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This Week in PNAS: Sep 5, 2017

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from the J. Craig Venter Institute, Human Longevity, and Human Longevity Singapore present a maximum entropy algorithm for bringing together diverse trait predictions from whole-genome sequence data. After exploring ties between genome features and phenotypes such as eye color, skin color, height, face shape, and more in 1,061 individuals from the San Diego region, the team attempted to re-identify 100 randomly selected individuals with the integrated trait prediction algorithm. The top 10 individuals sharing the traits predicted housed the individual of interest roughly 88 percent of the time, the authors report. GenomeWeb has more on the study, here.

A team from Dana-Farber Cancer Institute, Harvard Medical School, and Brigham and Women's Hospital consider expression quantitative trait loci (eQTL) networks in dozens of tissue types or cell lines. Starting with available RNA sequence data generated for the GTEx project, representing 50 tissue types and two cell lines, the researchers imputed genotype profiles and put together bipartite networks spelling out apparent gene expression shifts that occur in the presence of a given genetic variant in 13 tissues that met all of their quality control criteria and data requirements. "We found clusters of eQTL linked to shared functions across tissues and tissue-specific clusters linked to tissue-specific functions, driven by genetic variants with tissue-specific regulatory potential," they write.

Finally, researchers from the National Institutes of Health and the University of California, San Diego, describe a non-syndromic hearing loss-related missense mutation in the innate immune gene NLRP3, which codes for an inflammasome component. The team began by exploring genome-wide linkage patterns in a North American family where progressive sensorineural hearing loss appeared to be passed down in an autosomal dominant manner, narrowing in on a suspicious region of chromosome 1 that encompassed NLRP3. Targeted sequencing led to a missense change in the gene that was subsequently identified in a second hearing loss-affected family, while the investigators' subsequent experiments pointed to the possibility of treating some forms of hearing loss by tackling autoinflammation.