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This Week in Nucleic Acids Research: Dec 11, 2013

National Center for Biotechnology Information representatives report on a publicly available resource for scrutinizing ties between a given variant in the human genome and potential phenotypic effects. That database — ClinVar — is linked to other variant and phenotypic databases, the team says, and includes information on variants deemed medically important from past studies, their apparent effects, data behind the proposed relationships, and so on. "Building from the foundation of the variants submitted with minimal phenotypic descriptions to dbSNP and dbVar, ClinVar now accepts directs submission with rich, structured details of phenotype, interpretation of functional and clinical significance, methodology used to capture variant calls and supporting evidence," study authors say.

A team from Germany and the US used Pacific Biosciences SMRT sequencing to tease apart genome-wide methylation patterns in the gastric ulcer-causing bacterial pathogen Helicobacter pylori. By generating single-molecule sequence data for two H. pylori strains, the researchers identified new and known methylation patterns and methyltransferase enzyme-coding genes in the genomes, together with methylated sequence motifs in each of the strains. According to those involved, "methylomes of these well-characterized H. pylori strains will provide a valuable resource for future studies investigating the role of H. pylori [restriction-modification] systems in limiting transformation as well as in gene regulation and host interaction."

Researchers with the National Human Genome Research Institute and the European Molecular Biology Laboratory's European Bioinformatics Institute report on recent improvements to the NHGRI GWAS catalog. In its current form, the manually curated collection contains information on SNP-trait associations for nearly 12,000 SNPs characterized in more than 1,750 publications, the study's authors note, along with maps for visualizing the chromosomal locales of these variants, search tools, and more.