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Processes for calculating phased fetal genomic sequences

  • US 10,289,800 B2
  • Filed: 05/20/2013
  • Issued: 05/14/2019
  • Est. Priority Date: 05/21/2012
  • Status: Active Grant
First Claim
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1. A process for determining the phased composition in a fetal heritable genomic region from a maternal sample comprising maternal DNA and fetal DNA, the process comprising the steps of:

  • isolating cell-free nucleic acids from the maternal sample comprising the maternal DNA and the fetal DNA, wherein the cell-free nucleic acids comprise selected nucleic acid regions;

    interrogating the selected nucleic acid regions in the fetal heritable genomic region using oligonucleotides to amplify the selected nucleic acid regions, the oligonucleotides comprising universal amplification sequences;

    applying the amplified selected nucleic acid regions to an array-based pull-out detection system to identify informative loci corresponding to a heritable genomic region of interest;

    providing, to a computer processor, phased sequence information from at least one corresponding parental heritable genomic region;

    identifying, by the computer processor, five or more informative loci in the fetal DNA corresponding to a heritable genomic region of interest from the phased sequence information of the at least one corresponding parental heritable genomic region;

    calculating, by the computer processor, a paternal contribution of the heritable genomic region of interest using the phased sequence information of the five or more informative loci;

    calculating, by the computer processor, the maternal contribution of the heritable genomic region of interest by comparing the paternal contribution of the heritable genomic region of interest to the selected nucleic acid regions in the fetal heritable genomic region; and

    generating, by the computer processor, a prediction of a likely phased composition of the heritable genomic region of interest in the fetal DNA using the maternal and paternal contributions of the heritable genomic region of interest.

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