In PLOS Genetics, researchers from the University of Colorado Denver and other centers in the US and UK describe an analytical approach and related software for finding new genetic associations in case-control studies with the help of publicly available sequence data from unaffected control individuals to boost detection power. The approach — known as the "Proxy external controls association test," or ProxECAT — "estimates enrichment of rare variants within a gene region using internally sequenced cases and external controls," the authors say. They applied ProxECAT to simulated and real data to estimate control allele frequencies in case-control analyses searching for variants contributing to childhood obesity.
For a paper appearing in PLOS One, investigators from Hungary's University of Szeged and elsewhere explore the genetic ancestry of a "conqueror" group believed to have introduced Finno-Ugric Hungarian language to Central Europe's Carpathian Basin. Using mitochondrial genome sequences from more than 100 individuals whose remains were left in cemeteries used by this group, the researchers detected ancestry that resembled genetic sequences in nomadic Eurasian steppe populations as well as Central Asian mitochondrial DNA lineages that lined up with Asian Scythian, Asian Hun, and other populations. "The large diversity of [mitochondrial DNA haplogroups] detected in the Conquerors reflects quite complex genetic history," the authors note.
A Polish Academy of Sciences-led team characterizes two viruses that infect Streptococcus pyogenes for another PLOS One study. The researchers did short-read genome sequencing, liquid chromatography- and mass spec-based proteomic profiling, host range analyses, phylogenetics, and other analyses on the bacteriophages, dubbed Str01 and Str03. Their results suggest the bacteriophages belong to unknown genera within the Siphoviridae virus family, containing some genes that are common to Streptococcus-infecting siphoviruses and others that are distinct.