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This Week in Genome Research: Mar 27, 2019

Investigators from France, Singapore, the US, and Germany considers a mutational signature associated with potentially carcinogenic acrylamide exposure in a pan-cancer analysis spanning 19 human tumor types. Using genome sequencing data for some 1,600 tumors originating in 14 organs, along with newly-generated experimental data, the team looked at the prevalence of this so-called glycidamide mutational signature, identifying it in 88 percent of the lung tumors analyzed, as well as 73 percent of the liver tumors and more than 70 percent of tumors from the kidney. "The numerous [glycidamide]-positive, [tobacco related SBS4 signature]-negative tumors are of particular interest," the authors say, "as they likely reflect dietary and/or occupational exposures to [acrylamide] unrelated to tobacco smoking." 

A University of Vermont-led team presents a computational platform for identifying early-stage viral integrations in cancer genomes. The approach, dubbed the "Viral Integration caller" (VIcaller), detects early stage clonal integrations involving known viruses, the researchers explain. After benchmarking the approach with several cancer datasets, they used VIcaller to track down new or known clonal integrations involving a wide range of viruses — from the human papillomavirus or hepatitis B virus to the Epstein-Barr or BK viruses. The analysis pointed to HPV and BKV in bladder cancer, for example, along with HBV integrations at specific liver cancer loci and non-Hodgkin's lymphomas containing EBV integrations.

Finally, a team led by researchers at 10X Genomics, Inscripta, and other centers in the US and UK shares a novel "Linked-Reads" strategy for assessing human genome variation. Using informatics, the investigators explain, they were able to match barcoded short read sequences back to their corresponding long DNA molecules to pick up both small variants and larger structural events from the same DNA library. The approach compared favorably with prior short read methods, they report, stretching out high-confidence variant calls and making it possible to map 38 million bases sequences missed with short read data alone. From these and other results, the authors suggest that "[b]oth Linked-Read whole-genome and whole-exome sequencing identify complex structural variations, including balanced events and single exon deletions and duplications."