Methods and materials for assessing allelic imbalance

• US 9,279,156 B2
• Filed: 12/17/2013
• Issued: 03/08/2016
• Est. Priority Date: 06/17/2011
• Status: Active Grant

• Current Assignee: Myriad Genetics, Inc.
• Original Assignee: Myriad Genetics, Inc.
• Inventors: Gutin, Alexander, Timms, Kirsten, Lanchbury, Jerry
• Primary Examiner(s): Martinell, James
• Application Number:
  US14/109,163
• Publication Number:
  US 20140162886A1
• Time in Patent Office: 812 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

Methods and systems for detecting allelic imbalance using nucleic acid sequencing are provided.

Claims

1. An in vitro method for detecting homozygosity at a plurality of single nucleotide polymorphism loci, comprising:

(1) providing a formalin-fixed paraffin-embedded sample comprising at least one tumor cell obtained from a patient;

(2) enriching the sample in (1) for test DNA molecules each comprising at least one locus from the plurality of single nucleotide polymorphism loci, wherein the plurality of single nucleotide polymorphism loci comprises at least 5,000 single nucleotide polymorphism loci and wherein there is at least one single nucleotide polymorphism locus located on average every 500 kb within each chromosome; and

(3) sequencing the test DNA molecules to determine whether each locus in the plurality of single nucleotide polymorphism loci is homozygous.

2. The method of claim 1, wherein the plurality of single nucleotide polymorphism loci comprises at least 10,000 single nucleotide polymorphism loci.

3. The method of claim 1, wherein the plurality of single nucleotide polymorphism loci comprises at least 50,000 single nucleotide polymorphism loci.

4. The method of claim 1, wherein there is at least one single nucleotide polymorphism locus located on average every 100 kb within each chromosome.

5. The method of claim 1, wherein there is at least one single nucleotide polymorphism locus located on average every 50 kb within each chromosome.

6. The method of claim 1, wherein there is at least one single nucleotide polymorphism locus located on average every 10 kb within each chromosome.

7. The method of claim 1, wherein the genomic spacing of the plurality of single nucleotide polymorphism loci is less than or equal to 50%.

8. The method of claim 1, wherein the genomic spacing of the plurality of single nucleotide polymorphism loci is less than or equal to 25%.

9. The method of claim 1, wherein the genomic spacing of the plurality of single nucleotide polymorphism loci is less than or equal to 10%.

10. A system for detecting homozygosity at a plurality of single nucleotide polymorphism loci, comprising:

(1) a sample analyzer for

(a) enriching a formalin-fixed paraffin-embedded sample comprising at least one tumor cell obtained from a patient for test DNA molecules each comprising at least one locus from the plurality of single nucleotide polymorphism loci, wherein the plurality of single nucleotide polymorphism loci comprises at least 5,000 single nucleotide polymorphism loci and wherein there is at least one single nucleotide polymorphism locus located on average every 500 kb within each chromosome; and

(b) sequencing the test DNA molecules to produce a plurality of quantitative signals representing the alleles for each locus in the plurality of single nucleotide polymorphism loci present in the test DNA molecules; and

(2) a computer program for analyzing the plurality of quantitative signals to determine whether each locus in the plurality of single nucleotide polymorphism loci is homozygous.

11. The method of system 10, wherein the plurality of single nucleotide polymorphism loci comprises at least 10,000 single nucleotide polymorphism loci.

12. The method of system 10, wherein the plurality of single nucleotide polymorphism loci comprises at least 50,000 single nucleotide polymorphism loci.

13. The method of system 10, wherein there is at least one single nucleotide polymorphism locus located on average every 100 kb within each chromosome.

14. The method of system 10, wherein there is at least one single nucleotide polymorphism locus located on average every 50 kb within each chromosome.

15. The method of system 10, wherein there is at least one single nucleotide polymorphism locus located on average every 10 kb within each chromosome.

16. The method of system 10, wherein the genomic spacing of the plurality of single nucleotide polymorphism loci is less than or equal to 50%.

17. The method of system 10, wherein the genomic spacing of the plurality of single nucleotide polymorphism loci is less than or equal to 25%.

18. The method of system 10, wherein the genomic spacing of the plurality of single nucleotide polymorphism loci is less than or equal to 10%.