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UniProt Consortium, Epicentre Biotechnologies, Wellcome Trust Sanger Institute, Milford Medical Laboratory, Myriad Genetics

The UniProt Consortium has released UniMES, the UniProt Metagenomic and Environmental Sequences database, a repository for metagenomic and environmental data. UniMES currently contains the data from the Global Ocean Sampling Expedition, comprising 28 million DNA sequences from oceanic microbes and nearly 6 million predicted proteins. UniMES combines these predicted protein sequences with automatic classification by InterPro, the European Bioinformatics Institute’s resource for protein families, domains, and functional sites. 

Epicentre Biotechnologies has released the ArrayPure nanoscale RNA purification kit, which includes reagents for purifying RNA from one or more eukaryotic cells, including quantities typically obtained with laser capture procedures. The company said it has developed a nanoscale protocol for the kit and tested it with quantitative real-time PCR on one to 10,000 eukaryotic cells.

The Wellcome Trust Sanger Institute’s Cancer Genome Project has released version 31 of the COSMIC (Catalog of Somatic Mutations in Cancer) database. COSMIC release 31 includes gene fusion/translocation somatic mutation data from the literature. It includes information from 515,535 experiments, 230,057 tumors, 3,302 genes, and 438 fusions.  

Milford Medical Laboratory has released a DNA sequencing-based test for human papillomavirus and other sexually transmitted diseases that the company said eliminates the false positive test results associated with other methods. The test is based on the company’s LoTemp PCR amplification technology and compares a “signature sequence” from the test sample against Genbank in order to accurately identify the causative agent. The company said that its test can identify HPV genotypes that are not targeted for detection by Digene’s HC2 assay.

Myriad Genetics has launched TheraGuide 5-FU, a DNA-based test to help predict which cancer patients are likely to suffer serious toxic reactions to the drug 5-Fluorouracil (5-FU) or the oral form of the drug, capecitabine. The test costs $1,100 and includes DNA sequence analysis of the DPYD and TYMS genes, which increase a patient's risk for toxicity to 5-FU chemotherapy.
Myriad said that around one third of all patients given 5-FU will experience severe to life-threatening dose-limiting toxicity. “The majority of these toxic reactions are due to genetic variations in the DPYD and TYMS genes,” the company said.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.