Data Sharing: Standards for Bioinformatic Cross-Talk
✍ Scribed by James Ostell
- Publisher
- John Wiley and Sons
- Year
- 2009
- Tongue
- English
- Weight
- 71 KB
- Volume
- 30
- Category
- Article
- ISSN
- 1059-7794
No coin nor oath required. For personal study only.
✦ Synopsis
The RefSeqGene and variation database (dbSNP) groups at NCBI welcome den Dunnen et al.'s review of the issues related to sharing data between LSDBs and centralized databases (Hum Mutat 30, 493-495, 2009). NCBI has made a special effort over the past three years to support the identification of genome variants with potential clinical relevance. In 2006, NCBI staff, in collaboration with the genetic testing community and LSDBs, began developing standard sequences for reporting human variation (RefSeqGene; www.ncbi.nlm.nih.gov/RefSeq/RSG/). To date, more than 85 LSDBs and testing laboratories have partnered with NCBI to create about 530 of the current 1,150 RefSeqGene records. Responding to community suggestions, NCBI released two web tools to facilitate submission of information about variation according to the HGVS standard and added a new viewer to simplify review of variation that may be of clinical significance (see www.ncbi.nlm.nih.gov/ RefSeq/RSG/LSDB.shtml.) Early in 2008, NCBI and GEN2PHEN (http://www.gen2phen.org) began an active collaboration to establish an internationally recognized sequence standard for reporting variation, the Locus Region Genomic or LRG, for which RefSeqGene will be an important starting point (see also www.ncbi.nlm.nih.gov/RefSeq/RSG/LRG.shtml.) Also in 2008, NCBI arranged with Dr. den Dunnen and Dr. Fokkema to become an LOVD host-site, and is currently loading LSDB data in support of several disorder-specific advocacy groups. Last year, dbSNP also included HGVS mutation names on its display of variants and added HGVS nomenclature as a query function. These tools and reports are founded on NCBI's commitment to (1) providing attribution to data submitters, (2) providing web links to specialized databases that have more detailed information, (3) standardizing access to submitted data, and (4) facilitating comparison of multiple submissions. We value our long relationship with LSDBs and the clinical genetics community and will continue to devote considerable resources to supporting the principles outlined by den Dunnen et al. We look forward to ongoing positive and complementary relationships with LSDBs.