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This Week in PLoS: Jan 4, 2010

This week in PLoS ONE, a pair of New Zealand researchers attempted to predict co-variation between genes based on phylogeny. The duo applied generalized linear models to try to determine the functions of genes in a handful of prokaryotic organisms using gene tree branch length information. Though the accuracy varied with gene ontology group, the researchers reported that the approach was especially accurate for some genes, including those involved in translation.

Australian and American researchers did a meta-population genetic analysis of promising potential malaria vaccine antigens. After assembling and comparing more than 4,500 Plasmodium falciparum antigen sequences, the team found haplotype sub-groups of varying diversity — and concluded that current malaria vaccines are based on a low prevalence haplotype from a single sub-group.

Unspliced HIV-1 RNA levels may help predict an individual's outcome following combination anti-retroviral therapy or cART, Vladimir Lukashov and his team report. They used semi-nested real-time PCR-based methods to measure proviral HIV-1 DNA, unspliced RNA, and multiply spliced RNA in blood samples from 26 cART-treated individuals with undetectable viral levels in their blood plasma. "Use of this quantitative assay in the standard laboratory practice could aid in monitoring the course of cART and facilitate the early detection of drug-resistant escape mutants before the actual failure of the therapy," they write.

In PLoS Computational Biology, Jos Jonkers and team described their computational methods for finding networks of copy number changes that occur together in tumor cell lines. By distinguishing co-occurring gains and losses from passenger and single mutations, they found a network of alterations affecting known cancer genes and other functionally informative genes. "Our findings suggest that large-scale, low-intensity copy number alterations may be an important feature of cancer development or maintenance by affecting gene dosage of a large interconnected network of functionally related genes," the researchers write.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.