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This Week in PNAS: Jul 11, 2017

In the early, online edition of the Proceedings of the National Academy of Sciences, a team from the UK, China, Denmark, Japan, and the US report on findings from a genome sequencing study of the sand rat, Psammomys obesus, a desert gerbil from North Africa and the Middle East that is prone to obesity, type 2 diabetes, and pancreatic failure in carbohydrate-rich environments. Using a combination of short reads, long reads, and transcriptomic clues, the researchers put together a sand rat genome assembly, uncovering an overabundance of guanine and cytosine bases — particularly across a region that contains the Pdx1 gene coding for an insulin regulating protein.

For another PNAS paper, J. Craig Venter and his colleagues present an algorithm called xHLA, for doing human leukocyte antigen (HLA) typing from iteratively mapped short read sequence alignments. In addition to outlining the rationale for, and overview of, xHLA, the researchers shared results from proof-of-principle analyses on HLA regions identified in half-a-dozen available whole genome sequence- or exome sequence-based datasets with xHLA or other existing algorithms. Based on their results, the authors argue that xHLA "is both fast and accurate in identifying HLA types from personal genome data and should be used to make HLA typing more readily available to individuals and their physicians."

A Singapore-led team takes a look at interactions between the immune system, tumor microenvironment, and cancer tissue in individuals with a form of liver cancer called hepatocellular carcinoma. With the help of proteomic, transcriptomic, and immunofluorescence data, the investigators identified a gradient of immune cells that included regulatory T cells, tissue resident memory CD8+ T cell, resident natural killer cells, and tumor-associated macrophages in the tumor microenvironment. The research "validated the concept of a cancer-immune gradient and demonstrated in primary [hepatocellular carcinoma] that immune cell subsets become progressively suppressive as they traverse the non-tumor to tumor microenvironment."