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This Week in Genome Biology: Oct 8, 2014

A study appearing online in Genome Biology spells out the genome sequence for an Indian strain of Anopheles stephensi, a mosquito species known for spreading malaria in India and the Middle East. An international team led by investigators at Virginia Tech used Roche 454, Illumina, and Pacific Biosciences sequencing reads to put together a 221 million base assembly spanning some 92 percent or more of An. stephensi genome. With the help of RNA sequence data and comparative genomics, the researchers went on to annotate the genome, identifying immune, salivary, and other genes important to the mosquito's biology and susceptibility to carrying malaria parasites.

Researchers from the Netherlands, Finland, and France did genome sequencing on almost 100 formalin-fixed, paraffin-embedded low-grade glioma samples to look for copy number aberrations that might offer information on glioma tumor aggressiveness. Along with a known, prognostically important co-deletion involving chromosomes 1 and 19, the team found additional, recurrent copy number changes that correlated with low-grade glioma survival. These included a chromosome 10 deletion that tended to turn up in sub-clones within tumors from low-grade glioma patients with relatively poor outcomes — patterns that the study authors verified through testing on hundreds of individuals in their validation and confirmation cohorts.

A team from South Korea, the US, and Australia present a draft genome sequence and annotation for a cold-tolerant teleost fish called the Antarctic bullhead notothen, Notothenia coriiceps, that's found in frigid waters in the Southern Ocean. Using Roche 454, Illumina, and Pacific Biosciences instruments, the researchers put together a 637 million base hybrid assembly for the fish, which contained an estimated 32,260 protein-coding genes. By analyzing the genome and comparing it with sequences from other fish, they began untangling clues to the Antarctic bullhead notothen's cold adaptation, including changes to genes coding for mitochondrial contributors, hemoglobin, and heat shock proteins.

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.