Methods and processes for non-invasive assessment of genetic variations

• US 10,504,613 B2
• Filed: 03/01/2013
• Issued: 12/10/2019
• Est. Priority Date: 12/20/2012
• Status: Active Grant

• Current Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Kim, Sung K., Deciu, Cosmin
• Primary Examiner(s): Woitach, Joseph
• Application Number:
  US13/782,883
• Publication Number:
  US 20140180594A1
• Time in Patent Office: 2,475 Days
• Field of Search: None
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• 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: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

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

Claims

1. A computer-implemented method for classifying nucleic acid for a fetal aneuploidy, comprising:

(a) identifying a subset of genomic sections of a reference genome consisting essentially of genomic sections to which an enriched amount of reads from fetal nucleic acid fragments are mapped by a process comprising;

(i) sequencing circulating cell-free nucleic acid from each sample from a group of pregnant females by a sequencer that generates sequence reads for each of the samples of the group;

(ii) measuring, for each of the samples of the group, the length of each fragment in the circulating cell-free nucleic acid from which each of the sequence reads originated using a microprocessor;

(iii) computing, using a microprocessor, a fragment length ratio X/Y for each genomic section for each sample, wherein;

(1) X is the sum of reads that (i) map to the genomic section, and (ii) are from nucleic acid fragments that are shorter than a first selected fragment length; and

(2) Y is the sum of reads that (i) map to the genomic section, and (ii) are from nucleic acid fragments that are shorter than a second selected fragment length, wherein the second selected fragment length is longer than the first selected fragment length;

(iv) computing an average fragment length ratio for each genomic section;

(v) determining a median fragment length ratio for a plurality of genomic sections; and

(vi) selecting the subset of genomic sections based on each genomic section of the subset having an average fragment length ratio that is greater than the median fragment length ratio;

(b) sequencing circulating cell-free nucleic acid from a test sample from a pregnant female bearing a fetus by a sequencer that generates sequence reads for the test sample;

(c) mapping, using a microprocessor, the test sample sequence reads to the subset of genomic sections selected in (a)(vi);

(d) calculating, using a microprocessor, the amount of test sample sequence reads mapped to the subset of genomic sections;

(e) outputting a classification of presence or absence of a fetal aneuploidy according to the amount determined in (d).

2. The method of claim 1, wherein the sequencer that generates sequence reads for the test sample is a genome-wide massively parallel sequencer.

3. The method of claim 1, wherein the fetal aneuploidy is a trisomy 21, trisomy 18, or trisomy 13.

4. The method of claim 1, wherein the method comprises comparing the amount in (d), or derivative thereof, to a threshold value, thereby providing a comparison.

5. The method of claim 4, wherein the presence or absence of a fetal aneuploidy is determined according to the comparison.

6. The method of claim 1, wherein the first selected fragment length is about 150 bases or less.

7. The method of claim 1, wherein the second selected fragment length is about 600 bases or less.

8. The method of claim 1, comprising normalizing the amount of test sample sequence reads in (d) to adjust for guanine and cytosine (GC) bias.

9. The method of claim 1, wherein about 30% to about 70% of test sample sequence reads are mapped to the subset of genomic sections.

10. The method of claim 1, wherein sequence coverage and/or sequence read count for test sample sequence reads mapped to the subset of genomic sections is reduced by about 60% to about 85%.

11. The method of claim 1, comprising performing a medical procedure comprising amniocentesis or chorionic villus sampling when presence of a fetal aneuploidy classified in (e).

12. The method of claim 1, wherein the subset of genomic sections are selected from genomic sections in TABLE 4.

13. The method of claim 1, wherein the sequencer that generates sequence reads in (a)(i) is a paired-end sequencer that generates paired-end sequence reads for each of the samples of the group.

14. The method of claim 13, wherein measuring the length of each fragment in (a)(ii) comprises mapping the paired-end reads to a reference genome, determining the length of genomic sequence between the paired-end mapped reads, and calculating the fragment length as the total of both paired-end read lengths and the length of the genomic sequence between the paired-end reads.

15. The method of claim 1, wherein the sequencer that generates sequence reads in (a)(i) is a single-end sequencer that generates single-end sequence reads for each of the samples of the group.

16. The method of claim 15, wherein measuring the length of each fragment in (a)(ii) comprises determining the length of a single-end read derived from the fragment.

17. The method of claim 1, wherein the sequencer that generates sequence reads in (b) is a single-end sequencer that generates single-end sequence reads for the test sample.

18. The method of claim 1, wherein the subset of genomic sections of a reference genome consisting essentially of genomic sections to which an enriched amount of reads from fetal nucleic acid fragments are mapped consists essentially of genomic sections to which a significant amount of reads from nucleic acid fragments shorter than about 150 bases are mapped.

19. The method of claim 1, wherein the second selected fragment length is about 1000 bases or less.

20. The method of claim 1, wherein the second selected fragment length is about 2000 bases or less.