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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.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.