Method for Non-Invasive Prenatal Testing Using Parental Mosaicism Data
Provided herein are methods for determining the ploidy state of one or more chromosome in a developing fetus. The subject methods provide for increase accuracy by utilizing information about the mosaicism level of one or more chromosomes of interest in the mother of fetus. The mosaicism level of one or more chromosomes of interest is determine for the maternal tissue that is used as the source of nucleic acid for genetic analysis that are used to determine the ploidy state of the fetal chromosome or chromosomes of interest. For example, if 5% white blood cells of mother are missing a copy of the X chromosome, this information can be used when determining fetal ploidy level, rather than operating under the assumption that the maternal X chromosome are present in two copies. Utilization of the mosaicism data can be used to increase the reliability and accuracy of the determination of the ploidy state of a chromosome of interest.
1 . A method of diagnosing the ploidy state of a chromosome in a gestating fetus, the method comprising the steps:
obtaining a sample comprising nucleic acid from the mother of the fetus,
obtaining a sample comprising nucleic acid from the fetus,
determining the single-nucleotide polymorphism (SNP) allele counts at a plurality of polymorphic loci in the sample comprising nucleic acid from the mother, and the sample comprising nucleic acid from the fetus, by sequencing the polymorphic loci,
determining the degree of mosaicism of the chromosome in a tissue of the mother of the fetus,
creating on a computer, a plurality of ploidy state hypotheses pertaining to different ploidy states of the chromosome in the fetus, wherein the chromosome comprises the polymorphic loci, wherein the ploidy state is selected from the group consisting of, nullsomy, monosomy, disomy, uniparental disomy, euploidy, trisomy, matching trisomy, unmatching trisomy, maternal trisomy, paternal trisomy, tetrasomy, balanced (2:2) tetrasomy, unbalanced (3:1) tetrasomy, pentasomy, hexasomy, other aneuploidy, and combinations thereof,
determining on a computer a relative probability of each ploidy state hypothesis by comparing the SNP allele counts from the polymorphic loci of the fetus to the SNP allele counts from the polymorphic loci of the mother and using the degree of mosaicism of the chromosome in a tissue of the mother of the fetus, and
outputting the ploidy state hypothesis with the highest probability as a diagnosis of the ploidy state of the chromosome of interest in the fetus.
2 . The method of claim 1 , wherein the chromosome is the X chromosome.
3 . The method of claim 1 , wherein the allele count is determined for at least 100 loci.
4 . The method of claim 1 , wherein the allele count is determined for at least 500 loci.
5 . The method of claim 1 , wherein the fetal nucleic acid is free floating nucleic acid obtained from maternal plasma.
6 . The method of claim 1 , wherein the fetal nucleic acid is cellular DNA obtained from a mixture comprising cells that are genetically fetal and cells that are genetically maternal.
7 . The method of claim 1 , wherein the maternal tissue is blood.
8 . The method of claim 7 , wherein the maternal tissue is huffy coat derived from the blood.
9 . The method of claim 1 , wherein the determining of the relative probability of each ploidy state hypothesis further comprises building a joint distribution model of the allele counts.
10 . The method of claim 1 , wherein the mosaicism level is determined by array hybridization.
11 . The method of claim 1 , wherein the mosaicism level is determined by quantitative PCR.
12 . The method of claim 1 , wherein the mosaicism level is determined by quantitative sequence counting.