A team from the Li Kay Shing Centre introduces a software package called multiSNV for calling somatic point mutations simultaneously in sequence data representing multiple tumor samples from the same individual in Nucleic Acids Research. The approach uses a Bayesian framework to call variants in data for all of the available samples rather than through pairwise analyses of the samples, the researchers note — an approach that shows promise for picking up relatively rare mutations. Using simulated data and real exome sequences generated using multiple samples apiece from individuals with clear-cell renal carcinoma, for example, they detected somatic mutations with allele frequencies around 3 percent.
German and Norwegian researchers present a high-resolution analytical pipeline aimed at characterizing genetic polymorphisms found in adaptive immune system genes at human leukocyte antigen (HLA) loci. The new HLA typing method, which hinges on the availability of high-throughput sequencing data, includes both an in-solution targeted capture step aimed at HLA class I and class II genes as well as an allele-calling algorithm. The team validated this approach using 357 commercially available DNA samples that had already been HLA typed, demonstrating that the automated method can call HLA alleles with high accuracy.
Centre for Genomic Regulation systems biology researcher Luis Serrano led a group of Spanish researchers who used a machine learning technique that integrates half a dozen structural features and sequence-based predictors to distinguish between non-promoters and promoters that are active or abortive in Mycoplasma pneumoniae, a microbe with a streamlined genome. "By using a combined approach, we now show that it is possible to distinguish promoters of full-length transcripts from abortive and non-productive promoters," the study's authors say, noting that "this work may aid in the species-specific design of synthetic promoters, allowing the researcher to predict beforehand whether or not the designed sequence will give rise to a productive transcription event."