Patent Document ID: 9977708
Application ID: 13801653
Patent Status: 1

Claim One:
1. A method of determining ancestry origin of a first chromosome and a second chromosome of a chromosome pair of autosomal chromosomes of an individual, comprising: (a) obtaining, from a data source and for the first chromosome and the second chromosome of the chromosome pair of autosomal chromosomes of the individual, unphased genotype data comprising a plurality of genetic markers associated with the first chromosome and the second chromosome of the chromosome pair; (b) applying, using one or more computer processors, a phasing method to the unphased genotype data of the first and second chromosomes of the chromosome pair of autosomal chromosomes of the individual to generate a first set of phased haplotype data for the first chromosome of the chromosome pair and a second set of phased haplotype data for the second chromosome of the chromosome pair; (c) dividing, using one or more computer processors and based on the plurality of genetic markers, the first set of phased haplotype data of the first chromosome of the chromosome pair into a first sequence of non-overlapping haplotype windows and the second set of phased haplotype data of the second chromosome of the chromosome pair into a second sequence of non-overlapping haplotype windows, wherein each haplotype window at a chromosome location of the first sequence of non-overlapping haplotype windows of the first chromosome of the chromosome pair is paired with a haplotype window at a same chromosome location of the second sequence of non-overlapping haplotype windows of the second chromosome of the chromosome pair; (d) assigning, using a classifier model and one or more computer processors, an initial ancestry classification to each haplotype window of the first sequence of non-overlapping haplotype windows of the first chromosome of the chromosome pair and to each haplotype window of the second sequence of non-overlapping haplotype windows of the second chromosome of the chromosome pair, wherein each initial ancestry classification classifies each haplotype window as originating from an ancestry associated with a single geographical region or a single ethnicity, thereby generating a sequence of observed states, wherein each observed state is an ordered pair of initial ancestry classifications at a given chromosome location; (e) inputting, using one or more computer processors, the sequence of observed states of (d) to an Autoregressive Pair Hidden Markov Model (APHMM); and (f) performing dynamic programming, by one or more computer processors, to apply the APHMM to the sequence of observed states of (d) to produce a likely sequence of hidden states for the chromosome pair, wherein each observed state at a position in the sequence of observed states depends on its underlying hidden state and depends on at least one observed state at a previous position in the sequence of observed states, and wherein each hidden state is an ordered pair of likely ancestry classifications for a pair of haplotype windows of the first and second chromosomes of the chromosome pair at a given chromosome location, and wherein each hidden state at a position in the likely sequence of hidden states depends on the hidden state at a previous position in the likely sequence of hidden states, and wherein at least one error in the initial ancestry classification and/or phasing of the first and second chromosome of the chromosome pair is corrected, thereby determining ancestry origin of the first chromosome and the second chromosome of the chromosome pair of autosomal chromosomes of the individual.