Haplotype Reconstruction in Large Pedigrees with Untyped Individuals through IBD Inference

Haplotypes, as they specify the linkage patterns between dispersed genetic variations, provide important information for understanding the genetics of human traits. However, haplotypes are not directly obtainable from current genotyping platforms, which pushes extensive investigations of computational methods to recover such information. Two major computational challenges arising in current family-based disease studies are large family sizes and many ungenotyped family members. Traditional haplotyping methods can neither handle large families nor families with missing members. In this article, we propose a method that addresses these issues by integrating multiple novel techniques. The method consists of three major components: pairwise identical-by-descent (IBD) inference, global IBD reconstruction, and haplotype restoring. By reconstructing the global IBD of a family from pairwise IBD and then restoring the haplotypes based on the inferred IBD, this method can scale to large pedigrees, and more importantly it can handle families with missing members. Compared with existing approaches, this method demonstrates much higher power to recover haplotype information, especially in families with many untyped individuals. Availability: http://sites.google.com/site/xinlishomepage/pedibd.