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This Week in PLOS: Dec 11, 2017

In PLOS One, researchers from India, Spain, and the UK explore HIV-1 genetic diversity in Bangalore, India. Using blood plasma samples from 20 HIV-positive individuals, including many individuals not yet treated for HIV, the team did pooled 6-amplicon sequencing to generate more than a million HIV reads per sample. After assembling full length or partial genomes de novo from most of the samples, the investigators turned to phylogenetics to untangle relationships for HIV-1 strains in the region, which primarily fell in a C subtype containing isolates from India, Myanmar, and China. "[I]ndia HIV-1 whole genome sequences converge to form a monophyletic lineage of subtype C, closely related to a southern African lineage, with sporadic cases of A1C recombinant forms exhibiting independent origins," they write.

A Chinese team takes a look at potential ties between noise-induced hearing loss and variants in the FOXO3 gene for another PLOS One paper. The researchers focused on three FOXO3 SNPs for the analysis, genotyping the variants in 566 individuals with noise-induced hearing loss and 566 without — all recruited from a textile factory in China and assessed with hearing tests and questionnaires. Their analysis highlighted alleles and haplotypes involving these SNPs that coincided with enhanced noise-induced hearing loss risk in individuals of Chinese ancestry, along with alleles associated with the condition in those with long-term noise exposure spanning more than 16 years.

Finally, a team from the Broad Institute, Harvard Medical School, and Dana Farber Cancer Institute present "The Connectivity Map" (CMAP), a resource tallying up gene expression effects of RNA interference using short hairpin RNAs in mammalian cell lines. For their PLOS Biology paper, the researchers report on Luminex assay-based expression patterns for almost 1,000 gene transcripts in nine cell lines subjected to gene silencing with more than 13,000 short hairpin RNAs or CRISPR-Cas9-based gene knockout using a collection of nearly 400 single guide RNAs in half a dozen of the cell lines. Those involve say the resulting expression-knockdown relationship "will guide the proper use and analysis of genetic perturbations and demonstrate the value of systematic, large-scale lookup tables, such as CMAP."