A fast and accurate method for detection of IBD shared haplotypes in genome-wide SNP data

BioRxiv : the Preprint Server for Biology
Douglas W BjellandMatthew C Keller

Abstract

Identical by descent (IBD) segments are used to understand a number of fundamental issues in genetics. IBD segments are typically detected using long stretches of identical alleles between haplotypes in whole-genome SNP data. Phase or SNP call errors in genomic data can degrade accuracy of IBD detection and lead to false positive calls, false negative calls, and under- or overextension of true IBD segments. Furthermore, the number of comparisons increases quadratically with sample size, requiring high computational efficiency. We developed a new IBD segment detection program, FISHR (Find IBD Shared Haplotypes Rapidly), in an attempt to accurately detect IBD segments and to better estimate their endpoints using an algorithm that is fast enough to be deployed on the very large whole-genome SNP datasets. We compared the performance of FISHR to three leading IBD segment detection programs: GERMLINE, refinedIBD, and HaploScore. Using simulated and real genomic sequence data, we show that FISHR is slightly more accurate than all programs at detecting long (greater than 3 cM) IBD segments but slightly less accurate than refinedIBD at detecting short (1 cM) IBD segments. Moreover, FISHR outperforms all programs in determining the true ...Continue Reading

Related Concepts

Germ-Line Mutation
Genome
Genome Assembly Sequence
Spastic Syndrome
Genomics
Inflammatory Bowel Diseases
Simulation
Alleles
Single Nucleotide Polymorphism
Sense of Identity (Observable Entity)

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