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This Week in PNAS: Jan 23, 2018

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from the University of California, Berkeley, Korea's Yonsei University, and the Lawrence Berkeley National Laboratory propose a supervised machine-learning method for predicting inherited susceptibility to 20 common cancer types. With the help of data from the Cancer Genome Atlas, the team came up with a multiple classification approach to try to tease genomic contributions to cancer risk from risk related to lifestyle and/or environmental exposures, classifying more than 5,900 Caucasian individuals into either a healthy phenotype or one of 20 cancer phenotypes. "[D]epending on the type, about [33 percent to 88 percent] of a cancer cohort have acquired its cancer type primarily due to the inherited genomic susceptibility factors," the authors report, noting that "the rest are primarily due to environmental/lifestyle factors."

A University of Toronto team takes a look at root microbiome features in relation to species variation in angiosperm plants. Using 16S ribosomal RNA sequencing, the researchers profiled members of microbial communities living in and on the roots of 30 angiosperm species grown in an experimental field from surface-sterilized seeds. Based on root microbiome patterns, in combination with phylogenetic information, they explored tracked microbiome changes related to environmental factors such as drought and characterized the consequences of root microbiome similarities and differences in related host plants. "Our results emphasize the causes of variation in root microbiomes and their ecological importance for plant performance in response to biotic and abiotic stressors."

Researchers from Japan's National Cancer Center Research Institute and elsewhere explore the relative cancer risk associated with genetic and epigenetic shifts in human tissues. By comparing the point mutation and DNA methylation patterns classified as showing low-, intermediate-, or high-cancer risk in stomach and esophageal tissue, for example, the team characterized the distinct genetic and epigenetic contributions to gastric cancer or esophageal squamous cell carcinomas (ESCC). "Our analyses demonstrated that the impacts of genetic and epigenetic alterations on cancer risk are strikingly different between ESCC and gastric cancer, and epigenetic alterations can have greater impact on cancer risk than genetic alterations for some types of cancers," the authors report.

The Scan

Gap in COVAX Doses

BBC News reports that COVAX is experiencing a vaccine shortfall, as the Serum Institute of India has paused exports.

Sanofi, GSK Report Promising Results

The Wall Street Journal reports that the candidate SARS-CoV-2 vaccine from Sanofi and GlaxoSmithKline has had encouraging early results.

Influence of Luck

The New York Times examines how the US avoided variant-fueled increases in COVID-19 cases.

PLOS Papers on Retina GWAS, Hantaan Virus, COVID-19 Phenome-Wide Association Study

In PLOS this week: genome-wide association study of retinal morphology, analysis of hantaan virus found in a mouse, and more.