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This Week in Nucleic Acids Research: Jun 7, 2017

Researchers from the US and the Netherlands report on efforts to recode the genome of Salmonella typhimurium LT2 bacteria using a so-called stepwise integration of rolling circle amplified segments (SIRCAS) approach. Using SIRCAS — a method that relies on yeast-based assembly of 10,000-base to 25,000-base synthetic DNA constructs, followed by rolling circle amplification — the team put together a recoded Salmonella genome that contained more than 1,500 codon replacements affecting almost 200 genes. "Beyond genome recoding," the authors write, "SIRCAS is a powerful enabling technology for building and testing large de novo designs that span hundreds of genes."

A team from the UK and Spain provides details on the Human Genome Variation Archive (HGVA), an open-access database designed for tapping into human genomic variation data, identifying genotypes involved in disease, tallying variant frequencies in human populations, and annotating their potential consequences. The paper's authors note that HGVA "is the result of a long-term effort supported by Genomics England, the National Institute for Health Research, the University of Cambridge, and the Spanish Network for Research in Rare Diseases."

Finally, Cornell University and University of Barcelona researchers introduce a cloud-based tool for prioritizing germline variants and focus in on those with potential ties to disease. The "Germline mutation scoring for next-generation sequencing data," or GeMSTONE, brings together bioinformatics tools and collections of data to analyze germline variants in a standardized and centralized analysis pipeline, the team explains. For their proof-of-principle study, the authors applied GeMSTONE to previously analyzed familial colorectal cancer dataset. "We expect our GeMSTONE will greatly aid in automating the (re)analysis of genome-wide genetic variation data and enhance the reproducibility of large-scale genomic studies," they conclude.