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Using size and number aberrations in plasma DNA for detecting cancer

  • US 10,364,467 B2
  • Filed: 01/12/2016
  • Issued: 07/30/2019
  • Est. Priority Date: 01/13/2015
  • Status: Active Grant
First Claim
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1. A method of analyzing a biological sample of an organism, the biological sample including nucleic acid molecules originating from normal cells and potentially from cells associated with cancer, wherein at least some of the nucleic acid molecules are cell-free in the biological sample, the method comprising:

  • identifying a plurality of chromosomal regions of the organism, each chromosomal region including a plurality of loci;

    for each of a plurality of the nucleic acid molecules in the biological sample;

    measuring a size of the nucleic acid molecule; and

    identifying a location of the nucleic acid molecule in a reference genome of the organism;

    for each of the plurality of chromosomal regions;

    identifying a respective group of nucleic acid molecules as being from the chromosomal region based on the identified locations, the respective group including at least one nucleic acid molecule located at each of the plurality of loci of the chromosomal region;

    calculating, with a computer system, a respective amount of the respective group of nucleic acid molecules; and

    comparing the respective amount to a count reference value to determine a count classification of whether the chromosomal region exhibits an aberration, the count classification for a first chromosomal region of the plurality of chromosomal regions indicating a first aberration;

    identifying a first group of nucleic acid molecules as being from the first chromosomal region based on the identified locations;

    calculating, with a computer system, a first statistical value of a first size distribution of the first group of nucleic acid molecules;

    comparing the first statistical value to a size reference value to determine a size classification of whether the first chromosomal region exhibits the first aberration;

    determining a final classification of whether the first chromosomal region exhibits the first aberration using the count classification and the size classification of the first chromosomal region; and

    determining whether cancer exists in the organism using the final classification.

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