In PLOS Genetics, researchers from Yale and Washington University describe almost four dozen candidate genes implicated in congenital heart disease with de novo variant-focused, network-assisted analyses. "Under the hypothesis that connected genes in protein-protein interaction (PPI) networks are more likely to share similar disease association status, we developed a Markov Random Field model that can leverage information from publicly available PPI databases to increase power in identifying risk genes," the team says. Using this approach, the authors tracked down 46 genes with known or suspected ties to congenital heart disease, based on the presence of one or more de novo variants in these genes. "The simulation studies and real data analysis on CHD suggest that the proposed method has improved power to identify risk genes over methods without integrating network information," they write.
A Ubiquitous Pharmacogenomics (U-PGx) Consortium team discusses pharmacogenomics-related clinical decision support strategies for a paper appearing in PLOS One. The researchers performed qualitative and quantitative analyses on pharmacogenomics clinical decision support systems rolled out at 15 clinical sites across Europe for the U-PGx study, using insights from nearly 6,900 genotyped samples and dozens of questionnaires to assess the implementation of the decision support approaches. "We demonstrated the feasibility of implementing a standardized PGx decision support solution in a multinational, multi-language, and multi-center setting," the authors note. "Remaining challenges for future wide-scale rollout include the harmonization of existing PGx information in guidelines and drug labels, the need for strategies to lower the barrier of PGx [clinical decision support] adoption for healthcare institutions and providers, and easier compliance with regulatory and legal frameworks."
A paper in PLOS Neglected Tropical Diseases explores features found in Cuban isolates of Treponema pallidum endemicum, a sub-species previously linked to a non-venereal condition known as bejel, or endemic syphilis. Using pooled or direct genome sequencing, coupled with bioinformatic analyses, investigators from the Czech Republic, Cuba, and the US characterized T. pallidum subsp. endemicum, or "TEN," isolates from four Cuban patients in an area not known to be endemic for bejel. Because the sequences pointed to non-clonal TEN isolates, they conclude that TEN isolates are persistent or have been introduced to the region multiple times rather than stemming from a lone outbreak. "Altogether, the findings presented in this study suggest that there are several different sequence types of TEN strains circulating in the population of Cuba," the authors write, noting that the analyzed TEN isolates appeared to have been sexually transmitted.