RT Journal
A1 Rodriguez, Jesse M.
A1 Bercovici, Sivan
A1 Huang, Lin
A1 Frostig, Roy
A1 Batzoglou, Serafim
T1 Parente2: a fast and accurate method for detecting identity by descent
JF Genome Research 
JO Genome Research 
YR 2015 
FD February 01 
VO 25 
IS 2 
SP 280 
OP 289 
DO 10.1101/gr.173641.114 
UL http://genome.cshlp.org/content/25/2/280.abstract 
AB Identity-by-descent (IBD) inference is the problem of establishing a genetic connection between two individuals through a genomic segment that is inherited by both individuals from a recent common ancestor. IBD inference is an important preceding step in a variety of population genomic studies, ranging from demographic studies to linking genomic variation with phenotype and disease. The problem of accurate IBD detection has become increasingly challenging with the availability of large collections of human genotypes and genomes: Given a cohort’s size, a quadratic number of pairwise genome comparisons must be performed. Therefore, computation time and the false discovery rate can also scale quadratically. To enable accurate and efficient large-scale IBD detection, we present Parente2, a novel method for detecting IBD segments. Parente2 is based on an embedded log-likelihood ratio and uses a model that accounts for linkage disequilibrium by explicitly modeling haplotype frequencies. Parente2 operates directly on genotype data without the need to phase data prior to IBD inference. We evaluate Parente2’s performance through extensive simulations using real data, and we show that it provides substantially higher accuracy compared to previous state-of-the-art methods while maintaining high computational efficiency.