Bioinformatics investigation of SNP distributions among human populations

World Congress on Human Genetics

November 07- 08, 2016 Barcelona, Spain

Alexei Fedorov

University of Toledo, USA

Scientific Tracks Abstracts: Human Genet Embryol

Abstract :

Next Generation Sequencing revealed an intricate distribution of millions of genetic variants among different human populations. Both rare and frequent genetic variants may bring to light important information about history, evolution and health status of humans. First, we present a novel computational method for detecting identical-by-descent (IBD) chromosomal segments between sequenced genomes. It utilizes the distribution patterns of very rare genetic variants (vrGVs), which have minor allele frequencies less than 0.2%. Contrary to the existing probabilistic approaches our method is rather deterministic, because it considers a group of very rare events which cannot happen together only by chance. This method has been applied for exhaustive computational search of shared IBD segments among 1092 sequenced individuals from 14 populations. It demonstrated that clusters of vrGVs are unique and powerful markers of genetic relatedness, that uncover IBD chromosomal segments between and within populations, irrespective of whether divergence was recent or occurred hundreds-to-thousands of years ago. We found that several IBD segments are shared by practically any possible pair of individuals belonging to the same population. Moreover, shared short IBD segments (median size 183 Kb) were found in 10% of inter-continental human pairs, each comprising of a person from Sub-Saharan Africa and a person from Southern Europe. The shortest shared IBD segments (median size 54 Kb) were found in 0.42% of inter-continental pairs composed of individuals from Chinese/Japanese populations and Africans from Kenya and Nigeria. Knowledge of inheritance of IBD segments is important in clinical casecontrol and cohort studies, since unknown distant familial relationships could compromise interpretation of collected data. Clusters of vrGVs should be useful markers for familial relationship and common multifactorial disorders. Lastly, we present whole-genome investigation of human most frequent genetic variants and their arrangement in common haplotypes in various geographical regions. Three prominent types of common haplotypes â�?�?Yinâ�?, Yangâ�? and â�?�?Mosaicâ�? are described as well as their continent distribution. They represent three principal ancient lineages of mankind.

Biography :

Alexei Fedorov is an Associate Professor in the Department of Medicine and Vice Director of Bioinformatics and Proteomics/Genomics Program at the University of Toledo, Ohio, USA. He has received his MS degree in Physics from Moscow State University, Russia and PhD degree in Molecular Genetics from the Institute of Molecular Genetics, Russian Academy of Science, Moscow. He has developed his programming skills being a Postdoctoral fellow in Walter Gilbert lab at Harvard. He has over 100 publications including 50 manuscripts as a principal author.

Email: alexei.fedorov@utoledo.edu