Allele frequency-free inference of close familial relationships from genotypes or low depth sequencing data

Abstract

Knowledge of how individuals are related is important in many areas of research and numerous methods for inferring pairwise relatedness from genetic data have been developed. However, the majority of these methods were not developed for situations where data is limited. Specifically, most methods rely on the availability of population allele frequencies, the relative genomic position of variants, and accurate genotype data. But in studies of non-model organisms or ancient human samples, such data is not always available. Motivated by this, we present a new method for pairwise relatedness inference, which requires neither allele frequency information nor information on genomic position. Furthermore, it can be applied to both genotype data and to low-depth sequencing data where genotypes cannot be accurately called. We evaluate it using data from SNP arrays and low-depth sequencing from a range of human populations and show that it can be used to infer close familial relationships with a similar accuracy as a widely used method that relies on population allele frequencies. Additionally, we show that our method is robust to SNP ascertainment, which is important for application to a diverse range of populations and species.