In PLOS Genetics, researchers from the National Cancer Institute and other centers in the US, Spain, and Italy explore common and rare variant contributions to conditions that cluster in families, developing a statistical strategy for finding families who might benefit from sequencing-based searches for rare variants. After demonstrating that polygenic risk scores (PRS) made up of common SNPs might help flag families with disease risk stemming from highly penetrant rare variants (HPRV), the team developed an approach that considers not only PRSs, but also information on family structures and families members affected by disease. The authors included the statistical strategy in an analysis of families affected by melanoma, finding further evidence that "PRS prioritization may be a useful future tool" to guide HPRV searches.
A Michigan State University team takes a look at gene expression variability in the blood in individuals with or without chronic obstructive pulmonary disease (COPD) for a paper appearing in PLOS One. Using array-based blood gene expression data for almost 1,300 individuals from seven cohorts, including nearly 700 COPD-affected individuals, the researchers uncovered more than 3,300 genes that appeared to be differentially expressed in blood samples from individuals with the lung condition. They went on to whittle that set down to 679 suspicious genes, highlighting immune and other pathways that appear to be altered in individuals with COPD. The public array data re-analysis led to "prospective gene and pathway associations that may be targeted for improving COPD diagnosis and treatment," the authors write, noting that the study "also highlighted disease genes that interact with smoking status."
Researchers from the Northern Arizona University and the American Museum of Natural History evaluate a feces-based metabarcode sequencing method for identifying bat species from guano for another PLOS One paper. The team looked at the sensitivity of a mini barcode-based DNA amplicon sequencing assay known as the "Species from Feces" test, focusing on DNA retrieval and sequencing differences related to humidity, time since sampling, and so on in dozens of samples stored for up to 30 months under different temperature and humidity conditions. Although the assay successfully picked up the presence of rare bat species in pooled guano samples collected from temperate or tropical roosts, the investigators report, the performance appeared to drop off more quickly when humidity was high than it did at dry, cool sites.