In PLOS Genetics, researchers from the National University of Singapore and the University of Toronto explore minor allele frequency differences for variants found on the X chromosome of male and female participants in large sequence sets. The team flagged more than 2,000 of these so-called "sex differences in minor allele frequencies" (sdMAF) across 245,825 X chromosome SNPs considered from phase 3 data from the 1000 Genomes Project, prompting further analyses of the variants in individuals from European and African American populations in gnomAD, as well as a closer look at the locations of these variants within DNA sequences and across chromosomes. "Better understanding of the different sources of sdMAF is critical to developing X chromosome-suitable analytical strategies," the authors explain," from improved data collection and imputation to more robust association methods for variants on the X chromosome."
For a paper appearing in PLOS Neglected Tropical Diseases, members of the Centers for Disease Control and Prevention's Rickettsial Zoonoses Branch present findings from a genomic analysis of endemic murine typhus-causing Rickettsia typhi isolates passed from rats to humans via fleas. The investigators tracked down more than two dozen SNPs, along with seven small insertion-deletion sites when they compared genome sequences from R. typhi isolates originating in the US, Myanmar, or Thailand, before coming up with mismatch amplification mutation assays to test for the variants in more than a dozen other international R. typhi isolates and in the R. prowazekii species behind epidemic forms of typhus. "[O]ne purpose of the present study was to develop [an] efficient and inexpensive method for R. typhi isolate discrimination for use in epidemiological investigations," they explain, adding that "we succeeded in applying this low technology to group isolates of R. typhi into specific lades based on their genomic sequence differences."
Using single-cell RNA sequencing, a team from Weill Cornell Medical College and other centers searched for clues to immune-related injury after kidney transplantation. As they report in PLOS One, the researchers used 10x Chromium-based scRNA-seq to assess kidney biopsy samples from a living transplant donor, and allograft kidney with deteriorating function, and an allograft kidney from a successful, rejection-free transplant. Based on data for more than 7,200 individual cells, the authors highlighted a dozen major cell type clusters in the biopsies, including donor- and recipient-derived fibroblast cells and cell types that with expression shifts depending on the biopsy sample considered. They note that "single-cell transcriptomics yielded novel mechanistic insights, which could pave the way for individualizing the care of transplant recipients."