VERY excited to announce a pre-print that represents the culmination of several years of work*: “On ARGs, pedigrees, and genetic relatedness matrices” doi.org/10.1101/2025... Led by Brieuc Lehmann with contributions from @epigenci.bsky.social Luke Anderson Trocme Jerome Kelleher and Peter Ralph - ThreadSky

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gregorgorjanc.bsky.social • 80 days ago

VERY excited to announce a pre-print that represents the culmination of several years of work*: “On ARGs, pedigrees, and genetic relatedness matrices”

https://doi.org/10.1101/2025.03.03.641310

Led by Brieuc Lehmann with contributions from @epigenci.bsky.social Luke Anderson Trocme Jerome Kelleher and Peter Ralph

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gregorgorjanc.bsky.social•80 days ago

Genetic relatedness is a central concept in genetics, underpinning studies of population and quantitative genetics. It is typically stored as a genetic relatedness matrix (GRM), whose elements are pairwise relatedness values between individuals.

gregorgorjanc.bsky.social•80 days ago

It has been defined in various contexts based on pedigree, genotype, phylogeny, coalescent times, and, recently, ancestral recombination graph (ARG).

gregorgorjanc.bsky.social•80 days ago

In this study we

1 Discuss the different definitions of relatedness in a unifying context, making use of the additive model of a quantitative trait to provide a definition of “branch relatedness” and the corresponding “branch GRM”

gregorgorjanc.bsky.social•80 days ago

2 Explore the relationship between branch relatedness and pedigree relatedness through a case study of French-Canadian individuals that have a known pedigree.

gregorgorjanc.bsky.social•80 days ago

3 Derive an efficient algorithm for computing products between the branch GRM and a general vector, without explicitly forming the branch GRM. This algorithm leverages the sparse encoding of genomes with the tree sequence and enables large-scale computations with the branch GRM.

gregorgorjanc.bsky.social•80 days ago

4 We demonstrate the power of this algorithm by developing a randomized principal components algorithm for tree sequences that easily scales to MILLIONS of genomes.

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