On region based inference in genome wide association study
Sergey V. Malov1, Alexey Antonik2, Andrey K. Shevchenko3
1St.-Petersburg State University, malovs@sm14820.spb.edu
2St.-Petersburg State University, alexey.antonik@gmail.com
3St.-Petersburg State University, andrey.k.shevchenko@gmail.com
We consider an advanced framework for genome wide association study (GWAS) based on the signal localization. Instead of looking for single genetic markers associated with the phenotype we attempt to discover regions of genetic markers, which are associated with phenotype. We focus on the localization by moving sums of negative logarithms of p-values, which is efficient for discovery of wide regions of genetic markers associated with phenotype. Particularly, we expect the method should be efficient for searching genes containing a number of genetic markers, if any reconstruction in a gene related to a phenotype. The method is implemented in GWATCH software for visualization and interpretation results of multiple statistical tests for genome associations. We discuss some features of the GWATCH software and apply them for HIV/AIDS cohort study from Botswana.