Connection Between Epigenome, Selective Mutability, Evolution, and Human Disease
Li, Harris et al., PLoS Genetics
Researchers at the Baylor College of Medicine and elsewhere propose a "connection between the epigenome, selective mutability, evolution, and human disease" based on the findings of their study on associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination mediated by low-copy repeats. "Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability," the Baylor-led team writes.
GPUs for GWAS
Because the computational burden to search for epistasis in genome-wide association study data is often prohibitive, a team from the Roslin Institute at the University of Edinburgh has attempted a powerful and cheap implementation of a search algorithm on GPUs using OpenCL. The team published a paper in Bioinformatics describing the GPU implementation, which achieved a 92 speed up of an exhaustive epistasis scan for a quantitative phenotype.
In their paper, the authors write that "to achieve a comparable computational improvement without a graphics card would require a large compute-cluster, an option that is often financially non-viable. The implementation presented uses OpenCL—an open-source library designed to run on any commercially available GPU and on any operating system."
Their software, called EpiGPU, is open-source and GPU-vendor independent, meaning that it will run on any GPU card.