PhD Proposal – Jingwen Pei

Title: Inferring the ancestry of parents and grandparents from genetic data Student: Jingwen Pei Major Advisor: Dr. Yufeng Wu Associate Advisors: Dr. Ion Mandoiu, Dr. Mukul Bansal Day/Time: Thursday, December 14, 2017 10:00am Location: Babbidge 1947 Conference Room Abstract: Inference of admixture proportions is a classical statistical problem in population genetics. Standard methods implicitly assume that both parents of an individual have the same admixture fraction. However, this is rarely the case in real data. In this project we show that the distribution and lengths of admixture tracts in a genome contains information about the admixture proportions of the ancestors of an individual. We develop a Hidden Markov Model (HMM) framework for estimating the admixture proportions of the immediate ancestors of an individual, i.e. a type of appropriation of an individual’s admixture proportions into further subsets of ancestral proportions in the ancestors. Based on a genealogical model for admixture tracts, we develop an efficient algorithm for computing the sampling probability of the genome from a single individual, as a function of the admixture proportions of the ancestors of this individual. This allows us to perform probabilistic inference of admixture proportions of ancestors only using the genome of an extant individual. Extensive simulations are conducted to quantify the error in the estimation of ancestral admixture proportions under various conditions. As an illustration, we also apply the method on real data from the 1000 Genomes Project.