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This Week in Genome Biology: Dec 19, 2012

Researchers from Singapore, India, and Canada characterize genetic glitches in gastric cancer in an early online Genome Biology study. The team started by profiling matched tumor-normal samples from two Singaporean individuals with gastric adenocarcinoma. Through massively parallel genome sequencing and DNA paired-end tag sequencing of these samples, they uncovered mutational signatures in gastric cancers showing microsatellite instability, chromosomal instability, or exposure to reactive oxygen or nitrogen species. The researchers verified and expanded their initial findings via exome sequencing or targeted testing on more than 100 additional stomach cancer samples.

Members of the St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project report on efforts to track telomeric DNA profiles in hundreds of pediatric cancer genomes. By sorting through whole-genome sequence data on matched tumor-normal samples from 235 children with cancer — finding sequence reads with characteristic telomere sequences and looking at their representation relative to overall genome sequence coverage — the group began defining telomeric DNA patterns in the pediatric cancers. For instance, nearly one-third of solid tumors exhibited telomere gains, as did a small fraction of brain tumors. In contrast, such gains were missing in hematopoietic cancers, which appeared somewhat more prone to telomeric loss.

A pair of researchers from the Israel Institute of Technology describes a new method developed for reconstructing and fleshing out metabolic networks using genomic data. The approach, known as "Metabolic Reconstruction via Functional Genomics," or MIRAGE, brings together functional genomics data together and metabolic flux patterns to find and fill in missing pieces in metabolic networks. In their Genome Biology study, for example, researchers used the approach to reconstruct metabolic networks in Escherichia coli and a cyanobacterial species from the Synechocystis genus before applying it to three-dozen more sequenced cyanobacterial species.

The Scan

And For Adolescents

The US Food and Drug Administration has authorized the Pfizer-BioNTech SARS-CoV-2 vaccine for children between the ages of 12 and 15 years old.

Also of Concern to WHO

The Wall Street Journal reports that the World Health Organization has classified the SARS-CoV-2 variant B.1.617 as a "variant of concern."

Test for Them All

The New York Times reports on the development of combined tests for SARS-CoV-2 and other viruses like influenza.

PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

In PNAS this week: evolution of oral microbiomes among hominids, comparative genomic analysis of snake toxins, and more.