The Taub Faculty of Computer Science Events and Talks

Abstract: Shared segments that are Identical-by-Descent (IBD) from a recent common ancestor of purported unrelateds provide unique source of information for population and medical genetics: IBD addresses recent, rare variation, and is therefore key for interpreting data on the seam between SNP-array and sequencing studies. We have developed a rapid algorithm to efficiently detect IBD segments, enabling such analysis in large cohorts. We formalize this analysis in the context of a likelihood model, and show the utility of IBD detection in exposing fine population structure and recent demopographic events with precision and dynamic range unavailable previously. We present results on simulated data as well as examples from East Africans, who demonstrate genetics consistent with tribal demography, and from Ashkenazi Jews, who are unique in having expanded rapidly from a bottleneck population of hundreds to a population of millions. In terms of medical applications, we develop a method that leverages IBD analysis for testing association to rare alleles. We apply this to SNP- and sequencing-data in isolated and general populations. We detect associated variants in publicly available data that had been reported by subsequent, larger studies, and replicate association signals from our own data. Combining both medical- and population-genetics aspects, we show how IBD enables affordable population-based sequencing.

As an appendix, I will tell the story of the first animal mutant to be mapped by whole genome sequencing.