Methods and Systems for Determining and Displaying Pedigrees

1 . A computer-implemented method comprising:

growing, by one or more processors, pedigrees for a plurality of genetically-related individuals, wherein the pedigrees are grown based on pairwise identity-by-descent (IBD) data between the genetically-related individuals;

combining, by the one or more processors, pairs of the pedigrees that share an amount of common IBD data above a pre-determined threshold into a combined pedigree;

identifying, by the one or more processors and among a portion of the genetically-related individuals not included in the combined pedigree, a closest relative of an individual included in the combined pedigree;

determining, by the one or more processors and from a probabilistic relationship model applied to pairwise IBD data of the closest relative and the individual, a plurality of relationship likelihoods respectively associated with a plurality of candidate relationships between the closest relative and the individual;

selecting, by the one or more processors and from the plurality of relationship likelihoods, a particular relationship likelihood meeting a criterion; and

adding, by the one or more processors and to the combined pedigree, a particular candidate relationship associated with the particular relationship likelihood.

2 . The computer-implemented method of claim 1 , wherein combining the pairs of the pedigrees comprises:

identifying a first set of individuals in a first pedigree of a particular pair of the pedigrees that share the amount of common IBD data above a further pre-determined threshold with individuals in a second pedigree of the particular pair of pedigrees;

identifying a second set of individuals in the second pedigree that share the amount of common IBD data above the further pre-determined threshold with individuals in the first pedigree;

determining a first common ancestor of the first set of individuals;

determining a second common ancestor of the second set of individuals;

inferring a degree of relatedness between the first common ancestor and the second common ancestor; and

connecting, in the combined pedigree, the first common ancestor and the second common ancestor.

3 . The computer-implemented method of claim 2 , wherein the first common ancestor is identified as a most recent common ancestor of the first set of individuals.

4 . The computer-implemented method of claim 2 , wherein determining the first common ancestor comprises:

identifying a most recent common ancestor of the first set of individuals;

identifying a set of relatives of the most recent common ancestor who are not descendants of the most recent common ancestor;

computing first IBD segments between the set of relatives and the first set of individuals;

computing second IBD segments between the second set of individuals and the first set of individuals;

identifying overlapping IBD segments between the first segments and the second segments;

determining that a total overlap of the overlapping IBD segments is greater than a predetermined fraction of a total IBD length of the first and second IBD segments; and

rejecting the most recent common ancestor.

5 . The computer-implemented method of claim 4 , wherein the predetermined fraction of the total IBD length of the first and second IBD segments is at least a value between 0.01 and 0.15.

6 . The computer-implemented method of claim 1 , wherein the plurality of candidate relationships comprises relationships between a 0th and a 15th degree.

7 . The computer-implemented method of claim 1 , wherein the probabilistic relationship model comprises a machine-learning model configured to model a probability distribution of the pairwise IBD data of the closest relative and the individual.

8 . The computer-implemented method of claim 7 , wherein the probability distribution is based on a Gaussian distribution, a Poisson distribution, or an exponential distribution.

9 . The computer-implemented method of claim 1 , wherein the plurality of candidate relationships between the closest relative and the individual comprise relationships of at least 4 meioses on a common-ancestor path.

10 . The computer-implemented method of claim 1 , wherein the pairwise IBD data between the genetically-related individuals has a total IBD length larger than an IBD threshold.

11 . The computer-implemented method of claim 10 , wherein the IBD threshold is 1 centimorgan (cM), 2 cM, 3 cM, 4 cM, 5 CM, 6 CM, 7 cM, 8 CM, 9 cM, 10 cM, 15 CM, 20 cM, 25 cM, 50 cM, 75 cM, 100 cM, 200 cM, or 500 cM.

12 . The computer-implemented method of claim 1 , wherein the pairwise IBD data between the genetically-related individuals is adjusted for a background IBD level by subtracting the background IBD from the pairwise IBD data.

13 . The computer-implemented method of claim 12 , wherein the background IBD level is inferred by estimating IBD segments between the pairs of individuals in the genetically-related individuals that are determined to be non-consanguineous.

14 . A system comprising one or more processors and one or more computer-readable storage media having stored thereon instructions for execution on the one or more processors that cause performance of a set of operations comprising:

growing pedigrees for a plurality of genetically-related individuals, wherein the pedigrees are grown based on pairwise identity-by-descent (IBD) data between the genetically-related individuals;

combining pairs of the pedigrees that share an amount of common IBD data above a pre-determined threshold into a combined pedigree;

identifying, among a portion of the genetically-related individuals not included in the combined pedigree, a closest relative of an individual included in the combined pedigree;

determining, from a probabilistic relationship model applied to pairwise IBD data of the closest relative and the individual, a plurality of relationship likelihoods respectively associated with a plurality of candidate relationships between the closest relative and the individual;

selecting, from the plurality of relationship likelihoods, a particular relationship likelihood meeting a criterion; and

adding, to the combined pedigree, a particular candidate relationship associated with the particular relationship likelihood.

15 . The system of claim 14 , wherein combining the pairs of the pedigrees comprises:

identifying a first set of individuals in a first pedigree of a particular pair of the pedigrees that share the amount of common IBD data above a further pre-determined threshold with individuals in a second pedigree of the particular pair of pedigrees;

identifying a second set of individuals in the second pedigree that share the amount of common IBD data above the further pre-determined threshold with individuals in the first pedigree;

determining a first common ancestor of the first set of individuals;

determining a second common ancestor of the second set of individuals;

inferring a degree of relatedness between the first common ancestor and the second common ancestor; and

connecting, in the combined pedigree, the first common ancestor and the second common ancestor.

16 . The system of claim 15 , wherein the first common ancestor is identified as a most recent common ancestor of the first set of individuals.

17 . The system of claim 15 , wherein determining the first common ancestor comprises:

identifying a most recent common ancestor of the first set of individuals;

identifying a set of relatives of the most recent common ancestor who are not descendants of the most recent common ancestor;

computing first IBD segments between the set of relatives and the first set of individuals;

computing second IBD segments between the second set of individuals and the first set of individuals;

identifying overlapping IBD segments between the first segments and the second segments;

determining that a total overlap of the overlapping IBD segments is greater than a predetermined fraction of a total IBD length of the first and second IBD segments; and

rejecting the most recent common ancestor.

18 . A non-transitory computer-readable medium having stored thereon instructions that, when executed by one or more processors, cause performance of a set of acts comprising:

growing pedigrees for a plurality of genetically-related individuals, wherein the pedigrees are grown based on pairwise identity-by-descent (IBD) data between the genetically-related individuals;

combining pairs of the pedigrees that share an amount of common IBD data above a pre-determined threshold into a combined pedigree;

identifying, among a portion of the genetically-related individuals not included in the combined pedigree, a closest relative of an individual included in the combined pedigree;

determining, from a probabilistic relationship model applied to pairwise IBD data of the closest relative and the individual, a plurality of relationship likelihoods respectively associated with a plurality of candidate relationships between the closest relative and the individual;

selecting, from the plurality of relationship likelihoods, a particular relationship likelihood meeting a criterion; and

adding, to the combined pedigree, a particular candidate relationship associated with the particular relationship likelihood.

19 . The non-transitory computer-readable medium of claim 18 , wherein combining the pairs of the pedigrees comprises:

identifying a first set of individuals in a first pedigree of a particular pair of the pedigrees that share the amount of common IBD data above a further pre-determined threshold with individuals in a second pedigree of the particular pair of pedigrees;

identifying a second set of individuals in the second pedigree that share the amount of common IBD data above the further pre-determined threshold with individuals in the first pedigree;

determining a first common ancestor of the first set of individuals;

determining a second common ancestor of the second set of individuals;

inferring a degree of relatedness between the first common ancestor and the second common ancestor; and

connecting, in the combined pedigree, the first common ancestor and the second common ancestor.

20 . The non-transitory computer-readable medium of claim 19 , wherein determining the first common ancestor comprises:

identifying a most recent common ancestor of the first set of individuals;

identifying a set of relatives of the most recent common ancestor who are not descendants of the most recent common ancestor;

computing first IBD segments between the set of relatives and the first set of individuals;

computing second IBD segments between the second set of individuals and the first set of individuals;

identifying overlapping IBD segments between the first segments and the second segments;

determining that a total overlap of the overlapping IBD segments is greater than a predetermined fraction of a total IBD length of the first and second IBD segments; and

rejecting the most recent common ancestor.