IDENTITY-BY-DESCENT RELATEDNESS BASED ON FOCAL AND REFERENCE SEGMENTS
Example embodiments relate to identity-by-descent (IBD) relatedness based on focal and reference segments. An example method includes determining, by a services platform based on personal information of a focal individual, a focal string. The method also includes retrieving, by the services platform from a reference database, a reference string of a reference individual. Additionally, the method includes computationally identifying, by the services platform, IBD segments between the focal string and the reference string. Further, the method includes determining, by the services platform and based on the merged set of IBD segments, a degree of relatedness between the focal individual and the reference individual. In addition, the method includes providing, by the services platform, access to the degree of relatedness via a user interface.
1 . A computer implemented method of processing haplotypes to reduce errors when determining identity-by-descent (IBD) segments between haplotypes, the method comprising:
providing two or more paired haplotype strings for identification of IBD segments therebetween, each of the two or more paired haplotype strings representing a sequence of allele values at polymorphic sites in a haplotype of an organism; and
computationally iterating through the two or more paired haplotype strings by:
(i) identifying a first potential IBD segment between the two or more paired haplotype strings by identifying matches among alleles of the haplotype strings;
(ii) comparing a first site of the first potential IBD segment to an end site of a previously identified second potential IBD segment;
(iii) determining that the end site of the second potential IBD segment and the first site of the first potential IBD segment are within a threshold number of sites of each other; and
(iv) merging the first potential IBD segment and the second potential IBD segment to form a combined potential IBD segment.
2 . The computer implemented method of claim 1 , wherein the first potential IBD segment and the second potential IBD segment are on different haplotypes, and wherein the method further comprises:
determining that a phase switch error occurred at a site between the first potential IBD segment and the second potential IBD segment; and
swapping the haplotypes from a position of the phase switch error onward.
3 . The computer implemented method of claim 1 , wherein the first potential IBD segment and the second potential IBD segment overlap.
4 . The computer implemented method of claim 1 , wherein the first potential IBD segment and the second potential IBD segment each span at least the threshold number of sites.
5 . The computer implemented method of claim 1 , wherein the threshold number of sites is between 1 and 500 SNPs.
6 . The computer implemented method of claim 1 , further comprising:
determining a third potential IBD segment among phased haplotype data for a plurality of individuals, wherein the third potential IBD segment has a start site;
determining that the end site of the combined potential IBD segment and the start site of the third potential IBD segments are within the threshold number of sites of each other; and
merging the combined potential IBD segments and the third potential IBD segments.
7 . The computer implemented method of claim 1 , further comprising:
determining that the combined potential IBD segments have a minimum length in centimorgans; and
storing the combined potential IBD segments as an IBD segment.
8 . A computer implemented method of determining identity-by-descent (IBD) segments, the method comprising:
determining first potential IBD segments among phased haplotype data for a plurality of individuals, wherein the first potential IBD segments have an end site;
determining second potential IBD segments among haplotype data for the plurality of individuals, wherein the second potential IBD segments have a start site;
determining that the end site of the first potential IBD segments and the start site of the second potential IBD segments are within a threshold number of sites of each other; and
merging the first potential IBD segments and the second potential IBD segments to form a combined potential IBD segment.
9 . The method of claim 8 , wherein the first potential IBD segments and the second potential IBD segments are on different haplotypes for an individual of the plurality of individuals, and the method further comprises:
determining that a phase switch error occurred at a site between the first potential IBD segment and the second potential IBD segment for the individual; and
swapping the haplotypes for the individual from a position of the phase switch error onward.
10 . The method of claim 8 , wherein the first potential IBD segment and the second potential IBD segment each span at least the threshold number of sites.
11 . The method of claim 8 , wherein the threshold number of sites is between 1 and 500 SNPs.
12 . A system for determining identity-by-descent (IBD) segments, the system comprising:
(a) one or more processors and associated memory; and
(b) computer readable instructions that, when executed by the one or more processors, cause the one or more processors to:
determine first potential IBD segments among phased haplotype data for a plurality of individuals, wherein the first potential IBD segments have an end site;
determine second potential IBD segments among haplotype data for the plurality of individuals, wherein the second potential IBD segments have a start site;
determine that the end site of the first potential IBD segments and the start site of the second potential IBD segments are within a threshold number of sites of each other; and
merge the first potential IBD segments and the second potential IBD segments to form a combined potential IBD segment.
13 . The system of claim 12 , wherein the first potential IBD segments and the second potential IBD segments are on different haplotypes for an individual of the plurality of individuals, and wherein the computer readable instructions, when executed by the one or more processors, further cause the processor to:
determine that a phase switch error occurred at a site between the first potential IBD segment and the second potential IBD segment for the individual; and
swap the haplotypes for the individual from a position of the phase switch error onward.
14 . The system of claim 12 , wherein the first potential IBD segments and the second potential IBD segments overlap for an individual of the plurality of individuals.
15 . The system of claim 12 , wherein the first potential IBD segment and the second potential IBD segment each span at least the threshold number of sites.
16 . The system of claim 12 , wherein the threshold number of sites is between 1 and 500 SNPs.
17 . The system of claim 12 , wherein the plurality of individuals do not share a parent-child relationship.
18 . The system of claim 12 , wherein the computer readable instructions, when executed by the one or more processors, further cause the one or more processors to:
determine a third potential IBD segment among phased haplotype data for a plurality of individuals, wherein the third potential IBD segment has a start site;
determine that the end site of the combined potential IBD segment and the start site of the third potential IBD segments are within the threshold number of sites of each other; and
merge the combined potential IBD segments and the third potential IBD segments.
19 . The system of claim 18 , wherein the combined potential IBD segment and the third potential IBD segment are on different haplotypes for an individual of the plurality of individuals, and the computer readable instructions, when executed by the one or more processors, further cause the one or more processors to:
determine that a phase switch error occurred at a site between the combined potential IBD segment and the third potential IBD segment for the individual; and
swap the haplotypes for the individual from a position of the phase switch error.
20 . The system of claim 12 , wherein the computer readable instructions, when executed by the one or more processors, further cause the one or more processors to:
determine that the combined potential IBD segments have a minimum length in centimorgans; and
store the combined potential IBD segments as IBD segments for the plurality of individuals.