A method of designating a genomic locus as a maternal or fetal marker by analyzing a sample from a female subject pregnant with a fetus, the method comprising: receiving a plurality of sequence reads, wherein the sequence 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 sequence reads in a reference sequence; identifying one or more informative loci, each of which is homozygous in a first entity for a corresponding first allele and which is heterozygous in a second entity for the corresponding first allele and a corresponding second allele, wherein the first entity is the pregnant female subject or the fetus, and the second entity is the other one of the pregnant female subject and the fetus; filtering the one or more informative loci to identify one or more filtered informative loci: that are located within an expressed region of the reference sequence, at which at least a first predetermined number of sequence reads in the plurality of sequence reads containing the corresponding first allele are located, and at which at least a second predetermined number of sequence reads in the plurality of sequence reads containing the corresponding second allele are located; and for each of the filtered informative loci: determining a first number of sequence reads located at the filtered informative locus and containing the corresponding first allele, determining a second number of sequence reads located at the filtered informative locus and containing the corresponding second allele, calculating a ratio of the first number and the second number, and designating the filtered informative locus as a marker for the second entity when the ratio exceeds a cutoff. receiving a plurality of sequence reads, wherein the sequence 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 sequence reads in a reference sequence; identifying one or more informative loci, each of which is homozygous in a first entity for a corresponding first allele and which is heterozygous in a second entity for the corresponding first allele and a corresponding second allele, wherein the first entity is the pregnant female subject or the fetus, and the second entity is the other one of the pregnant female subject and the fetus; filtering the one or more informative loci to identify one or more filtered informative loci: that are located within an expressed region of the reference sequence, at which at least a first predetermined number of sequence reads in the plurality of sequence reads containing the corresponding first allele are located, and at which at least a second predetermined number of sequence reads in the plurality of sequence reads containing the corresponding second allele are located; and that are located within an expressed region of the reference sequence, at which at least a first predetermined number of sequence reads in the plurality of sequence reads containing the corresponding first allele are located, and at which at least a second predetermined number of sequence reads in the plurality of sequence reads containing the corresponding second allele are located; and for each of the filtered informative loci: determining a first number of sequence reads located at the filtered informative locus and containing the corresponding first allele, determining a second number of sequence reads located at the filtered informative locus and containing the corresponding second allele, calculating a ratio of the first number and the second number, and designating the filtered informative locus as a marker for the second entity when the ratio exceeds a cutoff. determining a first number of sequence reads located at the filtered informative locus and containing the corresponding first allele, determining a second number of sequence reads located at the filtered informative locus and containing the corresponding second allele, calculating a ratio of the first number and the second number, and designating the filtered informative locus as a marker for the second entity when the ratio exceeds a cutoff.