Patent ID: 11970742
Assignee: THE CHINESE UNIVERSITY OF HONG KONG
Field: Computer technology (Electrical engineering)
Classification: CPC C  G | IPC C  G

Claim 0:
1. A method of determining, in a sample from a female subject pregnant with a fetus, a portion of RNA that is of fetal origin, the method comprising:
receiving a plurality of reads, wherein the reads are obtained from an analysis of RNA molecules obtained from the sample, the sample containing a mixture of maternal- and fetal-derived RNA molecules;
identifying, by a computer system, locations of the reads in a reference sequence, wherein the reference sequence is a reference genome;
identifying one or more informative maternal loci, each of which is homozygous in the fetus for a corresponding first allele and which is heterozygous in the pregnant female subject for the corresponding first allele and a corresponding second allele;
filtering the one or more informative maternal loci to identify one or more filtered informative maternal loci:
that are located within an expressed region of the reference sequence,
at which at least a first predetermined number of reads in the plurality of reads containing the corresponding first allele are located, and
at which at least a second predetermined number of reads in the plurality of reads containing the corresponding second allele are located,

for each of the filtered informative maternal loci:
determining a first number of reads located at the filtered informative maternal locus and containing the corresponding first allele,
determining a second number of reads located at the filtered informative maternal locus and containing the corresponding second allele,
calculating a sum of the first number and the second number,
calculating a maternal ratio of the second number divided by the sum,
determining a scalar representing a total expression at the filtered informative maternal locus relative to expression of the corresponding second allele in the pregnant female subject,
multiplying the maternal ratio by the scalar to obtain a maternal contribution,
calculating a fetal contribution as one minus the maternal contribution, and

determining a portion of RNA in the sample that is of fetal origin, wherein the portion is an average of the fetal contributions for the filtered informative maternal loci.