SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA FROM TARGET INDIVIDUALS USING GENETIC DATA FROM GENETICALLY RELATED INDIVIDUALS

摘要

A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.

主权项

1. 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 sample from the biological mother of the fetus 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 comprises single nucleotide polymorphisms; collecting genetic material from one or both biological parents of the fetus; measuring genetic data from the biological parent of the fetus by determining 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, for each of the hypotheses, expected genetic data for the plurality of loci in the fetus from the measured genetic data from the biological parent; comparing, on a computer, the expected genetic data for each of the hypotheses to the measured genetic data to determine a probability that each hypothesis is true; ranking one or more of the hypotheses according to the probability that the hypothesis is true; 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.