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GNF Gene Expression Atlas 2, dbSNP, SynaBase, caBIOperl

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The UCSC Genome Browser now contains expression data from the GNF Gene Expression Atlas 2, from the Genomics Institute of the Novartis Foundation, at http://genome. ucsc.edu/cgi-bin/hgNear?db=hg16&near. order=expGnfAtlas2&near.col.gnfHumanAtlas2Id.vis=on. The data includes two replicates of 61 mouse tissues and 79 human tissues analyzed with Affymetrix microarrays. More information on the data will be available in a paper now in press at PNAS.


Build 120 of dbSNP is now available from the NCBI at ftp://ftp.ncbi.nih.gov/snp/. The mean SNP density for human genome Build 34 in dbSNP 120 is 0.002784 SNPs per base (27.844 SNPs per 10 kb). The mean spacing is 359.1473 bases per SNP.


Synamatix has released SynaBase, a database application for comparative genomics. SynaBase stores genetic data in a hierarchical format that reduces the amount of disk space required for storing large amounts of genetic data, according to the company. Using the database, “We conducted cross species genome analysis using multiple whole genome data sets in milliseconds per query,” said Robert Hercus, founder and managing sirector of Synamatix.


The National Cancer Institute Center for Bioinformatics has released a new Perl API for caBIO. The API, called caBIOperl, allows users to instantiate caBIO objects directly as Perl objects. It is available at http://ncicb.nci.nih.gov/download.

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The Scan

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Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.