System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals

An ex vivo method for determining a number of copies of a chromosome of interest, or section of the chromosome, in the genome of a fetus, comprising;

• collecting a maternal sample comprising at least one fetal cell,
• obtaining measured genetic data from the sample by measuring the quantity of each allele at each of the plurality of loci in genetic material from the fetus, wherein the plurality of loci comprises single nucleotide polymorphisms, and wherein the plurality of loci comprises loci on the chromosome of interest or section of the chromosome of interest;
• collecting genetic material from one or both biological parents of the fetus,
• obtaining measured genetic data from the parental cells by determining the allele present at each of the plurality of loci in genetic material from the parent;
• creating, on a computer, a plurality of hypotheses specifying the number of copies of the chromosome of interest or section of the chromosome of interest present in the genome of the fetus;
• creating, on a computer, for each of the hypotheses, a probability distribution of the expected quantity of each allele at each of the plurality of loci in the fetus from the (i) the measured genetic data from the one biological parent and (ii) the probability of one or more crossovers that may have occurred during the formation of a gamete that contributed a copy of the chromosome or interest or section of the chromosome of interest to the fetus;
• calculating, on a computer, a fit, for each of the hypotheses, between (1) the measured genetic data of the fetus and (2) the probability distribution of the expected quantity of each allele at each of the plurality of loci in the fetus for that hypothesis;
• ranking one or more of the hypotheses according to the calculated fit;
• and
• selecting the hypothesis that is ranked the highest, thereby determining the number of copies of the chromosome of interest or the section of the chromosome of interest in the genome of a fetus.

An ex vivo method for determining a number of copies of a chromosome of interest, or section of the chromosome, in the genome of a fetus that makes use of the genetic data of a biological parent of the fetus, the method comprising:

• collecting a maternal sample comprising at least one fetal cell;
• measuring genetic data from the fetal cell by determining the quantity of each allele at a plurality of loci in genetic material from the fetal cell, wherein the plurality of loci comprise single nucleotide polymorphisms;
• collecting genetic material from a biological parent of the fetus;
• measuring genetic data from one or both biological parents of the fetus by determining the identity of each allele at a plurality of the loci in genetic material from the biological parent;
• creating, on a computer, a plurality of hypotheses specifying the number of copies of the chromosome of interest or section of the chromosome of interest present in the genome of the fetus;
• calculating, on a computer, for each of the hypotheses, a probability distribution for expected genetic data of the fetus from the measured quantity of each allele at the loci;
• calculating, on a computer, a fit, for each of the hypotheses, between (1) the measured genetic data and (2) the probability distribution for the expected genetic data of the fetus for that hypothesis;
• ranking one or more of the hypotheses according to the calculated fit;
• and
• selecting the hypothesis that is ranked the highest, thereby determining the number of copies of the chromosome of interest or the section of the chromosome of interest in the genome of the fetus.