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PLOS Papers on Imputed Variants, Cholera Evolution, Diffuse Glioma

In PLOS Genetics, researchers from the University of North Carolina and elsewhere flesh out the genotyping-based genetic architecture of admixed African and Hispanic/Latino individuals with imputation using more than 100,000 phased whole-genome sequences generated for the National Heart, Lung, and Blood Institute's "Trans-Omics in Precision Medicine" (TOPMed) program. With this strategy, the team unearthed rare variants missed using reference sequences generated for efforts such as the 1000 Genomes Project. And in subsequent association analyses that included some 21,600 individuals with African ancestry and around 21,700 Hispanic/Latino individuals, the authors found that the improved imputation possible with the TOPMed genomes led to rare HBB gene variants involved in hematological traits in individuals with African or Hispanic/Latino ancestry.

A team from Denmark, Tanzania, and Singapore takes a look at the evolution of Vibrio cholerae isolates contributing to a recent cholera outbreak in Tanzania for a paper in PLOS Neglected Tropical Diseases, focusing on V. cholerae representatives from the O1 serogroup. After generating genome sequences for 22 clinical isolates collected between 2015 and 2017, the researchers compared these sequences to genome-wide data for environmental isolates of V. cholerae O1 from Lake Victoria and almost 600 so-called "seventh cholera pandemic" strains profiled from Tanzania and beyond over the last three decades. "From 1993 to 2017, most sub-lineages found in patients were also found in the aquatic environment," the authors report, "and the close phylogenetic relationships between strains from the two niches suggest that the African Great Lakes may act as a reservoir for cholera outbreak strains."

Researchers at the Translational Genomics Research Institute, the GE Research Center, and elsewhere brought together genomic, proteomic, imaging, and other data to characterize and compare dozens of diffuse glioma tumors with or without IDH1 mutations. Based on exome sequence, RNA sequence, single-cell protein marker data, and other profiles generated for paired central nervous system tumor and normal samples from 20 individuals with untreated glioma and 16 recurrent  glioblastoma cases, the team tracked down seven biomarker-based groups and identified features that marked IDH1-mutant tumors. For example, the authors note that stretched out overall survival times that have been documented in glioma patients with IDH1-mutated tumors "may reflect mutation driven alterations in cellular, molecular, and spatial heterogeneity which manifest in discernible radiological manifestations."