Methods and processes for non-invasive assessment of genetic variations

• US 10,497,462 B2
• Filed: 07/02/2013
• Issued: 12/03/2019
• Est. Priority Date: 01/25/2013
• 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
• Primary Examiner(s): Brusca, John S
• Application Number:
  US13/933,935
• Publication Number:
  US 20130304392A1
• Time in Patent Office: 2,345 Days
• 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 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation
• 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: G16H 50/20 for computer-aided diagnosis, e.g. based on medical expert systems

Abstract

Provided herein are methods, processes, systems and apparatuses for non-invasive assessment of a chromosome aneuploidy in a fetus according to a comparison of ratios of counts of sequence reads mapped to certain chromosomes. Also provided herein are methods, processes, systems and apparatuses for non-invasive assessment of a copy number variation in a fetus.

Claims

1. A computer-implemented method for outputting a classification of presence or absence of a chromosome aneuploidy for sequenced test sample nucleic acid from a pregnant female, comprising:

(a) sequencing test sample nucleic acid by a massively parallel sequencer that generates sequence reads, which test sample nucleic acid comprises circulating cell-free nucleic acid from blood of a pregnant female bearing a fetus, wherein the sequencing is at about 1-fold coverage or less;

(b) mapping, using a microprocessor, the sequence reads to portions of a reference genome;

(c) counting, using a microprocessor, the sequence reads mapped to the portions, which counting generates counts of sequence reads mapped to the portions;

(d) normalizing, using a microprocessor, the counts of sequence reads mapped to chromosomes 13, 18, and 21, or segments thereof, according to guanine-cytosine (GC) content, which normalizing generates normalized counts;

(e) calculating, using a microprocessor, three ratios from the normalized counts, wherein the three ratios consist of;

(i) a ratio between counts mapped to chromosome 13, or segment thereof, to counts mapped to chromosome 21, or segment thereof,

(ii) a ratio between counts mapped to chromosome 13, or segment thereof, to counts mapped to chromosome 18, or segment thereof, and

(iii) a ratio between counts mapped to chromosome 18, or segment thereof, to counts mapped to chromosome 21, or segment thereof;

(f) computationally comparing, using a microprocessor, the three ratios to corresponding ratios of one or more euploid samples, which comparing generates a comparison; and

(g) outputting, using a microprocessor, a classification of the presence of absence of a chromosome aneuploidy for the test sample according to the comparison generated in (f).

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

3. The method of claim 1, comprising generating and transmitting a laboratory prenatal test report comprising a classification of presence or absence of three copies of a chromosome for the test sample.

4. The method of claim 3, wherein the report comprises one or more of a sensitivity, specificity and confidence interval for the classification.

5. The method of claim 4, wherein the sensitivity is 95% or greater and the specificity is 99% or greater.

6. The method of claim 1, comprising monitoring health of the fetus and pregnant female from whom the test sample was obtained based on the number of copies of a chromosome in the fetus.

7. The method of claim 6, comprising performing a medical procedure comprising amniocentesis or chorionic villus sampling when the classification is presence of three copies of a chromosome.

8. The method of claim 1, wherein the comparison is a Cartesian coordinate in three-dimensional space.

9. The method of claim 1, wherein the comparing in (f) comprises plotting the three ratios calculated in (e) in three dimensions, which dimensions are the ratios, and the comparison is a point for the subject on a three dimensional plot.

10. The method of claim 9, wherein the outputting the classification in (g) comprises calculating the distance between the point for the subject to a point or points for the one or more euploid samples.

11. The method of claim 1, wherein the sequencing is by a genome-wide massively parallel sequencer.

12. The method of claim 1, wherein the comparison generated in (f) is not based on segments of the genome other than in chromosomes 13, 18 and 21.