Global ancestry determination system
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.
1. 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 a plurality 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, an inter-window hidden Markov model (HMM) that comprises:
(i) a plurality of node groups, each node group representing one of the windows that comprises a set of SNPs, 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 wherein the inter-window HMM is trained by:
receiving phased haplotype datasets corresponding to sequences of alleles of individuals;
building per-window models for the plurality of windows;
receiving a set of reference panel samples; and
training the per-window models using the set of reference panel samples to generate an emission probability for each node of each window in the inter-window HMI; and
generating information on the individual using the inter-window HMM.
2. The computer implemented method of claim 1 , wherein the information on the individual comprises one or more of: a set of possible ethnic origins of the individual and percentage compositions of the set of the possible ethnic origins, a set of possible paternal origins and percentage compositions of the set of possible paternal origins, or a set of possible maternal origins and percentage compositions of the set of possible maternal origins.
3. The computer implemented method of claim 1 , wherein the information on the individual comprises one or more of: a visualization of the individual's ancestry composition by chromosome painting, information about a particular trait of the individual, a percentage of DNA shared with a relative of the individual, a set of similarities and differences in a first genotype dataset of a first parent of the individual and a second genotype dataset of a second parent of the individual, or information on individuals genetically related to the individual.
4. The computer implemented method of claim 1 , wherein the plurality of nodes in each node group represents permutations of different first parent labels and second parent labels.
5. The computer implemented method of claim 1 , wherein a switching of order of the first parent label and the second parent label corresponds to a switching of the first and second parent labels from one node group to a next node group.
6. The computer implemented method of claim 1 , wherein generating the inter-window HMM further comprises:
initiating label probabilities, each label probability for a particular label representing a probability distribution of the particular label among other possible labels;
initiating label change probabilities, each label change probability representing a likelihood of a change of label from one window to another window;
initiating a label switch probability representing a likelihood of a switching of order of the first parent label and the second parent label from one window to another window;
adjusting the label probabilities, label change probabilities, and the label switch probability through iterations;
determining transition probabilities based on the label probabilities, the label change probabilities, and the label switch probability, each transition probability associated with a particular edge and representing a likelihood of the first node connected by the particular edge from one node group transitioning to the second node connected by the particular edge from another node group; and
connecting the nodes with edges, each edge corresponding to a determined transition probability.
7. The computer implemented method of claim 1 , wherein each node is associated with the emission probability based on the pair of phased haplotype datasets.
8. 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 a plurality 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, an inter-window hidden Markov model (HMM) that comprises:
(i) a plurality of node groups, each node group representing one of the windows that comprises a set of SNPs, 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 wherein the inter-window HMI is trained by:
receiving phased haplotype datasets corresponding to sequences of alleles of individuals;
building per-window models for the plurality of windows;
receiving a set of reference panel samples; and
training the per-window models using the set of reference panel samples to generate an emission probability for each node of each window in the inter-window HMM; and
generating information on the individual using the inter-window HMM.
9. The non-transitory computer-readable storage medium of claim 8 , wherein the information on the individual comprises one or more of: a set of possible ethnic origins of the individual and percentage compositions of the set of the possible ethnic origins, a set of possible paternal origins and percentage compositions of the set of possible paternal origins, or a set of possible maternal origins and percentage compositions of the set of possible maternal origins.
10. The non-transitory computer-readable storage medium of claim 8 , wherein the information on the individual comprises one or more of: a visualization of the individual's ancestry composition by chromosome painting, information about a particular trait of the individual, a percentage of DNA shared with a relative of the individual, a set of similarities and differences in a first genotype dataset of a first parent of the individual and a second genotype dataset of a second parent of the individual, or information on individuals genetically related to the individual.
11. The non-transitory computer-readable storage medium of claim 8 , wherein the plurality of nodes in each node group represents permutations of different first parent labels and second parent labels.
12. The non-transitory computer-readable storage medium of claim 8 , wherein a switching of order of the first parent label and the second parent label corresponds to a switching of the first and second parent labels from one node group to a next node group.
13. The non-transitory computer-readable storage medium of claim 8 , wherein generating the inter-window HMM further comprises:
initiating label probabilities, each label probability for a particular label representing a probability distribution of the particular label among other possible labels;
initiating label change probabilities, each label change probability representing a likelihood of a change of label from one window to another window;
initiating a label switch probability representing a likelihood of a switching of order of the first parent label and the second parent label from one window to another window;
adjusting the label probabilities, label change probabilities, and the label switch probability through iterations;
determining transition probabilities based on the label probabilities, the label change probabilities, and the label switch probability, each transition probability associated with a particular edge and representing a likelihood of the first node connected by the particular edge from one node group transitioning to the second node connected by the particular edge from another node group; and
connecting the nodes with edges, each edge corresponding to a determined transition probability.
14. The non-transitory computer-readable storage medium of claim 8 , wherein each node is associated with the emission probability.
15. 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 a plurality 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, an inter-window hidden Markov model (HMM) that comprises:
(i) a plurality of node groups, each node group representing one of the windows that comprises a set of SNPs, 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 wherein the inter-window HMM is trained by:
receiving phased haplotype datasets corresponding to sequences of alleles of individuals;
building per-window models for the plurality of windows;
receiving a set of reference panel samples; and
training the per-window models using the set of reference panel samples to generate an emission probability for each node of each window in the inter-window HMI; and
generating information on the individual using the inter-window HMM; and
a graphical interface configured to display the information.
16. The system of claim 15 , wherein the information on the individual comprises one or more of: a set of possible ethnic origins of the individual and percentage compositions of the set of the possible ethnic origins, a set of possible paternal origins and percentage compositions of the set of possible paternal origins, or a set of possible maternal origins and percentage compositions of the set of possible maternal origins.
17. The system of claim 15 , wherein the information on the individual comprises one or more of: a visualization of the individual's ancestry composition by chromosome painting, information about a particular trait of the individual, a percentage of DNA shared with a relative of the individual, a set of similarities and differences in a first genotype dataset of a first parent of the individual and a second genotype dataset of a second parent of the individual, or information on individuals genetically related to the individual.
18. The system of claim 15 , wherein the plurality of nodes in each node group represents permutations of different first parent labels and second parent labels.
19. The system of claim 15 , wherein a switching of order of the first parent label and the second parent label corresponds to a switching of the first and second parent labels from one node group to a next node group.
20. The system of claim 15 , wherein generating the inter-window HMM further comprises:
initiating label probabilities, each label probability for a particular label representing a probability distribution of the particular label among other possible labels;
initiating label change probabilities, each label change probability representing a likelihood of a change of label from one window to another window;
initiating a label switch probability representing a likelihood of a switching of order of the first parent label and the second parent label from one window to another window;
adjusting the label probabilities, label change probabilities, and the label switch probability through iterations;
determining transition probabilities based on the label probabilities, the label change probabilities, and the label switch probability, each transition probability associated with a particular edge and representing a likelihood of the first node connected by the particular edge from one node group transitioning to the second node connected by the particular edge from another node group; and
connecting the nodes with edges, each edge corresponding to a determined transition probability.