Kinship type determination for first-degree relationships using different patterns of allele sharing along the genome

There is no widely accepted and commonly used way to differentiate between different types of first-degree relationships, especially for low coverage, pseudohaploid data, which is common in ancient DNA (aDNA) studies. To address this question, we have developed a new, straightforward, rule-based method that makes use of the different patterns of allele sharing between sibling pairs and parent-offspring pairs along the genome. Our method is well-suited for most ancient DNA datasets, as it can be used on low coverage, pseudohaploid data, and is able to robustly determine the first-degree relationship type of two samples that share as low as 20,000 SNPs (TPR=94%, FPR=4%, for parent-offspring couples and TPR=96%, FPR=6% for siblings). We have tested our method using both simulated data for different numbers of overlapping SNPs between the simulated individuals of known relatedness, and published, real aDNA data. Using our new approach, we were able to determine the relationship type of three first-degree pairs from Aşıklı, which had not been settled before.