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This Week in Genome Research: Jan 2, 2019

Researchers from the University of Texas MD Anderson Cancer Center and elsewhere explore the genomic features of oral squamous cell carcinoma tumors accompanied by human papillomavirus infections. The researchers used a combination of somatic mutation profiles from tumor and matched normal sequences, RNA sequences, and other data to compare 149 HPV-positive OSCC cases with 335 cases deemed HPV-negative, including samples from the Cancer Genome Atlas project, and identified mutational signatures marking OSCC tumors with or without HPV, along with frequently mutated genes in the OSCCs. Based on their results, the authors argue that "virus-host interactions
cooperatively shape the unique genetic features of these [HPV-positive OSCC] cancers, distinguishing them from their HPV-negative counterparts."

A Weill Cornell Medicine team describes an algorithm aimed at deconvoluting linked, short metagenomic reads with shared barcodes without relying on a reference genome or alignment-based approaches. The graph-based strategy, known as Minerva, "uses information from sequence overlap between read clouds to approximately solve the barcode deconvolution problem for metagenomic samples," the researchers explain. They demonstrate the utility of the approach by applying Minerva to two real datasets made up of mock microbial communities with defined bacterial and/or fungal species.

Finally, members of the "Deciphering Developmental Disorders" study describe potentially pathogenic splice site variations detected with the help of exome sequence data for more than 7,800 individuals with developmental disorders and their unaffected parents. Together with Exome Aggregation Consortium data representing more than 60,000 exomes and mutational burden analyses, the team used the protein-coding sequences from DD-affected individuals to narrow in on non-canonical splice sites with likely diagnostic de novo alterations in 18 individuals with DD. "We provide an unbiased, exome wide view of the signatures of selection and the relative contribution of pathogenic splice altering mutations between the [canonical splice site dinucleotides] and other, near splice positions," the researchers explain.