Using GMQL-web for querying, downloading and integrating public with private genomic datasets

Abstract

Recent integrative analyses using data from TCGA permit GWAS investigation of the genetic variants function, providing more insight than single-platform approaches. Although there has been much progress, the integration across data sets and data types remains limited. In this work we illustrate a workflow, based on the use of GMQL-Web, for combining private cancer datasets with datasets of genomic features and biological/clinical metadata sourcing from ENCODE, Roadmap Epigenomics, TCGA, as well as annotations from GENCODE and RefSeq. GMQL-Web is a web-based interface with the goal of providing a user-friendly intuitive environment for bioinformaticians and biologists who need to query genomic processed data (including public dataset not already available in the GMQL Repository) and combine them with their private datasets. Finally, we present a case study that illustrates the workflow steps to find samples extracted from a pharmacogenomic drug metabolism multi-gene platform, i.e. the Affymetrix DMET Plus platform that contain single-nucleotide polymorphisms (SNPs) that overlap with exon regions. The DMET platform is able to identify the relationship among the patients’ genomic variations and drug metabolism by detecting SNPs on genes related to drug metabolism. From the obtained result, we identify only the SNPs overlapping with genes whose expression level is above a given threshold.