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This Week in Genome Research: Sep 30, 2009

In Genome Research this week, NHGRI's Gary Temple details the progress of the Mammalian Gene Collection, an effort to clone every human and mouse gene with a RefSeq transcript and at least 6,200 rat genes. Scientists used directed RT-PCR cloning and DNA synthesis to clone 92 percent of human and 89 percent of mouse genes with RefSeq transcripts, in addition to more than 6,300 rat genes.

Gerald Schumann at the Paul-Ehrlich-Institut in Langen, Germany, is the senior author on a paper that studied the structural diversity of SVA retrotransposons across the human genome. Looking at 116 SVA elements on chromosome 19, his team classified SVA elements into seven structural variants, with 5'-transduced SVA elements making up about 8 percent. Their data, they say, "indicate that SVA-mediated 5' transduction events involve alternative RNA splicing at cryptic splice sites," and that these "represent a novel source of genomic rearrangements contributing to genomic diversity," they say in the abstract.

University of Pennsylvania researchers also studied the human retrotransposon SVA, finding a new subfamily of SVA, "which apparently formed after an alternative splicing event where the first exon of the MAST2 gene spliced into an intronic SVA and subsequently retrotransposed," they say in the abstract. Further experimentation showed that a number of functional 3' splice sites exist within many transcribed SVAs in both the human and chimpanzee genomes. "These data imply that an SVA residing within an intron in the same orientation as the gene may alter normal gene transcription either by gene-trapping or by introducing [premature termination codons] through exonization, possibly creating differences within and across species."

Scientists from the National University of Singapore, the University of Oxford, and the Genome Institute of Singapore report on the Singapore Genome Variation Project, a public database of 1.6 million SNPs spanning individuals of Chinese, Malay, and Indian descent in Southeast Asia. In this paper, they clustered data from the HapMap and Human Genome Diversity projects, "providing useful insights into the population structure of the three major population groups in Asia."

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.