In PLOS Genetics, a University of Michigan-led team takes a look at several polygenic risk scores for skin cancer, using a phenome-wide association approach to look at primary and secondary traits linked to potential PRS for three skin cancer subtypes. Starting with publicly available data from the UK Biobank project and other efforts, the team assessed multiple PRS construction approaches, settling on a set of melanoma, basal cell carcinoma, and squamous cell carcinoma PRS for a PheWAS based on genetic and electronic health record data for 30,702 individuals of European descent from the Michigan Genomics Initiative biorepository and UK Biobank-based validation testing. "The various PRS-phenotype associations identified in this paper demonstrate ways to explore shared and subtype specific phenotypes," the authors say, noting that their skin cancer PRS interactions can be explored through an online visualization catalog called PRSweb.
Researchers from the University of Glasgow, University of Edinburgh, and the Karolinska Institute present findings from a chronic pain genome-wide association study for another PLOS Genetics paper. Using data for some 380,000 UK Biobank participants, the team searched for SNPs associated with a form of pain known as multi-site chronic pain. The search highlighted more than three-dozen risk loci, pointing to potential roles for nervous system, synaptic plasticity, and other genes in the complex, polygenic trait. "Overall, our findings support the proposition that chronic pain involves a strong nervous system component with implications for our understanding of the physiology of chronic pain," the investigators report.
For a paper in PLOS One, a team from Brazil, South Africa, and the UK uses genomic and phylogenetics to follow Chikungunya virus (CHIKV) diversity and dynamics during an outbreak in Rio de Janeiro. With a portable, real-time nanopore sequencing, the researchers produced near-complete genome sequences for 11 CHIKV isolates, which were collected in the southeastern Brazilian city from 2016 to 2018 and already screened by RT-qPCR. Their subsequent phylogenetic analysis, including 229 CHIKV full or partial genomes sequences reported in the past, placed the Rio de Janeiro outbreak strains in an East-Central-South African (ECSA) CHIKV lineage that appears to have entered the region in the spring of 2015. "[O]ur data suggests that the circulation of the CHIKV-ECSA lineage to Rio de Janeiro may have resulted from at least two separate introduction events from the north-eastern region," the authors write, "where this lineage was first detected in late 2014."