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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
First Claim
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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).

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