Methods and compositions for analyzing nucleic acid

• US 9,920,361 B2
• Filed: 03/01/2013
• Issued: 03/20/2018
• Est. Priority Date: 05/21/2012
• 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): Weiler, Karen S.
• Application Number:
  US13/782,857
• Publication Number:
  US 20130310260A1
• Time in Patent Office: 1,845 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• 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
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR

Abstract

Technology provided herein relates in part to methods, processes, compositions and apparatuses for analyzing nucleic acid.

Claims

1. A method for sequencing nucleic acid from a pregnant female, comprising:

(a) sequencing test sample nucleic acid by a genome-wide massively parallel sequencing process, thereby generating sequence reads, which test sample nucleic acid comprises circulating cell-free nucleic acid from blood of a pregnant female bearing a fetus, and obtaining counts of the sequence reads mapped to genomic sections of a reference genome;

(b) measuring the length of nucleic acid fragments from which the sequence reads are obtained;

(c) selecting counts for reads from nucleic acid fragments that are shorter than about 160 bases in silico, thereby generating selected counts;

(d) normalizing the selected counts for the test sample according to a bias for the test sample, a bias for each of multiple samples from multiple pregnant females, and counts of nucleotide sequence reads mapped to each of the genomic sections for the multiple samples, thereby generating normalized selected counts;

(e) determining the presence of a chromosome aneuploidy according to the normalized selected counts; and

(f) performing a medical procedure comprising amniocentesis or karyotyping for the pregnant female after (e).

2. The method of claim 1, further comprising comparing the normalized selected counts, or derivative thereof, to a threshold value, thereby providing a comparison.

3. The method of claim 2, wherein determining the presence of a chromosome aneuploidy is according to the comparison.

4. The method of claim 1, wherein sequence coverage of reads from nucleic acid fragments shorter than about 160 bases is reduced relative to sequence coverage of reads not restricted by fragment length.

5. The method of claim 1, wherein sequence read count of reads from nucleic acid fragments shorter than about 160 bases is reduced relative to sequence read count of reads not restricted by fragment length.

6. The method of claim 5, wherein sequence read count is reduced by at least about 50%.

7. The method of claim 1, wherein measuring the length of the nucleic acid fragments comprises a paired-end sequencing method.

8. The method of claim 1, wherein sequence read length is about 15 bases to about 25 bases.

9. The method of claim 1, wherein the sample is blood, serum or plasma.

10. The method of claim 1, wherein the chromosome aneuploidy is a trisomy.

11. The method of claim 10, wherein the trisomy is trisomy 21, trisomy 18, or trisomy 13.

12. The method of claim 1, wherein the bias for the test sample in (d) is a guanine and cytosine (GC) bias, and the bias for each of multiple samples from multiple pregnant females in (d) is a guanine and cytosine (GC) bias.

13. The method of claim 12, wherein the normalizing in (d) comprises 1) determining a guanine and cytosine (GC) bias coefficient for the test sample based on a fitted relation between (i) the counts of the nucleotide sequence reads mapped to each of the genomic sections and (ii) GC content for each of the genomic sections, 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) determining a fitted relation, for each of the genomic sections, between (i) a GC bias coefficient for each of the multiple samples from multiple pregnant females and (ii) counts of nucleotide sequence reads mapped to each of the genomic sections for the multiple samples.

14. The method of claim 1, wherein presence of a chromosome aneuploidy is determined for the fetus with a sensitivity of about 1.00 and a specificity of at least about 0.99.

15. The method of claim 1, further comprising

mapping the sequence reads to the genomic sections of the reference genome and counting the sequence reads mapped to the genomic sections, thereby obtaining counts of sequence reads mapped to the genomic sections.