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Methods and processes for non-invasive assessment of genetic variations

  • US 10,699,800 B2
  • Filed: 05/23/2014
  • Issued: 06/30/2020
  • Est. Priority Date: 05/24/2013
  • Status: Active Grant
First Claim
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1. A computer-implemented method for determining the presence or absence of a microduplication or microdeletion in a fetus, comprising:

  • (a) receiving input information comprising nucleic acid sequence reads obtained by non-targeted multiplexed massively parallel sequencing of circulating cell-free nucleic acid from a test sample from a pregnant female bearing a fetus, and mapping the nucleic acid sequence reads to portions of a reference genome;

    (b) normalizing, using a microprocessor, counts of the nucleic acid sequence reads mapped to portions of the reference genome, wherein the normalizing comprises normalization of guanine and cytosine (GC) bias and an adjustment according to a principal component analysis, thereby providing normalized counts;

    (c) segmenting, using a microprocessor, the normalized counts of the portions or the normalized counts in a subset of the portions, thereby providing one or more discrete segments;

    (d) identifying, using a microprocessor, a candidate segment among the one or more discrete segments, wherein the candidate segment is identified according to an area under a curve (AUC) analysis, wherein;

    i) the AUC analysis is based on a number of portions covered by the segment and an absolute value of a level of normalized counts for the segment, wherein the level corresponds to a negative value of normalized counts for a deletion or a positive value of normalized counts for a duplication; and

    ii) the candidate segment has the largest AUC of all the segments on the same chromosome; and

    (e) determining the presence or absence of the microduplication or microdeletion according to the candidate segment.

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