METHODS AND PROCESSES FOR NON-INVASIVE ASSESSMENT OF GENETIC VARIATIONS

• US 20130338933A1
• Filed: 03/14/2013
• Published: 12/19/2013
• 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
• Granted Patent: US 10,424,394 B2
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2537/16 Assays for determining copy number or wherein the copy number is of special importance
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• 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 method for determining a fraction of fetal nucleic acid in circulating cell-free nucleic acid from blood of a pregnant female, comprising:

(a) obtaining counts of nucleic acid sequence reads mapped to genomic sections of a reference genome, which sequence reads are reads of circulating cell-free nucleic acid from the blood of a pregnant female bearing a male fetus;

(b) from the counts in (a), generating an experimental Y chromosome representation, which experimental Y chromosome representation is a ratio of (i) counts of sequence reads mapped to the genomic sections of the reference genome in the Y chromosome, and (ii) counts of sequence reads mapped to genomic sections of the reference genome in the genome or segment thereof;

(c) determining the fraction of the fetal nucleic acid in the blood of the pregnant female according to the experimental Y chromosome representation generated in (b) and a fitted relationship, wherein;

the fitted relationship is between (i) an experimental Y chromosome representation determined from a set of pregnant females bearing a male fetus and (ii) an X chromosome representation determined from a set of pregnant females; and

the fitted relationship is fitted to a median chromosome X representation and a median chromosome Y representation for a set of pregnant females bearing a female fetus.

2. The method of claim 1, wherein the X chromosome representation in (c)(ii) is an experimental X chromosome representation.

3. The method of claim 1, wherein the X chromosome representation is a ratio of (i) counts of sequence reads mapped to the genomic sections of the reference genome in the X chromosome, and (ii) counts of sequence reads mapped to genomic sections of the reference genome in the genome or segment thereof.

4. The method of claim 1, wherein the X chromosome representation in (c)(ii) is determined from a set of pregnant females bearing a male fetus.

5. The method of claim 1, wherein the fitted relationship is linear.

6. The method of claim 5, wherein the fraction of the fetal nucleic acid is determined according to the slope and intercept of the fitted relationship, the experimental Y chromosome representation generated in (b) and a median X chromosome representation for a set of pregnant females bearing a female fetus.

7. The method of claim 6, wherein the fraction of the fetal nucleic acid is determined according to equation (62):

8. The method of any one of claim 1, wherein the fitted relationship in (c) is determined prior to (a).

9. The method of any one of claim 1, wherein the counts in (a) are obtained from a pregnant female bearing a male fetus having a chromosome aneuploidy.

10. The method of claim 9, wherein the chromosome aneuploidy is a trisomy 21, trisomy 18 and/or trisomy 13.

11. The method of claim 9, wherein the chromosome aneuploidy is a sex chromosome aneuploidy.

12. The method of claim 1, wherein the set of pregnant females in (c)(i) is a set of about 500 females or more.

13. The method of claim 1, wherein the set of pregnant females in (c)(ii) is a set of about 500 females or more.

14. The method of any one of claim 1, comprising normalizing the counts in (a), thereby providing normalized counts mapped to the genomic sections of the reference genome;

and which counts in (b) are normalized counts.

15. The method of claim 14, wherein the counts in (b) are normalized by GC content, bin-wise normalization, GC LOESS, PERUN, GCRM, or combinations thereof.

16. The method of claim 1, wherein the fetal fraction is provided with an accuracy of equal to or greater than 90% and/or a precision equal to or greater than 90%.

17. The method of claim 1, which comprises determining the presence or absence of nucleic acid sequence reads mapped to the Y chromosome in the reference genome.

18. The method of claim 17, wherein determining the presence or absence of nucleic acid sequence reads mapped to the Y chromosome is performed before performing (b).

19. The method of claim 1, which comprises determining the gender of the fetus.

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

which memory comprises instructions executable by the one or more processors and which memory comprises (i) counts of nucleic acid sequence reads mapped to genomic sections of a reference genome, which sequence reads are reads of circulating cell-free nucleic acid from the blood of a pregnant female bearing a male fetus and (ii) a fitted relationship between (i) an experimental Y chromosome representation determined from a set of pregnant females bearing a male fetus and (ii) an X chromosome representation determined from a set of pregnant females;

and wherein the fitted relationship is fitted to a median chromosome X representation and a median chromosome Y representation for a set of pregnant females bearing a female fetus, and

which instructions executable by the one or more processors are configured to;

(a) from the counts, generate an experimental Y chromosome representation, which experimental Y chromosome representation is a ratio of (i) counts of sequence reads mapped to the genomic sections of the reference genome in the Y chromosome, and (ii) counts of sequence reads mapped to genomic sections of the reference genome in the genome or segment thereof; and

(b) determine the fraction of the fetal nucleic acid in the blood of the pregnant female according to the experimental Y chromosome representation generated in (b) and the fitted relationship.