In PLOS Genetics, researchers from Stanford University and the Massachusetts Institute of Technology explore polygenic risk scores related to more than 1,500 traits, starting with data for hundreds of thousands of UK Biobank participants. With the help of an algorithm called "Batch Screening Iterative Lasso (BASIL), the team described 813 sparse PRS models for predicting traits. Along with follow-up analyses on the models and their ability to predict binary or quantitative traits, the authors considered the performance of the models in individuals from non-European ancestry groups. "Our transferability assessment of PRS models in UK Biobank revealed that the sparse PRS models trained on individuals of European ancestry had a lower predictive performance for individuals of African and Asian ancestry groups," they write.
A team from Tunisia, the US, and Qatar consider breast cancer susceptibility in individuals from Tunisia for a paper appearing in PLOS One. Using array-based genotyping, the researchers profiled germline variant patterns in nine cancer-related genes in 135 healthy individuals with no personal or family history of breast cancer, including 103 men and 32 women enrolled at sites across the country. From there, they dug into related haplotype, population structure, and functional features tied to the risk variants, uncovering allele frequency and regulatory features that were distinct from those found in European ancestry individuals in the past. "Our findings will help to better understand the genetic basis of breast cancer by guiding upcoming genome-wide studies in the Tunisian population," the authors note. "Putative functional SNPs may be used to develop an efficient polygenic risk score to predict breast cancer risk, leading to better disease prevention and management."
Finally, investigators in Senegal and the US trace Salmonella enterica antimicrobial resistance (AMR) factors found in the clinic in Senegal back to chickens for another paper in PLOS One. The team used whole-genome sequencing and antimicrobial susceptibility profiling to characterize 72 Salmonella strains, spanning isolates originally obtained from patients treated for diarrheal disease as well as isolates from chicken meat in Dakar markets. The analyses uncovered resistance features related to antibiotics most often used to treat invasive Salmonella today, while resistance to older, less often used treatments appeared to be relatively uncommon. From AMR levels in the clinical and poultry isolates, combined with phylogenetic analyses, the authors saw hints that antimicrobial use in chickens may be spawning AMR in the clinic. "These results stress the need for active surveillance of Salmonella and AMR in order to address invasive salmonellosis caused by non-typhoidal Salmonella strains and other important bacterial diseases in [sub-Saharan Africa]," they write.