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PLOS Papers on Tuberculosis in Colombia, Cancer Inflammation Signatures, Liver eQTLs Among African Americans

Investigators from Colombia and the Netherlands present findings from a genomic analysis of multidrug-resistant Mycobacterium tuberculosis strains collected from a region in Colombia's southwestern, Pacific coast region for a study in PLOS One. Starting with a collection of 311 clinical isolates collected in Colombia between 2002 and 2010 — which spanned more than three dozen Beijing M. tuberculosis strains — the team did high-resolution "Mycobacteria Interspersed Repetitive Unit-Variable Number Tandem Repeat" typing and mutation analyses on the strains, along with whole-genome sequencing on one drug-susceptible and one multidrug resistant strain. "[T]he two strains evaluated by whole genome sequencing shared most of the genetic features with the sub-lineage 2.2.1 'modern' Beijing previously characterized from Asian strains," the authors report, providing clues to the origins of such strains in Colombia.

A team from the University of California, Los Angeles, and Gilead Pharmaceuticals explore inflammatory response signatures in relation to cancer type, and other tumor or cancer patient characteristics, for another PLOS One paper. Using their online Signature Visualization Tool, known as SaVanT, the researchers amalgamated gene expression profiles for samples from seven cancer types from the Cancer Genome Atlas project and Molecular Signatures Database (MSigDB), identifying apparent ties between inflammation signatures and cancer features ranging from patients' sex and age at diagnosis to their tumor stage and cancer type. "We believe our results demonstrate the potential clinical utility in the continued establishment of personalized medicine and care for cancer patients," the authors write, "while further establishing the utility of SaVanT as a clinical tool."

In PLOS Genetics, researchers from Northwestern University share findings from an expression quantitative trait locus (eQTL) analysis that uncovered thousands of new candidate eQTLs in hepatocyte liver cells originating from African Americans, a population that appears particularly prone to metabolic conditions, differences in drug metabolism, and side effects. With the help of a local ancestry adjusted analytical method called LAMatrix, the team uncovered nearly 19,800 eQTLs and 277 genes with one of more eQTLs using array-based SNP profiles and transcriptome sequence data from 60 primary hepatocyte cultures developed from African-American participant samples. The eQTL set included more than 7,400 eQTLs not been described in individuals from other populations in the past, influencing the expression of dozens of genes.