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Genome Biology Papers Look at Structural Variant Effects in Cancer, Gut Microbiomes, More

A Baylor College of Medicine- and University of Texas MD Anderson Cancer Center-led team considers the DNA methylation and related regulatory consequences of somatic structural variants in cancer. The researchers focused on whole-genome and RNA sequence data for more than 2,300 tumors profiled for the Cancer Genome Atlas or Pan-Cancer Analysis of Whole Genomes projects, including 1,482 samples with accompanying array-based methylation data, searching for structural variant breakpoints falling at sites that upend typical gene expression or cytosine methylation profiles. In the process, they unearthed examples of somatic structural changes that boosted cytosine methylation at promoters, along with lower-than-usual methylation at within-gene sites hit with such alterations, and broader molecular signatures built on combined DNA, RNA, and methylation insights.

Researchers at Northwestern University and elsewhere compare gut microbial communities in humans and non-human primates, uncovering unexpected similarities between gut microbiomes in humans and representatives from an Old World monkey sub-family that includes baboons. By bringing together gut 16S ribosomal RNA gene and metagenomic sequences for individuals from more than a dozen industrialized and non-industrialized human populations and those from 18 non-human primates, the team found that human gut microbiomes shared more features with gut microbiomes in baboons than those found in more closely related ape species, though gut microbial communities still varied considerably from one human to the next. "Overall," the authors conclude, "these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome."

Finally, a team led by investigators at the Chinese Academy of Sciences and Shanghai Tech University introduces an online resource known as PGG.SNV that is designed to dial down ancestral bias in related variant and disease risk analyses, while increasing the availability of ancient genetic information on indigenous Asian populations. After analyzing new sequence data generated for more than 1,000 individuals through the Asian Admixed Genomes Consortium, the researchers put together a collection of single nucleotide variants gleaned from almost 220,150 diverse contemporary human genomes and 1,018 ancient genomes spanning nearly 1,000 populations from around the world. The site currently houses some 265 million annotated single nucleotide variants, the authors report, arguing that PGG. SNV "enables studies of variants that are rare or not existing in well-studied populations."