GRUPS-rs, a high-performance ancient DNA genetic relatedness estimation software relying on pedigree simulations
Résumé
The study of fine-grain genetic kinship ties (parents, siblings, cousins, etc.) from ancient remains is now gaining significant interest and prominence within the field of paleogenetics, as a means of deciphering the social organization of past societies. However, despite sustained research efforts, kinship analyses are in practice often quite difficult to apply within paleogenetic studies, and may carry a high degree of uncertainty in the results they provide, especially when working with lowly covered, highly degraded samples – as is typically the case in the context of ancient DNA studies – or studying poorly characterized populations. To overcome these challenges, most of the methods dedicated to kinship estimation between ancient DNA samples either refrain from inferring kinship past the second-degree of relatedness (e.g.: half-siblings), and/or rely on the use of a cohort of individuals to obtain a satisfactory statistical significance. Thus, the current state of the art remains intrinsically limited when attempting to estimate kinship on a small number of individuals, or when trying to detect more distant relationships (e.g.: cousins). Here, we present an update and complete reimplementation of "GRUPS" (Get Relatedness Using Pedigree Simulations): an ancient DNA kinship estimation software based on the methods originally developed in (Martin D. et al – 2017)[8]. GRUPS both computes an estimate of relatedness from randomly sampled pseudo-haploidized variant calls, and leverages high-definition pedigree simulations to bypass the use of a cohort of individuals, making this method especially suitable when attempting to perform kinship analysis on a single pair of low-coverage individuals. We highlight that GRUPS can provide with a sufficient statistical significance to estimate genetic relatedness past the second degree, while taking into account contamination and sequencing error estimates when simulating individuals. Finally, our updated method, "GRUPS-rs" offers an estimated 2200-fold speed-up in runtime performance compared to its predecessor – allowing the joint estimation of kinship between dozens of individuals in a matter of minutes – and is now bundled with a user-friendly Shiny interface, in which users can interactively visualize their results
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