Reducing sequence read count error in assessment of complex genetic variations

• US 9,984,198 B2
• Filed: 03/12/2013
• Issued: 05/29/2018
• Est. Priority Date: 10/06/2011
• Status: Active Grant

• Current Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Deciu, Cosmin, Dzakula, Zeljko, Ehrich, Mathias, Jensen, Taylor Jacob
• Primary Examiner(s): Vanni, G. Steven
• Application Number:
  US13/797,930
• Publication Number:
  US 20130325360A1
• Time in Patent Office: 1,904 Days
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/40 Population genetics; Linkage disequilibrium
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

Claims

1. A computer-implemented method for detecting presence or absence of a complex genetic variation, comprising:

(a) obtaining counts of sequence reads mapped to portions of a reference genome, which sequence reads are of circulating cell-free nucleic acid from a test sample from a pregnant female;

(b) reducing error in the counts of the sequence reads, wherein the error is reduced according to a process comprising;

(1) assigning a guanine and cytosine (GC) bias coefficient to the test sample based on a fitted relation between (i) the counts of the sequence reads mapped to each of the portions and (ii) GC content for each of the portions, wherein the GC bias coefficient is a slope for a linear fitted relation or a curvature estimation for a non-linear fitted relation; and

(2) calculating a genomic section level for each of the portions for the test sample based on the counts of (a), the GC bias coefficient of (b)(1), and a fitted relation, for each of the portions, between (i) the GC bias coefficient for each of multiple samples and (ii) the counts of the sequence reads mapped to each of the portions for the multiple samples, thereby providing calculated genomic section levels, whereby error in the counts of the sequence reads is reduced; and

(c) outputting a classification of the presence or absence of a complex genetic variation for the test sample according to the calculated genomic section levels, wherein the complex genetic variation comprises two or more copy number variations chosen from a whole chromosome aneuploidy, a microduplication, and a microdeletion, and wherein a measure of deviation between (i) calculated genomic section levels for portions that include a copy number variation and (ii) expected genomic section levels for portions that include no copy number variation is larger for counts with error reduction according to (b) than a measure of deviation between (i) and (ii) for counts with no error reduction according to (b).

2. The method of claim 1, wherein the GC bias coefficient in (b)(1) is a slope for a linear fitted relation determined by linear regression.

3. The method of claim 1, wherein the GC bias coefficient in (b)(1) is a curvature estimation determined by a non-linear fitted relation.

4. The method of claim 1, wherein the fitted relation of (b)(2) is linear.

5. The method of claim 4, wherein a slope of the fitted relation in (b)(2) is determined by linear regression.

6. The method of claim 5, wherein the GC bias coefficient for each of the multiple samples in (b)(2)(i) is the slope of a fitted linear relation, for each of the multiple samples, between (i) the counts of the sequence reads mapped to each of the portions and (ii) GC content for each of the portions.

7. The method of claim 6, wherein a calculated genomic section level L is calculated for the test sample for each portion of the reference genome according to Equation B:

L=(M−

GS)/I 

 

Equation B

wherein M is the counts of the sequence reads mapped to the portion for the test sample, G is the GC bias coefficient for the test sample, I is an intercept of the fitted linear relation of (b)(2) for the portion, S is a slope of the linear relationship of (b)(2) for the portion.

8. The method of claim 1, comprising filtering one or more portions and removing counts associated with the one or more portions for the classification of the presence or absence of the complex genetic variation in part (c).

9. The method of claim 8, comprising (i) normalizing the counts in (a) according to (b), thereby generating normalized counts, and removing normalized counts associated with one or more filtered portions, thereby yielding filtered normalized counts;

or (ii) removing counts associated with one or more filtered portions prior to (b), and normalizing the counts in portions that were not removed according to (b), thereby yielding filtered normalized counts.

10. The method of claim 8, wherein the one or more filtered portions are selected according to one or more criteria chosen from measure of error or mappability, or measure of error and mappability.

11. The method of claim 10, wherein the one or more filtered portions are selected according to one or more criteria chosen from portions having no guanosine and cytosine (GC) content, portions consistently receiving no counts, and repeat masking.

12. The method of claim 10, wherein the measure of error is an R factor.

13. The method of claim 12, wherein portions of the reference genome having an R factor of about 7% or greater were selected as filtered portions.

14. The method of claim 13, wherein portions of the reference genome having an R factor of about 7% to about 10% were selected as filtered portions.

15. The method of claim 10, comprising performing a secondary normalization of the filtered normalized counts or the levels.

16. The method of claim 15, wherein the secondary normalization is a LOESS normalization.

17. The method of claim 16, comprising (i) identifying a copy number variation in the calculated genomic section levels, and (ii) adjusting the calculated genomic section levels associated with the copy number variation.

18. The method of claim 17, comprising (1) identifying a first elevation in the calculated genomic section levels significantly different than a second elevation in the calculated genomic section levels, which first elevation is for a first set of genomic section levels, and which second elevation is for a second set of genomic section levels, (2) determining an expected elevation range for a homozygous and heterozygous copy number variation according to an uncertainty value for a segment of the genome, (3) adjusting the first elevation by a predetermined value when the first elevation is within one of the expected elevation ranges, thereby providing adjusted genomic section levels, and (4) identifying the presence or absence of the copy number variation according to the adjusted genomic section levels.

19. The method of claim 1, wherein the whole chromosome aneuploidy is a trisomy of a chromosome selected from chromosome 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 19, 20, 22, X and Y.

20. The method of claim 1, wherein the complex genetic variation is a double chromosome aneuploidy.

21. The method of claim 1, wherein the complex genetic variation is a fetal genetic variation.

22. The method of claim 1, wherein the microdeletion and/or microduplication is located in a chromosome selected from chromosome 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, X and Y.

23. The method of claim 1, wherein each portion of the reference genome comprises a nucleotide sequence of a predetermined length.

24. The method of claim 23, wherein the length is about 50 kilobases.

25. The method of claim 1, wherein (b)(1 ) or (b)(2), or (b)(1) and (b)(2), are implemented using at least one microprocessor.

26. The method of claim 1, comprising generating the sequence reads of the circulating, cell-free nucleic acid from the test sample by a sequencing apparatus.

27. The method of claim 26, comprising mapping the sequence reads to the portions of the reference genome, and counting the mapped sequence reads, thereby generating the counts of the sequence reads mapped to the portions of the reference genome.

28. The method of claim 1, comprising monitoring health of the fetus and pregnant female from whom the test sample was obtained according to the presence or absence of the complex genetic variation classified in (c) from the genomic section levels calculated in (b)(2).

29. The method of claim 28, comprising performing a medical procedure comprising amniocentesis or chorionic villus sampling when presence of a complex genetic variation is classified for the test sample from the calculated genomic section levels.

30. The method of claim 28, comprising performing a medical procedure consistent with a euploid pregnancy when absence of a complex genetic variation is classified for the test sample from the calculated genomic section levels.

31. The method of claim 1, comprising sequencing the test sample by a genome-wide massively parallel sequencing process.

32. The method of claim 31, wherein the sequencing is at about 1-fold coverage or less.

33. The method of claim 31, wherein the sequencing is at about 1- fold coverage or greater.

34. The method of claim 1, wherein the nucleic acid is from blood plasma or blood serum.

35. The method of claim 1, comprising generating and transmitting a laboratory prenatal test report comprising a classification of presence or absence of a complex genetic variation for the test sample.

36. The method of claim 35, wherein the report comprises one or more of a sensitivity, specificity and confidence interval for the classification.

37. The method of claim 1, comprising after (b) generating at least one Z-score from the calculated genomic section levels.

38. A system comprising one or more processors and memory,

which memory comprises instructions executable by the one or more processors and which memory comprises counts of sequence reads mapped to portions of a reference genome, which sequence reads are of circulating cell-free nucleic acid from a test sample from a pregnant female, which instructions executable by the one or more processors are configured to perform a process comprising:

(a) reducing error in the counts of the sequence reads, wherein the error is reduced according to a process comprising;

(1) assigning a guanine and cytosine (GC) bias coefficient to the test sample based on a fitted relation between (i) the counts of the sequence reads mapped to each of the portions and (ii) GC content for each of the portions, wherein the GC bias coefficient is a slope for a linear fitted relation or a curvature estimation for a non-linear fitted relation; and

(2) calculating a genomic section level for each of the portions for the test sample based on the counts of the sequence reads mapped to each of the portions, the GC bias coefficient of (a)(1), and a fitted relation, for each of the portions, between (i) the GC bias coefficient for each of multiple samples and (ii) the counts of the sequence reads mapped to each of the portions for the multiple samples, thereby providing calculated genomic section levels, whereby error in the counts of the sequence reads is reduced; and

(b) outputting a classification of the presence or absence of a complex genetic variation for the test sample according to the calculated genomic section levels, wherein the complex genetic variation comprises two or more copy number variations chosen from a whole chromosome aneuploidy, a microduplication, and a microdeletion, and wherein a measure of deviation between (i) calculated genomic section levels for portions that include a copy number variation and (ii) expected genomic section levels for portions that include no copy number variation is larger for counts with error reduction according to (a) than a measure of deviation between (i) and (ii) for counts with no error reduction according to (a).

39. The system of claim 38, wherein the system comprises a sequencing apparatus.