OMICS and Bioinformatics Laboratory
Bioinformatics tool development to integrate epigenomic data from data derived from the public domain. Efforts have been centered on patient-focused studies to discover the molecular changes in primary tumors by harnessing advances in next-generation sequencing and microarrays. Many projects have only profiled genomic and transcriptomic alterations, but the identification of frequent mutations in epigenetic modifier genes has focused a spotlight on epigenomic and chromatin profiling as a candidate for tumor progression and onset. DNA methylation, a prominent epigenetic marker due to the widespread availability of DNA and the stability of this covalent modification, has long been recognized as an important biological event in normal development; however, the biology underlying these changes is not well understood in cancer. Whole-genome sequencing has allowed large-scale data integration across multiple chromatin markers (ChIP-seq), revealing a more complete picture of DNA methylation patterns as a reflection of larger changes to chromatin ‘state.’ As part of the Epigenomic Characterization Center for TCGA, elucidating the connections between DNA methylation and these other gene regulatory features has spawned great interest in a variety of tumor studies including gliomas. Yet the analytic tools required for this type of integration are not readily available to most cancer biologists. The reference maps themselves require a domain knowledge of gene regulatory features that is beyond the scope of many clinical research groups, and the publicly available datasets are too often the result of heterogeneous and frequently shifting analysis pipelines.
As a result, we have developed an important R/Bioconductor tool called TCGAbiolinks which aids users in the downloading, processing, preparation and analyzation of TCGA-related data (Calaprico A, et al., NAR, 2015); however, to fully harness the publicly available data across cell lines (ENCODE), primary tissue (NIH Epigenomics Roadmap) and cancer tissue (TCGA), efforts in our lab are currently underway to develop user-friendly open-source tools for cancer biologists.
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Genomics and Epigenomics