We have been analyzing germline and somatic genomics, transcriptomics, epigenomics, and immunomics in human tumors. Using massively parallel sequencing (next generation sequencing) technology, we have sequenced whole exome of over 1,000 colorectal carcinomas with high dimensional annotations, and have calculated tumor neoantigen load. In addition, we have obtained data on transcriptome of over 200 colorectal carcinomas (by RNA sequencing). Some of our data have been published in Giannakis M et al. Nat Genet 2014, and Giannakis M et al. Cell Rep 2016. In all of the method disciplines that we pursue, genomics, particularly somatic genomic variations, has been our recent focus.
Giannakis et al. Nat Genet 2014 (free access). We identified RNF43 as a major driver gene mutated in nearly 20% of colorectal and endometrial carcinomas and associated positively with microsatellite instability (MSI) (and inversely with APC mutation in colorectal cancer).
www.ncbi.nlm.nih.gov/pmc/articles/PMC4283570/
Giannakis et al. Cell Rep 2016 (free access). We discovered that the neoantigen load calculated from whole exome sequencing and HLA genotyping data correlates with tumor-infiltrating lymphocytes (TIL) and other measures of adaptive T-cell immune response to tumor.
http://www.cell.com/cell-reports/fulltext/S2211-1247(16)30364-3
We presented two talks on immuno-genomics at AACR Tumor Immunology and Immunotherapy Meeting in Oct 2017.
www.aacr.org/Meetings/Pages/MeetingDetail.aspx?EventItemID=122&DetailItemID=651#.Wec5Bo9Szb0
Ma et al. CRC transcriptomics meta-analysis in Genome Biology 2018.
We continue working on the topics. New papers are forthcoming!
