On ARGs, pedigrees, and genetic relatedness matrices.
Genetic relatedness is a central concept in genetics, underpinning studies of population and quantitative genetics in human, animal, and plant settings. It is typically stored as a genetic relatedness matrix, whose elements are pairwise relatedness values between individuals. This relatedness has be...
| Published in: | Genetics Vol. 232; no. 1; pp. 1 - 23 |
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| Main Authors: | , , , , , |
| Format: | equations & formulas pictorial research tables/charts Journal Article |
| Published: |
Oxford University Press / USA
Jan2026
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| Online Access: | View this record in EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=190773580&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 190773580 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 00166731 GNT jtl: Genetics issn: 00166731 maglogo: N pubinfo: dt: Jan2026 vid: 232 iid: 1 pid: 622 pub: Oxford University Press / USA artinfo: ui: 190773580 190773580 190773580 10.1093/genetics/iyaf219 190773580 ppf: 1 ppct: 22 formats: tig: atl: On ARGs, pedigrees, and genetic relatedness matrices. aug: au: Lehmann, Brieuc Lee, Hanbin Anderson-Trocmé, Luke Kelleher, Jerome Gorjanc, Gregor Ralph, Peter L affil: Department of Statistical Science, University College London, London, WC1E 7HB, United Kingdom sug: subj: Genetics Pedigree Algorithms Models, Theoretical Conceptual Framework Quebec Human Funding Source Bioinformatics Genetic Variation Genome Models, Biological Family Statistics Factor Analysis Phylogenetics Poisson Distribution Alleles Genotype Simulations Descriptive Statistics Random Sample Data Analysis Software Reproducibility of Results ab: Genetic relatedness is a central concept in genetics, underpinning studies of population and quantitative genetics in human, animal, and plant settings. It is typically stored as a genetic relatedness matrix, whose elements are pairwise relatedness values between individuals. This relatedness has been defined in various contexts based on pedigree, genotype, phylogeny, coalescent times, and, recently, ancestral recombination graph. For some downstream applications, including association studies, using ancestral recombination graph-based genetic relatedness matrices has led to better performance relative to the genotype genetic relatedness matrix. However, they present computational challenges due to their inherent quadratic time and space complexity. Here, we first 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 genetic relatedness matrix". We explore the relationship between branch relatedness and pedigree relatedness (i.e. kinship) through a case study of French–Canadian individuals that have a known pedigree. Through the tree sequence encoding of an ancestral recombination graph, we then derive an efficient algorithm for computing products between the branch genetic relatedness matrix and a general vector, without explicitly forming the branch genetic relatedness matrix. This algorithm leverages the sparse encoding of genomes with the tree sequence and hence enables large-scale computations with the branch genetic relatedness matrix. We demonstrate the power of this algorithm by developing a randomized principal components algorithm for tree sequences that easily scales to millions of genomes. All algorithms are implemented in the open source tskit Python package. Taken together, this work consolidates the different notions of relatedness as branch relatedness and, by leveraging the tree sequence encoding of an ancestral recombination graph, provides efficient algorithms that enable computations with the branch genetic relatedness matrix that scale to mega-scale genomic datasets. pubtype: Academic Journal doctype: equations & formulas pictorial research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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