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:
partitioning genetic data into intervals;
determining, based on the genetic data and frequencies of genotypes appearing in the intervals for each of a set of reference populations, geographic origins for one or more of the intervals;
generating, for display on a graphical user interface, representations of the intervals indicating the geographic origins for the one or more of the intervals; and
providing, to the graphical user interface, the representations of the intervals.
2 . The computer-implemented method of claim 1 , further comprising:
determining, based on the genetic data and the frequencies of genotypes appearing in the intervals for each of the set of reference populations, one or more further intervals with no known geographic origins, wherein the representations of the intervals indicate that there are no known geographic origins for the one or more further intervals.
3 . The computer-implemented method of claim 1 , wherein the intervals are based on non-overlapping adjacent words of consecutive single-nucleotide polymorphisms.
4 . The computer-implemented method of claim 1 , wherein the 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, and wherein selection 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 for the one or more of the intervals.
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 the geographic 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 the geographic origins for a Y haplogroup or a mitochondrial haplogroup.
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 an individual with the genetic data, wherein the migration patterns are based on known human migration patterns and a geographic 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 the 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 genotypes appearing in the intervals for each of the set of reference populations by, for each respective interval of the intervals:
determining a first number of individuals within each respective reference population of the reference populations exhibiting a respective genotype; and
dividing the first number by a second number representing a total of the individuals within the reference populations.
15 . The computer-implemented method of claim 1 , wherein the frequencies of genotypes appearing in the intervals for each of the set of reference populations include at least one synthetic rate of genotype occurrence for a synthetic reference population of mixed geographic origins.
16 . The computer-implemented method of claim 1 , wherein determining the geographic origins for the one or more of the intervals comprises:
determining, for a specific interval of the one or more of the intervals, a ratio of a largest frequency of genotype occurrence to a second largest frequency of genotype 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 for a genotype associated with the largest frequency of genotype occurrence.
17 . The computer-implemented method of claim 1 , wherein determining the geographic origins for one or more of the intervals comprises:
arranging, for a specific interval of the one or more of the intervals, a window of n consecutive intervals including the specific interval; and
assigning, to the specific interval, a majority 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:
partitioning genetic data of an individual into intervals;
determining, based on the genetic data and frequencies of genotypes appearing in the intervals for each of a set of reference populations, geographic origins for one or more of the intervals;
generating, for display on a graphical user interface, representations of the intervals indicating the geographic origins for the one or more of the 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:
partitioning genetic data into intervals;
determining, based on the genetic data and frequencies of genotypes appearing in the intervals for each of a set of reference populations, geographic origins for one or more of the intervals;
generating, for display on a graphical user interface, representations of the intervals indicating the geographic origins for the one or more of the intervals; and
providing, to the graphical user interface, the representations of the intervals.