the patient is a carrier of the Mendelian recessive hereditary disorder.
[0014] In some aspects the invention provides a method of identifying splice forms (sometimes called isoforms). The method includes exposing a sample comprising cDNA or RNA to a plurality of molecular inversion probes (MIPs). Two of the MIPs via arms that have hybridized to the same cDNA or RNA molecule are connected together to create an inter-probe product, which is detected. The method includes identifying a splice form of an RNA transcript of a gene in the genome. The two MIPs may be connected together by filling in a gap between them along the cDNA molecular using a polymerase and using a ligase. Where the sample contains RNA, the polymerase may be a reverse transcriptase. The ligase could be, for example, a PBCV-1 DNA Ligase or Chlorella virus DNA Ligase, which catalyzes the ligation of adjacent, single-stranded DNA splinted by a complementary RNA strand. The method my further include sequencing the inter-probe product to produce sequence reads and analyzing the sequence reads to report one or more splice forms present in the sample.

BRIEF DESCRIPTION OF THE DRAWINGS

[0015] FIG. 1 diagrams a method for carrier screening that includes the ability to detect structural variant breakpoints using molecular inversion probes.
[0016] FIG. 2 illustrates use of MIPs to capture regions of target genomic material.
[0017] FIG. 3 illustrates the formation and detection of a “cross-probe”, or inter-probe, product.
[0018] FIG. 4 gives a diagram of a workflow for deletion detection.
[0019] FIG. 5 gives a diagram of a system of the invention.

DETAILED DESCRIPTION

[0020] The invention provides methods useful to identify large deletion variants in patient samples using a molecular inversion probe (MIP) assay that may be used in conjunction with sequencing such as next-generation short-read sequencing. Method of the invention provide for identification of otherwise difficult-to-characterize and often-deleterious variants. Assays that use MIP capture reactions and sequencing without employing methods of the invention may be found to be prone to false positive and false negative large deletion calls, thereby necessitating the use of extrinsic secondary tests. Methods of the invention are beneficial in addressing the high volume of output from next-generation sequencing (NGS) instruments. Particularly where NGS instruments have an extremely short read length, their ability to characterize indels larger than tens of bases is extremely limited. As many highly important deleterious variants are of large size (including CFTR del84, CFTR delExon2-3, HEXA del7.6 kb, NEB delExon55, and MCOLN del6.4 kb), NGS methods may not be adequate for genomic analysis of many important variants. Even where present MIP capture reactions are used to detect a specific deletion of interest, that deletion must be spanned by a single MIP. While efforts have been made to identify indels through depth of coverage, those efforts not only often require a known negative sample for comparison but also are susceptible to skewed read depth distributions due to uncontrollable changes in experimental conditions, making coverage comparisons challenging. The invention provides methods that avoid those limitations. Methods of the invention provide a complete carrier screening assay that can reliably report on variants in a patient's genome where the described and reported variants include both small variants such as mutations and short indels (e.g., between about 1 and tens of base pairs) as well as large deletions.
[0021] FIG. 1 diagrams a method 101 for to carrier screening that includes the ability to detect structural variant breakpoints using molecular inversion probes. In the depicted embodiment, the method includes obtaining 105 a nucleic acid sample from a person and exposing 109 the nucleic acid to a plurality of probes. Any suitable probe can be used where each probe provides a linked pair of targeting arms designed to hybridize upstream and downstream of a target in a genome. In a preferred embodiment, the probes are MIPs, e.g., as described in U.S. Pub. 2013/0274146, each incorporated by reference. Two of the probes are hybridized to the nucleic acid and attached 113 together to create an inter-probe product. After or as part of any optional amplification step, the inter-probe product is detected 117 and detection of the inter-probe product is used for reporting 121 a structural variant of the genome in the nucleic acid. An important benefit of the described method 101 is that the steps can be integrated within a MIP-based carrier screening assay where, for example, a plurality of MIPs are designed to tile along a target of interest, such as a portion of a gene known to harbor mutations associated with a genetic disorder. Such an assay can include sequencing the inter-probe product to produce sequence reads, which are then compared to a reference to describe a location of the structural variant within a gene associated with a Mendelian recessive hereditary disorder. Moreover, this may be done within an assay wherein at least some probes that hybridize to the nucleic acid by both targeting arms are enzymatically converted into covalently closed circles and some or all of the covalently closed probes are also sequenced. The resulting information produced by sequencing can be used to describe one or more mutations in the nucleic acid from the person in comparison to the reference genome. This provides an NGS-based platform for genetic carrier screening in a clinical setting. The MIPs can be designed and used to isolate a number of target regions of interest, for example, part or all of genes associated with known disorders, from genomic DNA by automated multiplex target capture. The isolated gDNA may be tagged with molecular barcodes, pooled, and sequenced, e.g., on an Illumina Hiseq system. Reads from each sample may be de-multiplexed, aligned to a reference, and integrated into accurate genotype calls which are then interrogated for pathogenic mutations. Using such methods, more than 40 k bp can be targeted by a set of MIPs designed to tile across the target such that each base is captured by at least three different probes.
[0022] For method 101, the sample that includes nucleic acid may be obtained 105 by any suitable method. The sample may be obtained from a tissue or body fluid that is obtained in any clinically acceptable manner. Body fluids may include mucous, blood, plasma, serum, serum derivatives, bile, blood, maternal blood, phlegm, saliva, sweat, amniotic fluid, menstrual fluid, mammary fluid, follicular fluid of the ovary, fallopian tube fluid, peritoneal fluid, urine, and cerebrospinal fluid (CSF), such as lumbar or ventricular CSF. A sample may also be a fine needle aspirate or biopsied tissue. A sample also may be media containing cells or biological material. Samples may also be obtained from the environment (e.g., air, agricultural, water and soil) or may include research samples (e.g., products of a nucleic acid amplification reaction, or purified genomic DNA, RNA, proteins, etc.).
[0023] Isolation, extraction or derivation of genomic nucleic acids may be performed by methods known in the art. Isolating nucleic acid from a biological sample generally includes treating a biological sample in such a manner that genomic nucleic acids present in the sample are extracted and made available for analysis. Generally, nucleic acids are extracted using techniques such as those described in Green & Sambrook, 2012, Molecular Cloning: A Laboratory Manual 4 edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2028 pages), the contents of which are incorporated by reference herein. A kit may be used to extract DNA from tissues and bodily fluids and certain such kits are commercially available from, for example, BD Biosciences Clontech (Palo Alto, Calif.), Epicentre Technologies (Madison, Wis.), Gentra Systems, Inc. (Minneapolis, Minn.), and Qiagen Inc. (Valencia, Calif.). User guides that describe protocols are usually included in such kits.
[0024] It may be preferable to lyse cells to isolate genomic nucleic acid. Cellular extracts can be subjected to other steps to drive nucleic acid isolation toward completion by, e.g., differential precipitation, column chromatography, extraction with organic solvents, filtration, centrifugation, others, or any combination thereof. The genomic nucleic acid may be resuspended in a solution or buffer such as water, Tris buffers, or other buffers. In certain embodiments the genomic nucleic acid can be re-suspended in Qiagen DNA hydration solution, or other Tris-based buffer of a pH of around 7.5.
[0025] Any nucleic acid may be analyzed using methods of the invention. Nucleic acids suitable for use in aspects of the invention may include without limit genomic DNA, genomic RNA, synthesized nucleic acids, whole or partial genome amplification product, and high molecular weight nucleic acids, e.g. individual chromosomes. In certain embodiments, a sample is obtained that includes double-stranded DNA, such as bulk genomic DNA from a subject, and the double-stranded DNA is then denatured. In some embodiments, a sample is obtained or prepared that includes cDNA and methods of the invention may be used to identify and quantify alternate splice forms or isoforms. As necessary or best-suited, double stranded nucleic acid may be denatured using any suitable method such as, for example, through the use of heat, detergent incubation, or an acidic or basic solution.
[0026] In some embodiments, it may be preferably to fragment the target nucleic acid for capture reactions. Without being bound by any mechanism, a set of probes may bind more successfully to target that has be fragmented. Nucleic acids, including genomic nucleic acids, can be fragmented using any of a variety of methods, such as mechanical fragmenting, chemical fragmenting, and enzymatic fragmenting. Methods of nucleic acid fragmentation are known in the art and include, but are not limited to, DNase digestion, sonication, mechanical shearing, and the like. U.S. Pub 2005/0112590 provides a general overview of various methods of fragmenting known in the art. Fragmentation of nucleic acid target is discussed in U.S. Pub. 2013/0274146.
[0027] Genomic nucleic acids can be fragmented into uniform fragments or randomly fragmented. In certain aspects, nucleic acids are fragmented to form fragments having a fragment length of about 5 kilobases or 100 kilobases. Desired fragment length and ranges of fragment lengths can be adjusted depending on the type of nucleic acid targets one seeks to capture and the design and type of probes such as molecular inversion probes (MIPs) that will be used. Chemical fragmentation of genomic nucleic acids can be achieved using methods such as a hydrolysis reaction or by altering temperature or pH. Nucleic acid may be fragmented by heating a nucleic acid immersed in a buffer system at a certain temperature for a certain period to time to initiate hydrolysis and thus fragment the nucleic acid. The pH of the buffer system, duration of heating, and temperature can be varied to achieve a desired fragmentation of the nucleic acid. Mechanical shearing of nucleic acids into fragments can be used e.g., by hydro-shearing, trituration through a needle, and sonication. The nucleic acid can also be sheared via nebulization, hydro-shearing, sonication, or others. See U.S. Pat. No. 6,719,449; U.S. Pat. No. 6,948,843; and U.S. Pat. No. 6,235,501. Nucleic acid may be fragmented enzymatically. Enzymatic fragmenting, also known as enzymatic cleavage, cuts nucleic acids into fragments using enzymes, such as endonucleases, exonucleases, ribozymes, and DNAzymes. Varying enzymatic fragmenting techniques are well-known in the art. Additionally, DNA may be denatured again as needed after the digestion and any other sample prep steps. For example, during a fragmentation step, ssDNA may anneal to form dsDNA and it may be desirable to again denature the dsDNA. In certain embodiments, the sample nucleic acid is captured or targeted using any suitable capture method or assay such as hybridization capture or capture by probes such as MIPs.
[0028] FIG. 2 illustrates use of MIPs 201 to capture regions of target genomic material 203 for amplification and sequencing. In order to provide for the accurate determination of large deletion variants using short-read sequencing, the invention provides an experimental and computational method to identify large deletion breakpoints using MIPs. Each MIP 201 contains a common backbone sequence and two complementary arms that are annealed to a DNA sample of interest. A polymerase 205 is utilized to fill in the gap between each of the two arms, and a ligase 221 is then utilized to create a set of circular molecules. Capture efficiency of the MIP to the target sequence on the nucleic acid fragment can be optimized by lengthening the hybridization and gap-filing incubation periods. (See, e.g., Turner et al., 2009, Massively parallel exon capture and library-free resequencing across 16 genomes, Nature Methods 6:315-316.) The resultant circular molecules 211 can be amplified using polymerase chain reaction to generate a targeted sequencing library. Here, the inventions provide methods wherein MIP capture reactions and sequencing/screening assays are extended to include the identification of arbitrarily large deletions and a variety of other classes of structural variations. These molecules can then be amplified using a common primer sequence present in the backbone, allowing a sequencing library to be generated from an arbitrary set of desired genomic target regions.
[0029] MIPs can be used to detect or amplify particular nucleic acid sequences in complex mixtures. Use of molecular inversion probes has been demonstrated for detection of single nucleotide polymorphisms (Hardenbol et al., 2005, Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay, Genome Res 15:269-75) and for preparative amplification of large sets of exons (Porreca et al., 2007, Multiplex amplification of large sets of human exons, Nat Methods 4:931-6 and Krishnakumar et al., 2008, A comprehensive assay for targeted multiplex amplification of human DNA sequences, PNAS 105:9296-301). One significant benefit of the method is in its capacity for a high degree of multiplexing, because generally thousands of targets may be captured in a single reaction containing thousands of probes. Thus the invention provides a multiplexed breakpoint detection and localization assay that may include identifying and reporting mutations or variants such as substitutions or small indels. The breakpoints detected in the multiplex assays may be associated with chromosomal rearrangements such as translocations, inversions, deletions, repetitions, wherein large segments (e.g., dozens or hundreds of base-pairs) of the genome are involved. Another significant benefit of the disclosed probe-based methods is that the methods may operate successfully with very small amounts of original target nucleic acid, unlike array-based methods, which require an abundance of target.
[0030] In some embodiments, the amount of target nucleic acid and probe used for each reaction is normalized to avoid any observed differences being caused by differences in concentrations or ratios. In some embodiments, in order to normalize genomic DNA and probe, the genomic DNA concentration is read using a standard spectrophotometer or by fluorescence (e.g., using a fluorescent intercalating dye). The probe concentration may be determined experimentally or using information specified by the probe manufacturer.
[0031] Once a locus has been captured, it may be amplified and/or sequenced in a reaction involving one or more primers. The amount of primer added for each reaction can range from 0.1 pmol to 1 nmol, 0.15 pmol to 1.5 nmol (for example around 1.5 pmol). However, other amounts (e.g., lower, higher, or intermediate amounts) may be used.
[0032] A targeting arm may be designed to hybridize (e.g., be complementary) to either strand of a genetic locus of interest if the nucleic acid being analyzed is DNA (e.g., genomic DNA). For MIP probes, whichever strand is selected for one targeting arm will be used for the other one. In the context of RNA analysis, a targeting arm should be designed to hybridize to the transcribed RNA. However, if cDNA is being targeted rather than RNA directly, the probes should be designed to be complementary to the reverse complement of the transcribed strand. It also should be appreciated that MIP probes referred to herein as “capturing” a target sequence are actually capturing it by template-based synthesis rather than by capturing the actual target molecule (other than for example in the initial stage when the arms hybridize to it or in the sense that the target molecule can remain bound to the extended MIP product until it is denatured or otherwise removed).
[0033] In certain embodiments, methods of the invention are used to identify a splice form. A sample that includes RNA or cDNA is exposed to a plurality of MIPs. Two of the MIPs are connected via arms that have hybridized to the same RNA or cDNA molecule to create an inter-probe product, which is detected and used to identify a splice form of an RNA transcript. The two MIPs may be connected using a polymerase and a ligase. Where the sample contains RNA, the polymerase may be a reverse transcriptase. The ligase could be, for example, a PBCV-1 DNA Ligase or Chlorella virus DNA Ligase, which catalyzes the ligation of adjacent, single-stranded DNA splinted by a complementary RNA strand. Once such ligase is the ligase sold under the trademark SPLINTR by New England BioLabs Inc. (Ipswich, Mass.).
[0034] A targeting arm may include a sequence that is complementary to one allele or mutation (e.g., a SNP or other polymorphism, a mutation, etc.) so that the probe will preferentially hybridize (and capture) target nucleic acids having that allele or mutation. Sequence tags (also referred to as barcodes) may be designed to be unique in that they do not appear at other positions within a probe or a family of probes and they also do not appear within the sequences being targeted. Uniformity and reproducibility can be increased by designing multiple probes per target, such that each base in the target is captured by more than one probe.
[0035] The length of a capture molecule on a nucleic acid fragment (e.g., a target nucleic acid or sub-region thereof) may be selected based upon multiple considerations. For example, where analysis of a target involves sequencing, e.g., with a next-generation sequencer, the target length should typically match the sequencing read-length so that shotgun library construction is not necessary. However, it should be appreciated that captured nucleic acids may be sequenced using any suitable sequencing technique as aspects of the invention are not limited in this respect.
[0036] Methods of the invention also provide for combining the method of fragmenting the nucleic acid prior to capture with other MIP capture techniques that are designed to increase target uniformity, reproducibility, and specificity. Other MIP capture techniques are shown in U.S. Pub. 2012/0165202, incorporated by reference.
[0037] Multiple probes, e.g., MIPs, can be used to amplify each target nucleic acid. In some embodiments, the set of probes for a given target can be designed to ‘tile’ across the target, capturing the target as a series of shorter sub targets. In some embodiments, where a set of probes for a given target is designed to ‘tile’ across the target, some probes in the set capture flanking non-target sequence. Alternately, the set can be designed to ‘stagger’ the exact positions of the hybridization regions flanking the target, capturing the full target (and in some cases capturing flanking non-target sequence) with multiple probes having different targeting arms, obviating the need for tiling. The particular approach chosen will depend on the nature of the target set. For example, if small regions are to be captured, a staggered-end approach might be appropriate, whereas if longer regions are desired, tiling might be chosen. In all cases, the amount of bias-tolerance for probes targeting pathological loci can be adjusted by changing the number of different MIPs used to capture a given molecule. Probes for MIP capture reactions may be synthesized on programmable microarrays to provide the large number of sequences required. See e.g., Porreca et al., 2007, Multiplex amplification of large sets of human exons, Nat Meth 4(11):931-936; Garber, 2008, Fixing the front end, Nat Biotech 26(10):1101-1104; Turner et al., 2009, Methods for genomic partitioning, Ann Rev Hum Gen 10:263-284; and Umbarger et al., 2014, Next-generation carrier screening, Gen Med 16(2):132-140. Using methods described herein, a single copy of a specific target nucleic acid may be amplified to a level that can be sequenced. Further, the amplified segments created by an amplification process such as PCR may be, themselves, efficient templates for subsequent PCR amplifications.
[0038] The result of MIP capture as described in FIG. 2 includes one or more circular target probes, which then can be processed in a variety of ways. Adaptors for sequencing may be attached during common linker-mediated PCR, resulting in a library with non-random, fixed starting points for sequencing. For preparation of a shotgun library, a common linker-mediated PCR is performed on the circle target probes, and the post-capture amplicons are linearly concatenated, sheared, and attached to adaptors for sequencing. Methods for shearing the linear concatenated captured targets can include any of the methods disclosed for fragmenting nucleic acids discussed above. In certain aspects, performing a hydrolysis reaction on the captured amplicons in the presence of heat is the desired method of shearing for library production. In addition to circularizing the MIPs for target capture, the invention includes the formation and detection of “cross-probe”, or inter-probe, product.
[0039] FIG. 3 illustrates the formation and detection of a “cross-probe”, or inter-probe, product 309. While probes normally self-ligate into circular molecules, in the case of a large deletion or other classes of structural variants, one probe may hybridize to the target by only one probe arm. One probe arm from each of two probes spanning a deletion become ligated to each other. This ligation can include an extension, or “fill-in”, step. This results in the formation of an inter-probe product 309 as shown in FIG. 3. Cross-probe products 309 may be amplified even when exonucleases are utilized to digest linear products. Inter-probe product 309 may be made resistant to exonuclease digestion via the inclusion of a phosphorothioate base or bases in the backbone of probes 201.
[0040] As described below, inter-probe product 309 may be sequenced along with circularized probe molecules. Additionally or alternatively, inter-probe product may be detected in parallel to or instead of sequencing to provide for detection of a deletion or other such chromosomal abnormality. Any suitable approach can be used to detect or describe deletion 303. In some embodiments, the detection of any inter-probe product 309 provides the inference that the patient's target DNA 203 includes the deletion 303 (that is, the very act of detection means that a breakpoint or deletion is included in a report). One approach to detection of deletions or breakpoints includes sequencing the inter-probe product 309. Methods may include attachment of amplification or sequencing adaptors or barcodes or a combination thereof to target DNA captured by probes.
[0041] Amplification or sequencing adapters or barcodes, or a combination thereof, may be attached to the fragmented nucleic acid. Such molecules may be commercially obtained, such as from Integrated DNA Technologies (Coralville, Iowa). In certain embodiments, such sequences are attached to the template nucleic acid molecule with an enzyme such as a ligase. Suitable ligases include T4 DNA ligase and T4 RNA ligase, available commercially from New England Biolabs (Ipswich, Mass.). The ligation may be blunt ended or via use of complementary overhanging ends. In certain embodiments, following fragmentation, the ends of the fragments may be repaired, trimmed (e.g. using an exonuclease), or filled (e.g., using a polymerase and dNTPs) to form blunt ends. In some embodiments, end repair is performed to generate blunt end 5′ phosphorylated nucleic acid ends using commercial kits, such as those available from Epicentre Biotechnologies (Madison, Wis.). Upon generating blunt ends, the ends may be treated with a polymerase and dATP to form a template independent addition to the 3′-end and the 5′-end of the fragments, thus producing a single A overhanging. This single A can guide ligation of fragments with a single T overhanging from the 5′-end in a method referred to as T-A cloning. Alternatively, because the possible combination of overhangs left by the restriction enzymes are known after a restriction digestion, the ends may be left as-is, i.e., ragged ends. In certain embodiments double stranded oligonucleotides with complementary overhanging ends are used.
[0042] In certain embodiments, one or more barcodes is or are attached to each, any, or all of the fragments. A barcode sequence generally includes certain features that make the sequence useful in sequencing reactions. The barcode sequences are designed such that each sequence is correlated to a particular portion of nucleic acid, allowing sequence reads to be correlated back to the portion from which they came. Methods of designing sets of barcode sequences is shown for example in U.S. Pat. No. 6,235,475, the contents of which are incorporated by reference herein in their entirety. In certain embodiments, the barcode sequences range from about 5 nucleotides to about 15 nucleotides. In a particular embodiment, the barcode sequences range from about 4 nucleotides to about 7 nucleotides. In certain embodiments, the barcode sequences are attached to the template nucleic acid molecule, e.g., with an enzyme. The enzyme may be a ligase or a polymerase, as discussed above. Attaching bar code sequences to nucleic acid templates is shown in U.S. Pub. 2008/0081330 and U.S. Pub. 2011/0301042, the content of each of which is incorporated by reference herein in its entirety. Methods for designing sets of bar code sequences and other methods for attaching barcode sequences are shown in U.S. Pat. Nos. 7,537,897; 6,138,077; 6,352,828; 5,636,400; 6,172,214; and 5,863,722, the content of each of which is incorporated by reference herein in its entirety. After any processing steps (e.g., obtaining, isolating, fragmenting, amplification, or barcoding), nucleic acid can be sequenced.
[0043] Sequencing may be by any method known in the art. DNA sequencing techniques include classic dideoxy sequencing reactions (Sanger method) using labeled terminators or primers and gel separation in slab or capillary, sequencing by synthesis using reversibly terminated labeled nucleotides, pyrosequencing, 454 sequencing, Illumina/Solexa sequencing, allele specific hybridization to a library of labeled oligonucleotide probes, sequencing by synthesis using allele specific hybridization to a library of labeled clones that is followed by ligation, real time monitoring of the incorporation of labeled nucleotides during a polymerization step, polony sequencing, and SOLiD sequencing. Separated molecules may be sequenced by sequential or single extension reactions using polymerases or ligases as well as by single or sequential differential hybridizations with libraries of probes.
[0044] A sequencing technique that can be used includes, for example, Illumina sequencing. Illumina sequencing is based on the amplification of DNA on a solid surface using fold-back PCR and anchored primers. Genomic DNA is fragmented, and adapters are added to the 5′ and 3′ ends of the fragments. DNA fragments that are attached to the surface of flow cell channels are extended and bridge amplified. The fragments become double stranded, and the double stranded molecules are denatured. Multiple cycles of the solid-phase amplification followed by denaturation can create several million clusters of approximately 1,000 copies of single-stranded DNA molecules of the same template in each channel of the flow cell. Primers, DNA polymerase and four fluorophore-labeled, reversibly terminating nucleotides are used to perform sequential sequencing. After nucleotide incorporation, a laser is used to excite the fluorophores, and an image is captured and the identity of the first base is recorded. The 3′ terminators and fluorophores from each incorporated base are removed and the incorporation, detection and identification steps are repeated. Sequencing according to this technology is described in U.S. Pat. No. 7,960,120; U.S. Pat. No. 7,835,871; U.S. Pat. No. 7,232,656; U.S. Pat. No. 7,598,035; U.S. Pat. No. 6,911,345; U.S. Pat. No. 6,833,246; U.S. Pat. No. 6,828,100; U.S. Pat. No. 6,306,597; U.S. Pat. No. 6,210,891; U.S. Pub. 2011/0009278; U.S. Pub. 2007/0114362; U.S. Pub. 2006/0292611; and U.S. Pub. 2006/0024681, each of which are incorporated by reference in their entirety.
[0045] Sequencing the inter-probe product 309 and the circularized MIPs produces a plurality of sequence reads. Reads generally include sequences of nucleotide data wherein read length may be associated with sequencing technology. For example, the single-molecule real-time (SMRT) sequencing technology of Pacific Bio produces reads thousands of base-pairs in length. For 454 pyrosequencing, read length may be about 700 bp in length. In some embodiments, reads are less than about 500 bases in length, or less than about 150 bases in length, or less than about 90 bases in length. In certain embodiments, reads are between about 80 and about 90 bases, e.g., about 85 bases in length. In some embodiments, these are very short reads, i.e., less than about 50 or about 30 bases in length. Sequence reads 251 can be analyzed to detect and describe the deletion 303 in target nucleic acid 203.
[0046] FIG. 4 gives a diagram of a workflow for deletion detection. Genomic DNA 203 is used as a starting sample and is exposed to a plurality of MIPs 201. Hybridization of the MIPs provides circularized probe product 211 and inter-probe product 309. Inter-probe product 309 is detected, which may include amplification, sequencing, micro-array detection, size fractionation, gel electrophoresis, other methods, or combinations thereof. In some embodiments, micro-arrays are used to detect inter-probe product. In certain embodiments, amplification and/or sequencing are used. Barcode PCR may be performed to provide amplicon material for sequencing and to attach sample-specific molecular barcodes. The amplicons and barcodes may then be sequenced and inter-probe product 309 detected. Sequencing produces a plurality of sequence reads that may be analyzed for breakpoint detection.
[0047] Sequence read data can be stored in any suitable file format including, for example, VCF files, FASTA files or FASTQ files, as are known to those of skill in the art. In some embodiments, PCR product is pooled and sequenced (e.g., on an Illumina HiSeq 2000). Raw.bcl files are converted to qseq files using bclConverter (Illumina). FASTQ files are generated by “de-barcoding” genomic reads using the associated barcode reads; reads for which barcodes yield no exact match to an expected barcode, or contain one or more low-quality base calls, may be discarded. Reads may be stored in any suitable format such as, for example, FASTA or FASTQ format.
[0048] FASTA is originally a computer program for searching sequence databases and the name FASTA has come to also refer to a standard file format. See Pearson & Lipman, 1988, Improved tools for biological sequence comparison, PNAS 85:2444-2448. A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (“>”) symbol in the first column. The word following the “>” symbol is the identifier of the sequence, and the rest of the line is the description (both are optional). There should be no space between the “>” and the first letter of the identifier. It is recommended that all lines of text be shorter than 80 characters. The sequence ends if another line starting with a “>” appears; this indicates the start of another sequence.
[0049] The FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. It is similar to the FASTA format but with quality scores following the sequence data. Both the sequence letter and quality score are encoded with a single ASCII character for brevity. The FASTQ format is a de facto standard for storing the output of high throughput sequencing instruments such as the Illumina Genome Analyzer. Cock et al., 2009, The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants, Nucleic Acids Res 38(6):1767-1771.
[0050] For FASTA and FASTQ files, meta information includes the description line and not the lines of sequence data. In some embodiments, for FASTQ files, the meta information includes the quality scores. For FASTA and FASTQ files, the sequence data begins after the description line and is present typically using some subset of IUPAC ambiguity codes optionally with “-”. In a preferred embodiment, the sequence data will use the A, T, C, G, and N characters, optionally including “-” or U as-needed (e.g., to represent gaps or uracil, respectively).
[0051] Following sequencing, reads may be mapped to a reference using assembly and alignment techniques known in the art or developed for use in the workflow. Various strategies for the alignment and assembly of sequence reads, including the assembly of sequence reads into contigs, are described in detail in U.S. Pat. No. 8,209,130, incorporated herein by reference. Strategies may include (i) assembling reads into contigs and aligning the contigs to a reference; (ii) aligning individual reads to the reference; (iii) assembling reads into contigs, aligning the contigs to a reference, and aligning the individual reads to the contigs; or (iv) other strategies known to be developed or known in the art. Sequence assembly can be done by methods known in the art including reference-based assemblies, de novo assemblies, assembly by alignment, or combination methods. Sequence assembly is described in U.S. Pat. No. 8,165,821; U.S. Pat. No. 7,809,509; U.S. Pat. No. 6,223,128; U.S. Pub. 2011/0257889; and U.S. Pub. 2009/0318310, the contents of each of which are hereby incorporated by reference in their entirety. Sequence assembly or mapping may employ assembly steps, alignment steps, or both. Assembly can be implemented, for example, by the program ‘The Short Sequence Assembly by k-mer search and 3′ read Extension’ (SSAKE), from Canada's Michael Smith Genome Sciences Centre (Vancouver, B.C., CA) (see, e.g., Warren et al., 2007, Assembling millions of short DNA sequences using SSAKE, Bioinformatics, 23:500-501). SSAKE cycles through a table of reads and searches a prefix tree for the longest possible overlap between any two sequences. SSAKE clusters reads into contigs.
[0052] Greater detail on sequence assembly or interpretation and variant calling is given below. Methods of the invention may be used to describe mutations both of a large structural type (e.g., large deletions or structural variants, chromosomal abnormalities, breakpoints) and of a small localized type (e.g., substitutions, small indels).
[0053] Any suitable approach can be used to detect or describe deletion or other structural variants 303 or splice forms or isoforms. In some embodiments, the detection of any inter-probe product 309 provides the inference that the patient's target DNA 201 includes the structural variant 303. In certain embodiments, analysis of the sequence reads (e.g., from the circularized MIPs) includes analysis designed to report the presence or location of the structural variant 303. One approach to reporting the presence or location of structural variant 303 is to identify any targeted regions from which an abundance of sequence reads from inter-probe product 309 are produced. Such reads can be detected by targeting arms from either end that are not from the same MIP (i.e., a circularized MIP may provide sequence reads with certain expected barcode ends). Where inter-probe product reads appear, a software program may be used to search for a candidate large deletion by attempting to identify a specific novel breakpoint in those “cross-probe” reads. This approach allows any known or novel large deletions to be identified as long as one or more MIPs cover the breakpoints.
[0054] By utilizing a software program to search for an enrichment or the presence of cross-probe products and then examining the individual reads to locate a breakpoint, known or novel large deletions can be identified even in a short-read sequencing experiment.
[0055] In certain embodiments, analysis of the sequence reads (e.g., from the circularized MIPs) includes analysis designed to report the presence or location of deletion 303. One approach to reporting the presence or location of deletion 303 is to identify any targeted regions from which an abundance of sequence reads from inter-probe product 309 are produced. Such reads can be detected by targeting arm sequence from either end that are not from the same MIP (i.e., a circularized MIP may provide sequence reads with certain expected barcode ends). Where inter-probe product reads appear, a software program may be used to search for a candidate large deletion by attempting to identify a specific novel breakpoint in those “cross-probe” reads. This approach allows any known or novel large deletions to be identified as long as one or more MIPs cover the breakpoints.
[0056] In some embodiments, large genomic structural variants are detected through the assembly and analysis of the sequence reads, which process may also be used to detect and describe small localized variants. Generally, read assembly and analysis will proceed through the use of one or more specialized computer programs.
[0057] One read assembly program is Forge Genome Assembler, written by Darren Platt and Dirk Evers and available through the SourceForge web site maintained by Geeknet (Fairfax, Va.) (see, e.g., DiGuistini et al., 2009, De novo sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data, Genome Biology, 10:R94). Forge distributes its computational and memory consumption to multiple nodes, if available, and has therefore the potential to assemble large sets of reads. Forge was written in C++ using the parallel MPI library. Forge can handle mixtures of reads, e.g., Sanger, 454, and Illumina reads.
[0058] Another exemplary read assembly program known in the art is Velvet, available through the web site of the European Bioinformatics Institute (Hinxton, UK) (Zerbino & Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research 18(5):821-829). Velvet implements an approach based on de Bruijn graphs, uses information from read pairs, and implements various error correction steps.
[0059] Read assembly can be performed with the programs from the package SOAP, available through the website of Beijing Genomics Institute (Beijing, Conn.) or BGI Americas Corporation (Cambridge, Mass.). For example, the SOAPdenovo program implements a de Bruijn graph approach. SOAPS/GPU aligns short reads to a reference sequence.
[0060] Another read assembly program is ABySS, from Canada's Michael Smith Genome Sciences Centre (Vancouver, B.C., CA) (Simpson et al., 2009, ABySS: A parallel assembler for short read sequence data, Genome Res., 19(6):1117-23). ABySS uses the de Bruijn graph approach and runs in a parallel environment.
[0061] Read assembly can also be done by Roche's GS De Novo Assembler, known as gsAssembler or Newbler (NEW assemBLER), which is designed to assemble reads from the Roche 454 sequencer (described, e.g., in Kumar & Blaxter, 2010, Comparing de novo assemblers for 454 transcriptome data, Genomics 11:571 and Margulies 2005). Newbler accepts 454 Flx Standard reads and 454 Titanium reads as well as single and paired-end reads and optionally Sanger reads. Newbler is run on Linux, in either 32 bit or 64 bit versions. Newbler can be accessed via a command-line or a Java-based GUI interface. Additional discussion of read assembly may be found in Li et al., 2009, The Sequence alignment/map (SAM) format and SAMtools, Bioinformatics 25:2078; Lin et al., 2008, ZOOM! Zillions Of Oligos Mapped, Bioinformatics 24:2431; Li & Durbin, 2009, Fast and accurate short read alignment with Burrows-Wheeler Transform, Bioinformatics 25:1754; and Li, 2011, Improving SNP discovery by base alignment quality, Bioinformatics 27:1157. Assembled sequence reads may preferably be aligned to a reference. Methods for alignment and known in the art and may make use of a computer program that performs alignment, such as Burrows-Wheeler Aligner.
[0062] Aligned or assembled sequence reads may be analyzed for the detection of deletion 303. For example, where inter-probe product 309 is present, the sequence reads that result from that inter-probe product may be aligned to a reference with a liberal allowance for a deletion. In fact, known alignment methods (e.g., Smith-Waterman) can be adjusted to prefer one large deletion for such a set of reads. Breakpoint detection may include methodologies discussed in Ye et al., 2009, Pindel: a pattern growth approach to detect break points of large deletions and medium size insertions from paired-end short reads, Bioinformatics 25(21):2865-2871. For additional background, see Furtado et al., 2011, Characterization of large genomic deletions in the FBN1 gene using multiplex ligation-dependent probe amplification, BMC Med Gen 12:119-125; Nuttle et al., 2014, Resolving genomic disorder-associated breakpoints within segmental DNA duplications using massively parallel sequencing, Nat Prot 9(6):1496-1513; and Okeniewski et al., 2013, Precise breakpoint localization of large genomic deletions using PacBio and IIlumina next-generation sequencers, Biotechniques 54(2):98-100. the contents of each of which are incorporated by reference.
[0063] Besides just detecting large deletions, methods of the invention can be used to detect and describe other types of mutations. Mutation calling is described in U.S. Pub. 2013/0268474. In certain embodiments, analyzing the reads includes assembling the sequence reads and then genotyping the assembled reads.
[0064] In certain embodiments, reads are aligned to hg18 on a per-sample basis using Burrows-Wheeler Aligner version 0.5.7 for short alignments, and genotype calls are made using Genome Analysis Toolkit. See McKenna et al., 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res 20(9):1297-1303 (aka the GATK program). High-confidence genotype calls may be defined as having depth≥50 and strand bias score≤0. De-barcoded fastq files are obtained as described above and partitioned by capture region (exon) using the target arm sequence as a unique key. Reads are assembled in parallel by exon using SSAKE version 3.7 with parameters “—m 30 —o 15”. The resulting contiguous sequences (contigs) can be aligned to hg18 (e.g., using BWA version 0.5.7 for long alignments with parameter “—r 1”). In some embodiments, short-read alignment is performed as described above, except that sample contigs (rather than hg18) are used as the input reference sequence. Software may be developed in Java to accurately transfer coordinate and variant data (gaps) from local sample space to global reference space for every BAM-formatted alignment. Genotyping and base-quality recalibration may be performed on the coordinate-translated BAM files using the GATK program.
[0065] In some embodiments, any or all of the steps of the invention are automated. For example, a Perl script or shell script can be written to invoke any of the various programs discussed above (see, e.g., Tisdall, Mastering Perl for Bioinformatics, O'Reilly & Associates, Inc., Sebastopol, C A 2003; Michael, R., Mastering Unix Shell Scripting, Wiley Publishing, Inc., Indianapolis, Ind. 2003). Alternatively, methods of the invention may be embodied wholly or partially in one or more dedicated programs, for example, each optionally written in a compiled language such as C++ then compiled and distributed as a binary. Methods of the invention may be implemented wholly or in part as modules within, or by invoking functionality within, existing sequence analysis platforms. In certain embodiments, methods of the invention include a number of steps that are all invoked automatically responsive to a single starting queue (e.g., one or a combination of triggering events sourced from human activity, another computer program, or a machine). Thus, the invention provides methods in which any or the steps or any combination of the steps can occur automatically responsive to a queue. Automatically generally means without intervening human input, influence, or interaction (i.e., responsive only to original or pre-queue human activity).
[0066] Mapping sequence reads to a reference, by whatever strategy, may produce output such as a text file or an XML file containing sequence data such as a sequence of the nucleic acid aligned to a sequence of the reference genome. In certain embodiments mapping reads to a reference produces results stored in SAM or BAM file (e.g., as shown in FIG. 4) and such results may contain coordinates or a string describing one or more mutations in the subject nucleic acid relative to the reference genome. Alignment strings known in the art include Simple UnGapped Alignment Report (SUGAR), Verbose Useful Labeled Gapped Alignment Report (VULGAR), and Compact Idiosyncratic Gapped Alignment Report (CIGAR). See Ning et al., 2001, SSAHA: A fast search method for large DNA database, Genome Research 11(10):1725-9. These strings are implemented, for example, in the Exonerate sequence alignment software from the European Bioinformatics Institute (Hinxton, UK).
[0067] In some embodiments, a sequence alignment is produced—such as, for example, a sequence alignment map (SAM) or binary alignment map (BAM) file—comprising a CIGAR string (the SAM format is described, e.g., in Li, et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, 2009, 25(16):2078-9). In some embodiments, CIGAR displays or includes gapped alignments one-per-line. CIGAR is a compressed pairwise alignment format reported as a CIGAR string. A CIGAR string is useful for representing long (e.g. genomic) pairwise alignments. A CIGAR string is used in SAM format to represent alignments of reads to a reference genome sequence.
[0068] A CIGAR string follows an established motif. Each character is preceded by a number, giving the base counts of the event. Characters used can include M, I, D, N, and S (M=match; I=insertion; D=deletion; N=gap; S=substitution). The CIGAR string defines the sequence of matches/mismatches and deletions (or gaps). For example, the CIGAR string 2MD3M2D2M will mean that the alignment contains 2 matches, 1 deletion (number 1 is omitted in order to save space), 3 matches, 2 deletions and 2 matches. In general, for carrier screening or other assays such as the NGS workflow depicted in FIG. 5, sequencing results will be used in genotyping.
[0069] Output from mapping may be stored in a SAM or BAM file, in a variant call format (VCF) file, or other format. In an illustrative embodiment, output is stored in a VCF file. A typical VCF file will include a header section and a data section. The header contains an arbitrary number of meta-information lines, each starting with characters ‘##’, and a TAB delimited field definition line starting with a single ‘#’ character. The field definition line names eight mandatory columns and the body section contains lines of data populating the columns defined by the field definition line. The VCF format is described in Danecek et al., 2011, The variant call format and VCFtools, Bioinformatics 27(15):2156-2158.
[0070] The data contained in a VCF file represents the variants, or mutations, that are found in the nucleic acid that was obtained from the sample from the patient and sequenced. In its original sense, mutation refers to a change in genetic information and has come to refer to the present genotype that results from a mutation. As is known in the art, mutations include different types of mutations such as substitutions, insertions or deletions (INDELs), translocations, inversions, chromosomal abnormalities, and others. By convention in some contexts where two or more versions of genetic information or alleles are known, the one thought to have the predominant frequency in the population is denoted the wild type and the other(s) are referred to as mutation(s). In general in some contexts an absolute allele frequency is not determined (i.e., not every human on the planet is genotyped) but allele frequency refers to a calculated probable allele frequency based on sampling and known statistical methods and often an allele frequency is reported in terms of a certain population such as humans of a certain ethnicity. Variant can be taken to be roughly synonymous to mutation but referring to a genotype being described in comparison or with reference to a reference genotype or genome. For example as used in bioinformatics variant describes a genotype feature in comparison to a reference such as the human genome (e.g., hg18 or hg19 which may be taken as a wild type). Methods described herein generate data representing a location of a breakpoint or deletion in the genome of a patient, which data may further also represent one or more mutations, or “variant calls.”
[0071] A description of a mutation may be provided according to a systematic nomenclature. For example, a variant can be described by a systematic comparison to a specified reference which is assumed to be unchanging and identified by a unique label such as a name or accession number. For a given gene, coding region, or open reading frame, the A of the ATG start codon is denoted nucleotide+1 and the nucleotide 5′ to +1 is −1 (there is no zero). A lowercase g, c, or m prefix, set off by a period, indicates genomic DNA, cDNA, or mitochondrial DNA, respectively.
[0072] A systematic name can be used to describe a number of variant types including, for example, substitutions, deletions, insertions, and variable copy numbers. A substitution name starts with a number followed by a “from to” markup. Thus, 199A>G shows that at position 199 of the reference sequence, A is replaced by a G. A deletion is shown by “del” after the number. Thus 223delT shows the deletion of T at nt 223 and 997-999del shows the deletion of three nucleotides (alternatively, this mutation can be denoted as 997-999delTTC). In short tandem repeats, the 3′ nt is arbitrarily assigned; e.g. a TG deletion is designated 1997-1998delTG or 1997-1998del (where 1997 is the first T before C). Insertions are shown by ins after an interval. Thus 200-201insT denotes that T was inserted between nts 200 and 201. Variable short repeats appear as 997(GT)N-N′. Here, 997 is the first nucleotide of the dinucleotide GT, which is repeated N to N′ times in the population.
[0073] Variants in introns can use the intron number with a positive number indicating a distance from the G of the invariant donor GU or a negative number indicating a distance from an invariant G of the acceptor site AG. Thus, IVS3+1C>T shows a C to T substitution at nt+1 of intron 3. In any case, cDNA nucleotide numbering may be used to show the location of the mutation, for example, in an intron. Thus, c.1999+1C>T denotes the C to T substitution at nt+1 after nucleotide 1997 of the cDNA. Similarly, c.1997-2A>C shows the A to C substitution at nt −2 upstream of nucleotide 1997 of the cDNA. When the full length genomic sequence is known, the mutation can also be designated by the nt number of the reference sequence.
[0074] Relative to a reference, a patient's genome may vary by more than one mutation, or by a complex mutation that is describable by more than one character string or systematic name. The invention further provides systems and methods for describing more than one variant using a systematic name. For example, two mutations in the same allele can be listed within brackets as follows: [1997G>T; 2001A>C]. Systematic nomenclature is discussed in den Dunnen & Antonarakis, 2003, Mutation Nomenclature, Curr Prot Hum Genet 7.13.1-7.13.8 as well as in Antonarakis and the Nomenclature Working Group, 1998, Recommendations for a nomenclature system for human gene mutations, Human Mutation 11:1-3. By such means, a mutation can be described in the property index file of a variant node.
[0075] Any suitable gene may be screened using methods of the invention. In a preferred embodiments, methods of the invention are used to screen for recessive Mendelian disorders. Certain genetic disorders and their associated genes that may be screened using methods of the invention include Canavan disease (ASPA), cystic fibrosis (CFTR), glycogen storage disorder type 1a (G6PC), Niemann-Pick disease (SMPD1), Tay-Sachs disease (HEXA), Bloom syndrome (BLM), Fanconi anemia C (FANCC), familial Hyperinsulinism (ABCC8), maple syrup urine disease type 1A (BCKDHA) and type 1B (BCKDHB), Usher syndrome type III (CLRN1), dihydrolipoamide dehydrogenase deficiency (DLD), familial dysautonomia (IKBKAP), mucolipidosis type IV (MCOLN1), and Usher syndrome type 1F (PCDH15).
[0076] Methods of the invention may include detecting and describing genotype features such as mutations in a patient's genome and using a database for look-up, comparisons, or storage. In some embodiments, where a novel mutation is detected, it is classified and if pathogenic according to classification criteria, then it is entered into a database for use in future assays and comparisons. For one suitable database architecture, see U.S. Pat. No. 8,812,422, incorporated by reference. Using methods of the invention, single nucleotide substitutions or insertions/deletions not exceeding 10 bp (e.g., that are located in exons or within the first 10 bp of an intron) as well as gross chromosomal rearrangements, such as deletions, translocations, and inversions may be detected or stored. Variants may be named according to HGVS-recommended nomenclature or any other systematic mutation nomenclature. Mutations in the database (e.g., for comparison to sequencing results from a MIP carrier screening) may be classified. Classification criteria described here apply to recessive Mendelian disorders and highly penetrant variants with relatively large effects. Classification criteria may follow recommendations in the literature: Richards et al., ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007, Genet Med 2008, 10:294-300; Maddalena et al., Technical standards and guidelines: molecular genetic testing for ultra-rare disorders, Genet Med 2005, 7:571-83; and Strom C M, Mutation detection, interpretation, and applications in the clinical laboratory setting, Mutat Res 2005, 573:160-7, each incorporated by reference. Classification may be based on any suitable combination of sequence-based evidence (e.g., being a truncating mutation), experimental evidence, or genetic evidence (e.g., classified as pathogenic based on genetic evidence if it was a founder variant, or if there was statistical evidence showing the variant was significantly more frequent in affected individuals than in controls; see MacArthur et al., Guidelines for investigating causality of sequence variants in human disease, Nature 2014, 508:469-76). For methods suitable for use in detection of variants detectable by the standard NGS protocol, see Umbarger et al., Next-generation carrier screening, Genet Med 2014, 16:132-40 and Hallam et al., Validation for Clinical Use of, and Initial Clinical Experience with, a Novel Approach to Population-Based Carrier Screening using High-Throughput, Next-Generation DNA Sequencing, J Mol Diagn 2014, 16:180-9, both incorporated by reference.
[0077] Functions described above such as sequence read analysis or assembly can be implemented using systems of the invention that include software, hardware, firmware, hardwiring, or combinations of any of these.
[0078] FIG. 5 gives a diagram of a system 501 according to embodiments of the invention. System 501 may include an analysis instrument 503 which may be, for example, a sequencing instrument (e.g., a HiSeq 2500 or a MiSeq by Illumina). Instrument 503 includes a data acquisition module 505 to obtain results data such as sequence read data. Instrument 503 may optionally include or be operably coupled to its own, e.g., dedicated, analysis computer 533 (including an input/output mechanism, one or more processor, and memory). Additionally or alternatively, instrument 503 may be operably coupled to a server 513 or computer 549 (e.g., laptop, desktop, or tablet) via a network 509.
[0079] Computer 549 includes one or more processors and memory as well as an input/output mechanism. Where methods of the invention employ a client/server architecture, steps of methods of the invention may be performed using the server 513, which includes one or more of processors and memory, capable of obtaining data, instructions, etc., or providing results via an interface module or providing results as a file. The server 513 may be engaged over the network 509 by the computer 549 or the terminal 567, or the server 513 may be directly connected to the terminal 567, which can include one or more processors and memory, as well as an input/output mechanism.
[0080] In system 501, each computer preferably includes at least one processor coupled to a memory and at least one input/output (I/O) mechanism.
[0081] A processor will generally include a chip, such as a single core or multi-core chip, to provide a central processing unit (CPU). A process may be provided by a chip from Intel or AMD.
[0082] Memory can include one or more machine-readable devices on which is stored one or more sets of instructions (e.g., software) which, when executed by the processor(s) of any one of the disclosed computers can accomplish some or all of the methodologies or functions described herein. The software may also reside, completely or at least partially, within the main memory and/or within the processor during execution thereof by the computer system. Preferably, each computer includes a non-transitory memory such as a solid state drive, flash drive, disk drive, hard drive, etc. While the machine-readable devices can in an exemplary embodiment be a single medium, the term “machine-readable device” should be taken to include a single medium or multiple media (e.g., a centralized or distributed database, and/or associated caches and servers) that store the one or more sets of instructions and/or data. These terms shall also be taken to include any medium or media that are capable of storing, encoding, or holding a set of instructions for execution by the machine and that cause the machine to perform any one or more of the methodologies of the present invention. These terms shall accordingly be taken to include, but not be limited to one or more solid-state memories (e.g., subscriber identity module (SIM) card, secure digital card (SD card), micro SD card, or solid-state drive (SSD)), optical and magnetic media, and/or any other tangible storage medium or media.
[0083] A computer of the invention will generally include one or more I/O device such as, for example, one or more of a video display unit (e.g., a liquid crystal display (LCD) or a cathode ray tube (CRT)), an alphanumeric input device (e.g., a keyboard), a cursor control device (e.g., a mouse), a disk drive unit, a signal generation device (e.g., a speaker), a touchscreen, an accelerometer, a microphone, a cellular radio frequency antenna, and a network interface device, which can be, for example, a network interface card (NIC), Wi-Fi card, or cellular modem.
[0084] Any of the software can be physically located at various positions, including being distributed such that portions of the functions are implemented at different physical locations.
[0085] System 401 or components of system 401 may be used to perform methods described herein. Instructions for any method step may be stored in memory and a processor may execute those instructions. System 401 or components of system 401 may be used for the analysis of genomic sequences or sequence reads (e.g., detecting deletions and variant calling).

INCORPORATION BY REFERENCE

[0086] References and citations to other documents, such as patents, patent applications, patent publications, journals, books, papers, web contents, have been made throughout this disclosure. All such documents are hereby incorporated herein by reference in their entirety for all purposes.

EQUIVALENTS

[0087] Various modifications of the invention and many further embodiments thereof, in addition to those shown and described herein, will become apparent to those skilled in the art from the full contents of this document, including references to the scientific and patent literature cited herein. The subject matter herein contains important information, exemplification and guidance that can be adapted to the practice of this invention in its various embodiments and equivalents thereof.
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Claims

1. A method of identifying a structural variant, the method comprising:
exposing a nucleic acid in a sample to a plurality of molecular inversion probes (MIPs), each MIP comprising two targeting arms designed to hybridize upstream and downstream of a target in a reference genome;
connecting together two of the MIPs via arms that have hybridized to the same molecule of the nucleic acid by only one of the two targeting arms of each MIP to create an inter-probe product;
detecting the inter-probe product;
identifying a structural variant of the genome in the nucleic acid;
describing one or more breakpoints in the nucleic acid based on the two MIPs that each hybridizes to the nucleic acid by only one of its two targeting arms.
2. The method of claim 1, further comprising:
sequencing the inter-probe product to produce sequence reads;
comparing the sequence reads to a reference genome; and
describing a location of the structural variant within a gene associated with a Mendelian recessive hereditary disorder.
3. The method of claim 2, wherein producing the sequencing reads also includes:
covalently closing at least some MIPs that hybridize to the nucleic acid by both targeting arms; and
sequencing at least a portion of the covalently closed MIPs, and further wherein the method comprises describing one or more substitution mutations in the gene.
4. The method of claim 1, wherein the plurality of MIPs are exposed to the nucleic acid free in solution and in one reaction volume.
5. The method of claim 1, further comprising circularizing some of the MIPs and sequencing the circularized MIPs and the inter-probe product.
6. The method of claim 1, wherein each MIP further comprises at least one moiety to resist exonuclease digestion of that probe.
7. The method of claim 6, further comprising digesting single-stranded nucleic acid material with an exonuclease prior to detecting the inter-probe product.
8. The method of claim 7, wherein the moiety comprises at least one phosphorothioate base.
9. The method of claim 1, wherein attaching the two MIPs together comprises using a DNA ligase.
10. The method of claim 9, wherein the attaching also comprises filling in a gap between the two MIPs along the strand of nucleic acid using a polymerase.
11. The method of claim 1, further comprising sequencing the inter-probe product to produce sequence reads and comparing the sequence reads to the genome to report the structural variant.
12. The method of claim 11, further comprising producing a report that identifies that a person is a carrier of a hereditary disorder.
13. The method of claim 12, further comprising identifying the structural variant as lying within an exon of gene associated with the hereditary disorder.
14. The method of claim 1, wherein the nucleic acid comprises cDNA and identifying the structural variant comprises identifying a splice form.
15. A method of identifying a structural variant, the method comprising:
exposing a nucleic acid from a patient to a plurality of probes, each probe comprising a linked pair of targeting arms comprising sequence designed to hybridize upstream and downstream of a target in a reference genome, wherein the plurality of probes are designed to cover at least a portion of a gene associated with a Mendelian recessive hereditary disorder;
ligating together two of the probes that each hybridize to the nucleic acid by only one targeting arm to create an inter-probe product;
circularizing at least some probes that hybridize to the nucleic acid by both targeting arms;
sequencing the inter-probe product and at least a portion of the circularized probes to produce sequence reads;
comparing the sequence reads to a reference genome; and
describing one or more substitution mutations and a structural variant within the gene as found in the nucleic acid from the patient.
16. The method of claim 15, wherein the plurality of probes are exposed to the nucleic acid all in one reaction volume with all of the probes freely in solution.
17. The method of claim 16, wherein each probe is designed to resist nuclease digestion.
18. The method of claim 17, further comprising digesting single-stranded nucleic acid material with a nuclease prior to the sequencing.
19. The method of claim 18, wherein ligating the two probes together comprises filling in a gap between the two probes along the strand of nucleic acid using a polymerase and using a DNA ligase.
20. The method of claim 19, wherein describing the structural variant includes describing a location of one or more breakpoints in the gene.
21. The method of claim 19, further comprising producing a report that identifies that the patient is a carrier of the Mendelian recessive hereditary disorder.
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