US 2020/0286579 A1 · GLOBAL ANCESTRY DETERMINATION SYSTEM

Abstract

An input genotype is divided into a plurality of windows, each including a sequence of SNPs. For each window, a diploid HMM is computed based on genotypes and/or phased haplotypes to determine a probability of a haplotype sequence being associated with a particular label. For example, the diploid HMM for a window is used to determine the emission probability that the window corresponds to a set of labels. An inter-window HMM, with a set of states for each window, is computed. Labels are assigned to the input genotype based on the inter-window HMM. Upper and lower bounds are estimated to produce a range of likely percentage values an input can be assigned to a given label. Confidence values are determined indicating a likelihood that an individual inherits DNA from a certain population. Maps are generated with polygons representing regions where a measure of ethnicity of population falls within specific ranges.

Claims20

Dependent claims

A computer implemented method comprising:

accessing a genotype dataset associated with an individual;
dividing the genotype dataset into a plurality of windows, each window comprising a set of single nucleotide polymorphisms (SNPs);
determining a pair of phased haplotype datasets from the plurality of windows of genotype dataset;
generating, using one or more processors and the pair of phased haplotype datasets, a directed acyclic graph that comprises:
(i) a plurality of node groups, each node group representing one of the windows, each node group comprising a plurality of nodes, each node representing a state of the window represented by the node group, the state comprising:
(1) a first parent label, and
(2) a second parent label, and
(ii) a plurality of edges, at least one edge connecting a first node to a second node and representing a transition from the first node to the second node;
and
generating information on the individual using the directed acyclic graph.

7 more elements

A non-transitory computer-readable storage medium storing executable computer program instructions, the computer program instructions, when executed by one or more processors, cause the one or more processors to perform steps comprising:

accessing a genotype dataset associated with an individual;
dividing the genotype dataset into a plurality of windows, each window comprising a set of single nucleotide polymorphisms (SNPs);
determining a pair of phased haplotype datasets from the plurality of windows of genotype dataset;
generating, using the pair of phased haplotype datasets, a directed acyclic graph that comprises:
(i) a plurality of node groups, each node group representing one of the windows, each node group comprising a plurality of nodes, each node representing a state of the window represented by the node group, the state comprising:
(1) a first parent label, and
(2) a second parent label, and
(ii) a plurality of edges, at least one edge connecting a first node to a second node and representing a transition from the first node to the second node;
and
generating information on the individual using the directed acyclic graph.

7 more elements

A system comprising:

one or more computer processors;
and
memory storing executable computer program instructions, the computer program instructions, when executed by the one or more computer processors, cause the one or more computer processors to perform steps comprising:
accessing a genotype dataset associated with an individual,
dividing the genotype dataset into a plurality of windows, each window comprising a set of single nucleotide polymorphisms (SNPs),
determining a pair of phased haplotype datasets from the plurality of windows of genotype dataset,
generating, using the pair of phased haplotype datasets, a directed acyclic graph that comprises:
(i) a plurality of node groups, each node group representing one of the windows, each node group comprising a plurality of nodes, each node representing a state of the window represented by the node group, the state comprising:
(1) a first parent label, and
(2) a second parent label, and
(ii) a plurality of edges, at least one edge connecting a first node to a second node and representing a transition from the first node to the second node, and
generating information on the individual using the directed acyclic graph;
and
a graphical interface configured to display the information.

11 more elements

Dependencies are inferred from the claim text.

Global ancestry determination system

Life of this patent

Global ancestry determination system

Life of this patent

Abstract

Claims20