In PLOS Genetics, researchers from the US and Nepal explore polygenic adaptations and related adaptive phenotypes related to life at high altitude in more than 1,000 indigenous women from Tibetan populations in Nepal who were profiled by low-density genotyping, as well as 53 Tibetan or Sherpa individuals assessed by whole-genome sequencing. Through genome-wide association analyses focused on nearly two dozen phenotypes, together with polygenic adaptation testing, the team uncovered apparent selection for certain reproduction-related alleles, including variants implicated in the number of births and pregnancy outcomes. "Lower hemoglobin level did not show clear evidence for polygenic adaptation," the authors note, "despite its strong association with an EPAS1 haplotype carrying selective sweep signals."
For another PLOS Genetics paper, a Translational Genomics Research Institute- and Arizona State University-led team characterizes canine malignant melanoma with whole-genome sequencing, RNA sequencing, targeted sequencing, array comparative genomic hybridization, and/or SNP genotyping. By profiling 37 canine melanoma tumor samples — including mucosal, acral, cutaneous, or uveal melanoma samples — and 17 matched normal control samples, the researchers saw recurrent truncating mutations involving the suspected tumor suppressor gene PTPRJ, along with activating RAS mutations, mutations affecting cell cycle control or proliferation genes, and subtype-specific alterations. In general, the tumors appeared prone to copy number or structural alterations, the authors note, but typically lacked ultraviolet light-associated mutational signatures, and were often more similar to sun-shielded human melanoma cases.
Researchers from the Chinese Academy of Sciences and elsewhere look at within-host evolution of the yellow fever virus (YFV) for a paper appearing in PLOS Neglected Tropical Diseases. The team did whole-genome sequencing on sequential samples from a dozen YFV cases treated in China in 2016 in workers returning from Angola during an outbreak there. By comparing samples from the same host to one another, and to YFV isolates profiled previously, the authors identified 234 SNPs and 101 within-host variants in the Chinese isolates, which were most closely related to the Angola 1971 strain.