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PLOS Papers Look at Gene-Lipid Trait Associations, Interactions Underlying B-ALL, More

For a paper in PLOS One, researchers from Loyola University search for genetic variants, genes, and tissue types contributing to lipid traits in Hispanic populations. The team began with a genome-wide association study involving more than 11,100 individuals from the Hispanic Community Health Study/Study of Latinos, using expression quantitative trait locus clues from the Genotype-Tissue Expression Project to predict corresponding transcriptomic features. After focusing in on two dozen SNPs with potential ties to total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglyceride levels, the investigators validated 14 genes and 59 gene-tissue-phenotype associations in a group of almost 3,900 multi-ethnic individuals, subsequently comparing their findings to those identified in a large, prior lipid genomic analysis involving close to 196,500 individuals.

In PLOS Genetics, a team from Sweden takes a look at the potential functional roles for PAX5 in human B-lineage leukemia, where the transcription factor is often mutated. Using a combination of BioID protein-protein interaction profiling, chromatin immunoprecipitation sequencing, proximity ligation-assisted ChIP-seq, RNA sequencing, and other approaches, the researchers teased out a network of genes and regulatory factors related to PAX5 that may be involved in B-cell acute lymphoblastic leukemia (B-ALL). Based on their results, the authors propose that "the transformation process in B-ALL involve[s] multiple mutations of genes being part of a regulatory network possibly causing an exacerbated effect on the transcriptional programming in the B-cell progenitor."

Chinese researchers present a potential reference genome for the parasitic flatworm Schistosoma japonicum for a paper appearing in PLOS Neglected Tropical Diseases. The team relied on Pacific Biosciences long-read and Illumina short-read sequences to improve on a prior draft genome for the disease-causing fluke, producing a 370.5 million base genome assembly that contained 10,089 predicted protein-coding genes, many gene families marked by expansions, and a raft of repetitive element sequences that spanned some 46.8 percent of the new high-quality genome. "Schistosomiasis is an acute and chronic disease that remains one of the most prevalent and serious of the parasitic diseases," the authors write, noting that the newly improved, annotated S. japonicum genome assembly "will provide [a] valuable genomic resource for future studies, especially functional genomic analysis for S. japonicum."