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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

Harvard Team Report One-Time Base Editing Treatment for Motor Neuron Disease in Mice

A base-editing approach restored SMN levels and improved motor function in a mouse model of spinal muscular atrophy, a new Science paper reports.

International Team Examines History of North American Horses

Genetic and other analyses presented in Science find that horses spread to the northern Rockies and Great Plains by the first half of the 17th century.

New Study Examines Genetic Dominance Within UK Biobank

Researchers analyze instances of genetic dominance within UK Biobank data, as they report in Science.

Cell Signaling Pathway Identified as Metastasis Suppressor

A new study in Nature homes in on the STING pathway as a suppressor of metastasis in a mouse model of lung cancer.