A0638
Title: Detection of short identity-by-descent segments using low-frequency variants
Authors: Lu Zhang - HKBU Institute for Research and Continuing Education, ShenZhen (Hong Kong) [presenting]
Abstract: Identity by descent (IBD) segments are shared inherited nucleotide sequences from common ancestors that have applications as biomarkers during lineage analysis, disease mutation mapping, and within broader fields of population genetics. Current methods used to detect IBD segments focus on identifying long IBD segments, with short IBD segments (i.e., those with a length shorter than 2cM) often going undetected. SILO, a method with a remarkably improved ability, is presented to detect short IBD segments compared to state-of-the-art methods. SILO detects IBD segments by considering both common and low-frequency variants (LFV), where each LFV is assumed to follow a Bernoulli distribution with probability $\theta$ following a Beta distribution. The Beta distribution could be learned from population genomic variants. SILO was benchmarked against five methods (GERMLINE2, hap-IBD, HapFABIA, Parente, and TRUFFLE) on simulated data and a pedigree from the 1000 Genomes Project. The results show that SILO has an unrivalled ability to detect short IBD segments and that its ability to detect long IBD segments is similar to that of current methods in the field.
