| CPC G16B 20/20 (2019.02) [G16B 20/00 (2019.02)] | 13 Claims |
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1. A method for identifying variants associated with a genetic disease or genetic trait, the method comprising:
mapping, using a processor, a plurality of nucleic acid reads from a plurality of subjects to a reference genome, the subjects comprising a proband, a first biological relative of the proband, and a second biological relative of the proband, wherein the proband is affected by the genetic disease or genetic trait and comprises a phenotype associated with the genetic disease or genetic trait, and one or both of the first biological relative and the second biological relative are unaffected by the genetic disease or genetic trait;
based on the mapping, determining, using the processor, differences between the plurality of nucleic acid reads and the reference genome as variant positions in nucleic acid sequences of the proband, the first biological relative, and the second biological relative;
generating, using the processor, a first list of variants potentially inherited by the proband from the first biological relative and a second list of variants potentially inherited by the proband from the second biological relative at the determined variant positions;
filtering, using the processor, the first list of variants and the second list of variants to remove variants that do not contribute to compound heterozygous positions in the proband;
identifying, using the processor, one or more trans-phased compound heterozygous variants for the proband based on the filtering of the first and second lists; and
outputting, using the processor, the one or more trans-phased compound heterozygous variants as a potential variant associated with the genetic disease or the genetic trait.
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