Ancestry painting
Displaying an indication of ancestral data is disclosed. An indication that a genetic interval corresponds to a reference interval that has a likelihood of having one or more ancestral origins is received. One or more graphic display parameters are determined based at least in part on the indication. An indication of the one or more ancestral origins is visually displayed using the one or more graphic display parameters.
1. A computer-implemented method comprising:
obtaining genetic data of an individual;
partitioning the genetic data into intervals based on known genetic intervals, wherein the known genetic intervals each contain one or more genotypes with corresponding frequencies of occurrence within reference populations, and wherein the reference populations are respectively associated with reference geographic origins of reference individuals with the corresponding genotypes;
determining, based on the genetic data of the individual and the frequencies of occurrence for the intervals, geographic origins for one or more of the intervals of the individual;
generating, for display on a graphical user interface, representations of the intervals indicating: one or more of the geographic origins for genotyped intervals, or that one or more of the geographic origins are unknown for un-genotyped intervals; and
providing, to the graphical user interface, the representations of the intervals.
2. The computer-implemented method of claim 1 , wherein the genetic data includes a pair of chromosomes of the individual, and wherein partitioning the genetic data into intervals comprises partitioning each of the chromosomes separately when the genetic data is phased and partitioning the pair of chromosomes when the genetic data is unphased.
3. The computer-implemented method of claim 1 , wherein the known genetic intervals are based on non-overlapping adjacent words of consecutive single-nucleotide polymorphisms.
4. The computer-implemented method of claim 1 , wherein the known genetic intervals are based on fixed-sized words of consecutive single-nucleotide polymorphisms.
5. The computer-implemented method of claim 1 , wherein the geographic origins include at least Europe, Asia, and Africa.
6. The computer-implemented method of claim 1 , wherein the graphical user interface includes a drop-down menu that lists a plurality of individuals, wherein the plurality of individuals contains the individual, and wherein selection of the individual by way of the drop-down menu causes the graphical user interface to display the representations of the intervals.
7. The computer-implemented method of claim 1 , wherein the graphical user interface includes a geographic map of the geographic origins that are known.
8. The computer-implemented method of claim 1 , wherein the graphical user interface includes a geographic map, and wherein the geographic map includes a spatial distribution of likely ancestral origins.
9. The computer-implemented method of claim 1 , wherein the graphical user interface includes a geographic map, and wherein the geographic map includes indications of likely ancestral origins for a Y haplogroup or a mitochondrial haplogroup of the individual.
10. The computer-implemented method of claim 1 , wherein the graphical user interface includes a geographic map, and wherein the geographic map includes indications of migration patterns for ancestors of the individual, wherein the migration patterns are based on known human migration patterns and a geographical location of a haplotype of the individual.
11. The computer-implemented method of claim 1 , wherein the intervals are arranged in the graphical user interface in a karyotype view including 22 autosomal chromosomes.
12. The computer-implemented method of claim 11 , wherein the intervals of the 22 autosomal chromosomes are represented as pairs, and wherein the geographic origins for intervals within each pair are separately indicated.
13. The computer-implemented method of claim 1 , wherein the geographic origins are each represented by different colors.
14. The computer-implemented method of claim 1 , further comprising:
determining the frequencies of occurrence within one or more of the reference populations by: determining, for each respective known genetic interval of the known genetic intervals, a first number of individuals within the one or more of the reference populations exhibiting the respective known genetic interval; and dividing the first number by a second number representing a total of the individuals within the one or more of the reference populations.
15. The computer-implemented method of claim 1 , wherein the frequencies of occurrence include at least one synthetic rate of occurrence for a synthetic reference population of mixed geographic origins.
16. The computer-implemented method of claim 1 , wherein determining the geographic origins for one or more of the intervals of the individual comprises:
determining, for a specific interval of the one or more intervals, a ratio of a largest frequency of occurrence to a second largest frequency of occurrence within the specific interval;
determining that the ratio is above a given threshold or a given quantile; and
based on the ratio being above the given threshold or the given quantile, assigning, to the specific interval, a geographic origin associated with the largest frequency of occurrence.
17. The computer-implemented method of claim 1 , wherein determining the geographic origins for one or more of the intervals of the individual comprises:
arranging, for a specific interval of the one or more intervals, a window of n consecutive intervals including the specific interval; and
assigning, to the specific interval, a dominant geographic origin of the n consecutive intervals within the window.
18. The computer-implemented method of claim 17 , wherein n is a value from 10 to 50.
19. A non-transitory computer-readable medium storing program instructions that, when executed by one or more processors of a computing system, cause the computing system to perform operations comprising:
obtaining genetic data of an individual;
partitioning the genetic data into intervals based on known genetic intervals, wherein the known genetic intervals each contain one or more genotypes with corresponding frequencies of occurrence within reference populations, and wherein the reference populations are respectively associated with reference geographic origins of reference individuals with the corresponding genotypes;
determining, based on the genetic data of the individual and the frequencies of occurrence for the intervals, geographic origins for one or more of the intervals of the individual;
generating, for display on a graphical user interface, representations of the intervals indicating: one or more of the geographic origins for genotyped intervals, or that one or more of the geographic origins are unknown for un-genotyped intervals; and
providing, to the graphical user interface, the representations of the intervals.
20. A computing system comprising:
one or more processors;
memory; and
program instructions, stored in the memory, that upon execution by the one or more processors cause the computing system to perform operations comprising:
obtaining genetic data of an individual;
partitioning the genetic data into intervals based on known genetic intervals, wherein the known genetic intervals each contain one or more genotypes with corresponding frequencies of occurrence within reference populations, and wherein the reference populations are respectively associated with reference geographic origins of reference individuals with the corresponding genotypes;
determining, based on the genetic data of the individual and the frequencies of occurrence for the intervals, geographic origins for one or more of the intervals of the individual;
generating, for display on a graphical user interface, representations of the intervals indicating: one or more of the geographic origins for genotyped intervals, or that one or more of the geographic origins are unknown for un-genotyped intervals; and
providing, to the graphical user interface, the representations of the intervals.