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Downloads and Upgrades : Aug 19, 2011


The National Center for Biotechnology Information has launched dbSNP build 134 for the human genome.

The complete data for build 134 can be found here in multiple formats.

The complete build summary for 134 is available here.

The release includes submissions from the 1000 Genomes Project interim phase I release and the National Heart, Lung, and Blood Institute Exome Sequencing Project. It adds 6,038,585 SNPs from 18 new organisms and an overall total of 108,182,122 new SNPs representing a total of 86 organisms.

The release includes new attributes that allow searching and filtering of human variation by clinical significance, allele origin, minor allele frequency, and suspected false SNPs.

NCBI has also released GenBank 185.0 via ftp.

Uncompressed 185.0 flatfiles require roughly 511 gigabytes for sequence files only or 550 gigabytes to include the short directory, index, and text files. The ASN.1 data require approximately 420 gigabytes.

The Protein Data Bank in Europe has released two modules for its PDBeMotif service, a program that’s used to analyze PDB entries in terms of structure, sequence, and chemistry. These tools provide users with information and statistics about ligands in PDB.

The first module retrieves residues with which a given ligand in the database interacts based on current PDB entries and plots the results on an interactive graph. The graph can be used to further view the PDB entries in which the interactions occur, or to do additional analyses using PDBeMotif.

The second tool lets users search for ligands in the database that interact with a
given set of residues and displays the results graphically.

This week, the genome browser team at the University of California, Santa Cruz, released Track Data Hubs, a new feature for the UCSC Genome Browser.

These hubs are web-accessible directories of genomic data that can be viewed on the browser alongside native annotation tracks. It provides access to datasets and lets users display tracks from any public track hub that has been registered with UCSC. Additionally, users can import data from unlisted hubs or can set up, display, and share their own track hubs.

The data that underlies the tracks in a hub lives on a remote server and is stored in compressed binary indexed files in bigBed, bigWig or BAM formats. As such, when a hub track is displayed in the browser, only the data needed to support the view of the current genomic region is transmitted, rather than the entire file.

The Scan

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.