NSF East Asia and Pacific Summer Institute (EAPSI) for FY 2013 in Japan

Johnston Ian, Boston MA

Investigators

Abstract

This action funds Ian Johnston of Boston University to conduct a research project in Biology during the summer of 2013 at Kyoto University's Institute for Chemical Research in Kyoto. The project title is "Developing Latent Genotypes for Genome-Wide Association Studies." The host scientist is Professor Hiroshi Mamitsuka. This research project rigorously vets a new technique for genome-wide association studies (GWAS) that combines a Bayesian statistical model with a novel concept of a "latent genotype" in an attempt to: formally address rare variants and linkage disequilibrium in GWAS data; and to exploit the underlying structure of single-nucleotide polymorphisms (SNPs) to then identify associations between SNPs and genes and diseases. The latent genotypes are obtained by transforming the original genotypes in such a way so as to correct for the strong correlation present in the data. In order to justify the use of the latent genotypes in GWAS, an additional goal of the project is to conduct a comparative analysis of current Bayesian and non-Bayesian methods using the original genotypes versus the latent genotypes. The product of this research project is an extensive comparative analysis that first investigates the usefulness of the latent genotypes and then investigates the usefulness of the novel Bayesian statistical model for GWAS, as well as software that implements the proposed model. Broader impacts of an EAPSI fellowship include providing the Fellow a first-hand research experience outside the U.S.; an introduction to the science, science policy, and scientific infrastructure of the respective location; and an orientation to the society, culture and language. These activities meet the NSF goal to educate for international collaborations early in the career of its scientists, engineers, and educators, thus ensuring a globally aware U.S. scientific workforce. Furthermore, the software to be produced by this research project can be used by industry professionals as well as in teaching examples. In particular, the cross-fertilization of ideas between statisticians and geneticists would be especially fruitful in establishing groundwork for future mutual projects as well as for the networks of communication that are ultimately necessary to achieve the overall goals of genetic studies.