Members of the Cancer Genome Atlas project share findings from an integrated genomic analysis of adult soft tissue sarcoma. Using genome, exome, RNA, and/or microRNA sequencing — coupled with array-based analyses — the team considered somatic mutations, copy number changes, expression profiles, and epigenetic patterns in 206 adult soft tissue sarcomas from half a dozen sarcoma types. The results indicate that copy number shifts typically eclipse sequence mutations in sarcoma, with most somatic mutations falling in a few main genes. The authors also identified molecular features in the tumor and microenvironment that appear to influence sarcoma patient outcomes.
Researchers from the UK and Belgium track neutral, positive, and negative selection contributions to cancer development using an evolutionary genomics framework. By applying its molecular evolutionary analysis to data from five healthy somatic tissue types and to 7,664 tumors from 29 cancer types, the team found that positive selection appeared to play a more prominent role in cancer development than negative or purifying selection. The number of protein-coding substitutions under positive selection varied by tumor type, ranging from fewer than one to more than 10 substitutions, on average. "We have found that negative selection is a surprisingly weak force during cancer development," authors write, "which in turn has allowed us to obtain the first exome-wide genetic estimates of the number of driver coding substitutions across a range of tumor types."
A TRACERx Consortium team follows loss of heterozygosity involving the human leukocyte antigen in individuals with non-small cell lung cancer during the process of tumor evolution. Starting with exome sequence data for 327 tumor samples and 100 matched normal samples for 100 TRACERx participants, the researchers used a bioinformatics approach called LOHHLA to uncover examples of allele-specific HLA loss and its effects on tumor neoantigen production, immune escape, and tumor evolution. Based on their results, the authors argue that the HLA LOH they detected in some 40 percent of the NSCLC tumors was linked to features consistent with immune escape and sub-clonal genome evolution.