A computational method for discovering regulatory noncoding variants in individual cancer genomes is reported in Nature Genetics this week. The method, called cis-X, combines whole-genome and transcriptome sequencing data from a single cancer sample, according to its developers at St. Jude Children's Research Hospital and their collaborators. It first identifies aberrantly cis-activated genes that exhibit allele-specific expression accompanied by an elevated outlier expression, then searches for causal noncoding variants that may introduce aberrant transcription factor binding motifs or enhancer hijacking by structural variations. Cis-X, they write, overcomes two major limitations of hotspot analysis and mutation-expression association: the need for a large cohort of samples usually only attainable in a pan-cancer study and the requirement that noncoding variants are recurrent to achieve statistical significance. The scientists demonstrate that their method can identify known and previously unknown regulatory noncoding variants targeting known oncogenes, as well as implicate putative oncogenes for subsequent studies to establish selective dependency.
By analyzing genomic data from Native Americans and individuals across the Polynesian islands, a team led by scientists from Stanford University provide evidence for prehistoric contact between these peoples. While it has been suggested that prehistoric South American populations played a role in the settlement of east Polynesia and particularly of Easter Island, most notably by the Norwegian explorer Thor Heyerdahl, molecular genetic studies have not provided any conclusive supporting evidence. To further investigate the issue, the researchers analyzed genome-wide variation in 807 individuals from 17 Polynesian populations and 15 Pacific coast Native American groups for signs of admixture. As reported in Nature, they uncover evidence of contact between Polynesians and Native Americans around 1200 AD. Their data also point to a single contact event that occurred in eastern Polynesia between Polynesian individuals and a Native American group most closely related to the indigenous inhabitants of present-day Colombia. GenomeWeb has more on this, here.