HiFi – A Computer Program for Haplotype Imputation from Incomplete Data
(2 p.m.-3:30 p.m., 11/4/2011, Friday, Department Conference Room)
Dr. Qing Song
Cardiovascular Research Institute
Morehouse School of Medicine
Computational haplotyping methods are currently limited by inaccuracies, ambiguities, and short phasing distance, and experimental methods are limited by labor, cost, and incompleteness. Here, we report on a computational/experimental integrated method to solve the single-individual haplotyping problem. We implemented this method in software (HiFi) and applied it to resolving the chromosomal haplotypes of 14 individuals. Each genome haplotype was determined in 2.5 minutes completely on all SNPs, with ~99.7% accuracy.
About the Speaker: Dr. Song received his PhD training in the area of hypertension and molecular genetics in Medical University of South Carolina. During 1992-2000, he studied the molecular mechanisms of essential hypertension in various animal models and in humans (population studies), and then he started to study the functional impact of single nucleotide polymorphisms (SNP) and haplotypes on human tissue kallikrein gene promoter and blood pressure regulation. In 2001, he joined The Cardiovascular Research Institute of Morehouse School of Medicine as a Research Instructor. During 2001-2008, he studied the functional roles of promoter SNPs in the genes of PPARgamma2, CRP, and PDE4D in cardiovascular in vitro cell culture system and studied their associations with coronary heart disease, atherosclerosis and ischemic stroke. At the end of 2007, he made a switch on his career to re-educate himself on new approaches, particularly on systemic and integrated approaches. The reason why he made this risky switch is that he found that those conventional molecular biology strategies and the computational methods were insufficient for elucidating the functional roles of non-coding regulatory variants. He started to build-in more systematic, in vivo, epigenetic, and computational components into his research projects. On this line of efforts, he has developed the first high-throughput experimental pipeline for genome-wide and chromosomal-range haplotyping (nature methods 2010), which enables him to study the long-range actual cis-interactions and chromatin remodeling in cardiovascular diseases. He is now close to finishing another high-throughput experimental pipeline for determining the genome-wide chromosome-range epi-haplotypes. All of these technologies are assisted by customized software programs that were developed in his laboratory. Now he is the director of a MSM core lab for genetic variants and a core laboratory for next-generation sequencing (454 and Illumina GAII), and a core lab for single-cell microdissection. His current research interest lies in the functional characterization of genetic alleles and epigenetic alleles and applications to cardiovascular diseases.