Screening for structural variants

• US 10,066,259 B2
• Filed: 01/06/2016
• Issued: 09/04/2018
• Est. Priority Date: 01/06/2015
• Status: Active Grant

• Current Assignee: Molecular Loop Biosciences, Inc.
• Original Assignee: Good Start Genetics, Inc. (Invitae Corporation)
• Inventors: Gore, Athurva, Umbarger, Mark
• Primary Examiner(s): Whisenant, Ethan C
• Application Number:
  US14/989,073
• Publication Number:
  US 20160194692A1
• Time in Patent Office: 972 Days
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides
• CPC Class Codes: C12Q 2531/125 Rolling circle

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.

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.