Analyzing copy number variation in the detection of cancer

Patent metadata

Field	Value
Publication number	US-10388403-B2
Application number	US-201213555010-A
Country	US
Kind code	B2
Filing date	Jul 20, 2012
Priority date	Jan 19, 2010
Publication date	Aug 20, 2019
Grant date	Aug 20, 2019

Abstract

The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.

First claim

What is claimed is:

1. A method, implemented at a computer system that includes one or more processors and system memory, for identifying the presence of a cancer and/or an increased risk of a cancer in a mammal, said method comprising:
(a) providing sequence reads of nucleic acids in a test sample from said mammal to the computer system, wherein said test sample comprises both genomic nucleic acids from cancerous or precancerous cells and genomic nucleic acids from constitutive cells, wherein the sequence reads are provided in an electronic format;
(b) aligning, by the one or more processors of the computer system, the sequence reads to one or more chromosome reference sequences, and thereby providing sequence tags corresponding to the sequence reads;
(c) identifying, by the one or more processors of the computer system, a number of sequence tags from the nucleic acids for one or more chromosomes of interest amplifications of which or deletions of which are known to be associated with cancers, or chromosome segments of interest amplification of which or deletions of which are known to be associated with cancers, wherein said chromosome or chromosome segments are selected from chromosomes 1-22, X, and Y and segments thereof and identifying a number of sequence tags for at least one normalizing chromosome sequence or normalizing chromosome segment sequence for each of the one or more chromosomes of interest or chromosome segments of interest;
(d) calculating, by the one or more processors of the computer system and using said number of sequence tags identified for each of said one or more chromosomes of interest or chromosome segments of interest and said number of sequence tags identified for each said normalizing chromosome sequence or normalizing chromosome segment sequence, a single chromosome or segment dose for each of said one or more chromosomes of interest or chromosome segments of interest,
wherein the at least one normalizing chromosome sequence or normalizing chromosome segment sequence is a chromosome or segment that was selected for the chromosome or segment of interest by (i) identifying a plurality of qualified samples for the chromosome or segment of interest; and (ii) selecting the normalizing chromosome sequence or normalizing chromosome segment sequence giving chromosome or segment doses for the chromosome or segment of interest having: (1) a smallest variability, (2) a greatest differentiability, (3) a smallest variability and a greatest differentiability, or (4) an optimal combination of small variability and large differentiability; and
(e) comparing, by the one or more processors of the computer system, each of said single chromosome doses for each of one or more chromosomes of interest or chromosome segments of interest to a corresponding threshold value for each of said one or more chromosomes of interest or chromosome segments of interest; and
(f) based on the comparing, determining the presence or absence of aneuploidies in said sample and the presence and/or increased risk of a cancer.

2. The method of claim 1 , wherein said aneuploidies comprise whole chromosome aneuploidies.

3. The method of claim 2 , wherein said whole chromosome aneuploidies comprise a loss.

4. The method of claim 2 , wherein said aneuploidies comprise a gain.

5. The method of claim 2 , wherein said whole chromosome aneuploidies comprise a gain or a loss as shown in Table 1.

6. The method of claim 1 , wherein said chromosomal segments of interest are substantially arm-level segments comprising a p arm or a q arm of any one or more of chromosomes 1-22, X and Y.

7. The method of claim 6 , wherein said aneuploidies comprise an amplification of a substantial arm level segment of a chromosome.

8. The method of claim 6 , wherein said aneuploidies comprise a deletion of a substantial arm level segment of a chromosome.

9. The method of claim 6 , wherein said chromosomal segments of interest substantially comprise one or more arms selected from the group consisting of 1q, 3q, 4p, 4q, 5p, 5q, 6p, 6q, 7p, 7q, 8p, 8q, 9p, 9q, 10p, 10q, 12p, 12q, 13q, 14q, 16p, 17p, 17q, 18p, 18q, 19p, 19q, 20p, 20q, 21q, and/or 22q.

10. The method of claim 9 , wherein said aneuploidies an amplification of one or more arms selected from the group consisting of 1q, 3q, 4p, 4q, 5p, 5q, 6p, 6q, 7p, 7q, 8p, 8q, 9p, 9q, 10p, 10q, 12p, 12q, 13q, 14q, 16p, 17p, 17q, 18p, 18q, 19p, 19q, 20p, 20q, 21q, 22q.

11. The method of claim 9 , wherein said aneuploidies a deletion of one or more arms selected from the group consisting of 1p, 3p, 4p, 4q, 5q, 6q, 8p, 8q, 9p, 9q, 10p, 10q, 11p, 11q, 13q, 14q, 15q, 16q, 17p, 17q, 18p, 18q, 19p, 19q, 22q.

12. The method of claim 1 , wherein said chromosomal segments of interest are segment that comprise a region and/or a gene shown in Table 3 and/or Table 5 and/or Table 4 and/or Table 6.

13. The method of claim 12 , wherein said aneuploidies comprise an amplification of a region and/or a gene shown in Table 3 and/or Table 5.

14. The method of claim 12 , wherein said aneuploidies comprise a deletion of a region and/or a gene shown in Table 4 and/or Table 6.

15. The method of claim 1 , wherein said chromosomal segments of interest are segments known to contain one or more oncogenes and/or one or more tumor suppressor genes.

16. The method of claim 15 , wherein said aneuploidies comprise an amplification of one or more regions selected from the group consisting of 20Q13, 19q12, 1q21-1q23, 8p11-p12, and the ErbB2.

17. The method of claim 15 , wherein said aneuploidies comprise an amplification of one or more regions comprising a gene selected from the group consisting of MYC, ERBB2 (EFGR), CCND1 (Cyclin D1), FGFR1, FGFR2, HRAS, KRAS, MYB, MDM2, CCNE, KRAS, MET, ERBB1, CDK4, MYCB, ERBB2, AKT2, MDM2 and CDK4.

18. The method of claim 1 , wherein said test sample comprises a sample selected from the group consisting of whole blood, a blood fraction, saliva/oral fluid, urine, a tissue biopsy, pleural fluid, pericardial fluid, cerebral spinal fluid, and peritoneal fluid.

19. The method of claim 1 , wherein the chromosome reference sequences have excluded regions that are present naturally in chromosomes but that do not contribute to the number of sequence tags for any chromosome or chromosome segment.

20. The method of claim 1 , further comprising storing in a computer readable medium, at least temporarily, sequence information for said nucleic acids in said sample.

21. The method of claim 1 , wherein step (d) comprises calculating a segment dose for a selected one of segments of interest as a ratio of the number of sequence tags identified for said one or more chromosomes of interest or chromosome segments of interest and the number of sequence tags identified for a corresponding at least one normalizing chromosome sequence or normalizing chromosome segment sequence for the selected segment of interest.

22. The method of claim 1 , wherein the one or more chromosome segments of interest comprise at least 5 different segments of interest.

23. The method of claim 1 , wherein at least 5 different aneuploidies are detected.

24. The method of claim 1 , wherein said at least one normalizing chromosome sequence comprise one or more chromosomes selected from the group consisting of chromosomes 1-22, X, and Y.

25. The method of claim 1 , wherein said at least one normalizing chromosome sequence comprises for each segment the chromosome corresponding

Assignees

• Rava Richard P
• Rhees Brian K
• Verinata Health Inc

Inventors

• Rava Richard P
• Rhees Brian K

Classifications

• A61P35/00

  Antineoplastic agents · CPC title

• G16H50/20

  for computer-aided diagnosis, e.g. based on medical expert systems · CPC title

• C12Q1/6886

  for cancer (immunoassay for cancer G01N33/575) · CPC title

• C12Q1/6806

  Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) · CPC title

• C12Q1/6869

  Methods for sequencing · CPC title