Tag Archives: genetic association

New and Updated Online Tutorials for dbGaP, GAD, and DGV

Comprehensive tutorials on the publicly available dbGaP, GAD, and DGV databases enable researchers to quickly and effectively use these invaluable resources.

Seattle, WA: July 16, 2009 — OpenHelix today announced the availability of new tutorial suites on dbGaP, Genetic Assocation Database (GAD) and Database of Genomic Variants (DGV). The dbGaP resource is a database of genotypes and phenotypes with extensive variation data and clinical details GAD is an annotated resource connecting human genes and polymorphisms to diseases and traits, and DGV or Database of Genomic Variants, catalogs and displays structural variation in the human genome. These three new tutorials in conjunction with additional OpenHelix tutorials on dbSNP, VISTA, HapMap, GeneSNPs, SeattleSNPs, Genome Variation Server and many others, give the researcher an excellent set of training resources to assist in their genetic association and variation research.

The tutorial suites, available for single purchase or through a low- priced yearly subscription to all OpenHelix tutorials, contain an online, narrated, multi-media tutorial, which runs in just about any browser connected to the web, along with slides with full script, handouts and exercises. These tutorials will teach users:

dbGaP

  • to perform basic and advanced searches and navigate the dbGaP site
  • to understand the displays for the main open access data types: studies, variables, documents, and analyses
  • to use the analysis browser to identify candidate genomic regions for genotype-phenotype associations and to manipulate and customize the browser displays GAD

GAD

  • to view GAD tables from different perspectives
  • to read detailed reports for unique genetic associations
  • to perform basic searches for genes, diseases, polymorphisms, environmental factors, and references
  • to perform advanced queries
  • to do a batch query for a large gene list
  • add a new genetic association or edit an existing one

DGV

  • to browse and search through DGV’s structural variant data
  • how to find, understand and link to more genomic variation details
  • to navigate and customize your data using the genome browser
  • how to perform a BLAT sequence search

With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. The scripts, handouts and other materials can also be used as a reference or for training others. To find out more about these and over 70 other tutorial suites visit the OpenHelix Catalog and OpenHelix. Or visit the OpenHelix Blog for up-to-date information on genomics and genomics resources.

About OpenHelix:
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web-based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

Linking phenotypes and genotypes.

Ok, that’s a really broad title for an important area. And it is a problem that we are starting to see addressed more and more with GWAS (genome wide association studies). ResearchBlogging.org If you came here hoping that I had solved this, I’m sorry to disappoint you. We are asked all the time for places to look for this kind of information. The relatively new “Phenotypes and Disease Association Tracks” on the human UCSC Genome Browser have been popular in the training sessions we have given (look at the human browser, and check the second group of tracks controls on the page). You can find OMIM data in Ensembl. You can add Morbid Map to your Map Viewer. Another resource that I just found out about is trying to get at the same types of data–but it is available from their interface and also on the HapMap browser.

MutaGeneSys is a tool with a very simple interface at their web site, but the data is also displayed as a track in the GBrowser at HapMap. The goal was to combine HapMap information + OMIM + whole-genome marker correlation data. The news page at HapMap that describes the addition of this track to HapMap says:

Predicted OMIM associations available in GBrowse

The OMIM associations track presents data from the MutaGeneSys database, which links genotype data from HapMap and whole genome association studies with the known disease variants reported by the OMIM database. Example of a region with multiple OMIM associations: Chr1:194923128..194933127

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