Genome Sciences Centre
Bioinformatics Graduate Program Exit Seminar
Cis-Regulatory Somatic Mutations and Gene-Expression Alteration in B Cell Lymphomas
Speaker: Calvin Lefebvre
NOTE: This session will take the place of the Friday Bioinformatics Seminar (BioTalk)
Friday, May 8, 2015
12:00 am – 1:00 pm
BCCRC Dorothy Lam Boardroom
BC Cancer Research Centre
675 West 10th Avenue
Substantial progress has been achieved in characterizing protein coding regions for cancer genomes, with large contributions coming from TCGA and the ICGC. In order to obtain a complete mutational profile of cancer genomes, the whole genome must be analyzed for two reasons: a large proportion of somatic mutations are within the non-coding region and 80% of the human genome is estimated to have some biological functionality. The dramatic cost reduction afforded by next generation sequencing has now made it tractable to sequence entire cancer genomes, allowing mutational profiling of the functional loci in the non-coding regions, such as cis-regulatory elements. Recent cancer genomic studies observed somatic mutations within cis-regulatory elements have the capacity to deregulate gene expression, but their impact remains underexplored.
Initial attempts to prioritize cis-regulatory mutations did not incorporate RNA-Seq. We used 84 B cell lymphoma samples to address this limitation by prioritizing disruptive cis-regulatory mutations based on their potential to be the cause of observable cascading expression changes throughout biological networks. BCL6, ROBO1, GNA13, HAS2 and MYC were dysregulated genes targeted with somatic mutations through different mechanisms. Mutations either targeted the genes directly (protein coding mutations), indirectly (cis-regulatory mutations) or both.
Our analyses demonstrates the importance of identifying genomically altered cis-regulatory elements, along with gene expression data, to interpret the mutational landscapes of cancers.
Kirsten San Juan
Canada’s Michael Smith Genome Sciences Centre
Suite 100 – 570 West 7th Avenue
Vancouver, BC V5Z 4S6