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PLOS Studies on eQTL Fine-Mapping, Leishmania Sequencing, and Elderly Burn Patients

In PLOS Genetics, a University of California, Los Angeles-led team outlines a computational method for fine-mapping expression quantitative trait loci (eQTL) by incorporating allelic imbalance — differences in gene expression between a site on one chromosome and its partner in a diploid pair. The approach relies on a meta-analysis statistic strategy to integrate allelic imbalance and total gene expression profiles, the researchers say, making it possible to focus in on causal eQTLs while weeding out some of the variants in linkage disequilibrium with them. In simulated datasets and in real data for 10 tissues profiled for the Genotype-Tissue Expression project, for example, they found that the method dialed down the number of putative causal variants, while shoring up potential eQTLs in parts of the genome known for having active chromatin states in prior analyses. "We show that by combining eQTL and [allelic imbalance] data, we can identify the true causal variants more efficiently and substantially decrease the number of putative causal variants for downstream analysis," the authors write. 

Sequencing Leishmania parasites directly from clinical samples may offer previously unappreciated clues to the biology and spread of the visceral leishmaniasis culprit, researchers from Belgium, the UK, and Nepal report in PLOS Neglected Tropical Diseases. The team sequenced L. donovani DNA pulled from clinical samples with Agilent SureSelect-based targeted enrichment. When they assessed L. donovani sequences in dozens of bone marrow or spleen aspirate samples from individuals in Nepal who had been diagnosed with visceral leishmaniasis, the authors successfully uncovered informative SNPs for genotyping 97 percent of the samples, while uncovering genome-wide sequence clues in more than 80 percent of those profiled. "Our study sheds a new light on the biology of Leishmania in the human host," they write, noting that the method appears to be "most suitable for clinical studies and for molecular tracking in the context of elimination programs." 

Researchers in Canada and the US explore gene expression patterns in blood samples from burn patients for a paper in PLOS One. Following from past research suggesting that elderly burn patients may fare worse than other adults with burns, the team did array-based gene expression profiling on blood samples from 10 elderly patients and 20 adult controls matched for sex and burn area. Along with lower-than-usual inflammatory gene expression during the acute phase of burn response in the elderly patients, the authors saw reduced expression of genes from cell signaling and antiviral pathways, among other differences. "Elderly patients demonstrate failure to initiate an appropriate inflammatory and stress response during the acute phase post-burn," they write, noting that elderly individuals with extensive body surface burn areas appeared particularly prone to enhanced expression of complement activation and other "destruction-related cellular pathways."