Tag Archives: GAD

Video Tip of the Week: list of genes associated with a disease

I am currently in Puerto Varas, Chile at an EMBO genomics workshop. The workshop is mainly for grad students and the instructors are, for the most part, alumni of the Bork group. I gave a tutorial on genomics databases.

Anyway, the last two days of the workshop is a challenge, in teams of 3-4 advised by an instructor, students are to develop a list of genes associated with epilepsy. Obviously, this could be a trivial task, just go to OMIM or GENECARDS and grab a list. But this challenge requires them to go behind that and use the available data and make predictions. My team attempted, on my suggestion, some brainstorming techniques to ensure a more creative solution than they could come up with individually or just jumping into normal group dynamics. It seemed to work, their solution was quite creative and we will find out today how that worked.

That was my long way of saying, in the process we came across many databases of gene-disease information. above you will find a video of rat gene disease associations from RGD, often used of course to investigate human gene disease associations.

Below you will find a list of some excellent databases and resources to find similar lists:

Gene Association Database  http://geneticassociationdb.nih.gov/

G2D http://g2d2.ogic.ca

OMIM http://www.omim.org

Diseases http://diseases.jensenlab.org/

GeneCards http://genecards.org

DisGeNET http://ibi.imim.es/web/DisGeNET/

Several NCBI resources http://www.ncbi.nlm.nih.gov/guide/howto/find-gen-phen/

UCSC Genome Browser’s tracks for disease and phenotype http://genome.ucsc.edu

There are several others I’m sure, if you have a favorite not on this list, please comment.

Reference for RGD:
Laulederkind S.J.F., Hayman G.T., Wang S.J., Smith J.R., Lowry T.F., Nigam R., Petri V., de Pons J., Dwinell M.R. & Shimoyama M. & (2013). The Rat Genome Database 2013–data, tools and users, Briefings in Bioinformatics, 14 (4) 520-526. DOI:

(one) Video Tip of the Week (to hold them all): Variation and Disease Databases

After again reading Daniel MacArthur’s good rundown about the state of databases of human disease-causing variation from last year (One database to hold them all), I thought it might be nice to do a tip comparing several of them. I couldn’t get it under our self-imposed 5 minute limit for our tips (and technical limit of software I’m using, but that’s about to change). But as I perused our tips and other sites, I found we and others have quite a list of how-to tips to use these databases. So in today’s tip I’ve gathered video tips for 3 of the databases listed in the linked post. Below those tips I’ll link to other how-to videos for additional human variation and disease.

The databases mentioned are OMIM, Human Gene Mutation Database (HGMD), MutaDATABASE and The Human Variome Project . There are video tips for the first three.

OMIM.

Last year OMIM moved to http://www.omim.org and had a entire new interface. Mary was on top of it and did a tip on the new OMIM interface with lots of information on the move and OMIM in the post:

Our full tutorial on the new OMIM is coming soon.

HGMD:
HGMD has a public site and a by-subscription site. The latter includes access to the most current data and some added features. The publicly accessible site is out-of-date by three years. Because of HGMD restrictions, we aren’t able to do a tutorial or a tip on HGMD, but they do have an introduction video to their database:

 

Additionally, there is a good background page for more information.

MutaDATABASE:

Mary did a tip on MutaDatabase last summer:

 

Another excellent resource is Gen2Phen. The Gen2Phen project “aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data, and to link this system into other biomedical knowledge sources via genome browser functionality.”  In that vein, they have quite an extensive list of Locus-specific databases and additional resources.

There are several other resources available for human disease variation including CGAP, dbGAP, GAD, PhenomicDB and several others. We have tutorials on all those if you wish to check those out.

Of course there’s dbSNP :D of which we have a tutorial and tip about searching human variation.

You can find an extensive list of other resources at Human Genome Variation Society (HGVS).

And an oft-asked question on Biostar is what kind of resources are there for this kind of data. You can find answers here, here and here.

Video Tip of the Week: VnD Resource for Genetic Variation and Drug Information


In today’s tip I am going to feature a resource that I found recently. I’ve been updating our dbSNP tutorial, which Mary & Trey will be presenting at workshops in Morocco, and also our free PDB tutorial, which is sponsored by the RCSB PDB team. I have therefore been thinking about protein structures and small sequence variations a lot lately. As I explored the latest Database issue of NAR looking for resources to do a tip on, I found an article describing the VnD (genetic Variation and Drug) resource, which can also be accessed at the URL www.vandd.org, according to the NAR article. The article is “VnD: a structure-centric database of disease-related SNPs and drugs“, and figure one shows a veritable Who’s Who of protein, variation and disease resources, so I had to investigate.

What I found at VnD made me sure that this was a resource that I wanted to feature in a tip. VnD is from the Korean Bioinformation Center, or KOBIC, who has a list of databases and tools that they provide. I’ll save the rest of the KOBIC resources for another post & concentrate on VnD here. Compiling data from resources such as RefSeq, OMIM, UniProt, PDB, DrugBank, dbSNP, GAD and more might have been cool enough, depending on how it was done, but the VnD also does their own structure modeling analysis on how the variation affects the protein structure and drug/ligand binding.

This tip movie isn’t long enough to really show you the breadth of what is available from the VnD, but I hope it will be enough to encourage you to read the NAR article (listed below), and to check out VnD. One thing to note: don’t expect to find every dbSNP rs# over there – one that I’ve been using in our tutorial isn’t over there. They are specifically interested in variations within genes that might effect drug binding. But hey, you can’t query DrugBank with rs#s, and I’ve never seen the structure modeling done like VnD, so it is a worthy resource that you may want to investigate if you are interested in how genetic variations connect with disease and drug therapies.

Quick links:

VnD: Variations and Drugs resource -  http://vnd.kobic.re.kr:8080/VnD/index.jsp

Korean Bioinformation Center (KOBIC) – http://www.kobic.re.kr/

RCSB PDB – http://www.pdb.org

OpenHelix Tutorial on the RCSB PDB – http://www.openhelix.com/pdb

dbSNP: Short Genetic Variations, from NCBI -  http://www.ncbi.nlm.nih.gov/projects/SNP/

OpenHelix Tutorial on NCBI’s dbSNP – http://www.openhelix.com/cgi/tutorialInfo.cgi?id=39

For links to other resources and OpenHelix tutorials mentioned in this post, please see our catalog of resources – http://www.openhelix.com/cgi/tutorials.cgi

Reference:
Yang, J., Oh, S., Ko, G., Park, S., Kim, W., Lee, B., & Lee, S. (2010). VnD: a structure-centric database of disease-related SNPs and drugs Nucleic Acids Research, 39 (Database) DOI: 10.1093/nar/gkq957

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.

New gene linked to ALS, in Science today

I didn’t expect to be doing another blog post today, but I found this story so compelling that I put off some other work to track this down. New Gene Nailed for ALS. (subscription required) ResearchBlogging.orgMy Science newsletter today had a link to a story about a new gene found that may be mutated in some cases of ALS, amyotrophic laterial sclerosis, or Lou Gehrig’s disease: This article describes the phenotype and the gene hunt a bit. It links to the research article in today’s Science as well.

From the abstract:

We identified neighbouring mutations in a highly conserved region of TARDBP in sporadic and familial ALS cases. TARDBPM337V segregated with disease within one kindred and a genome-wide scan confirmed that linkage was restricted to chromosome 1p36, which contains the TARDBP locus. Mutant forms of TDP-43 fragmented more readily than wild-type in vitro and caused neural apoptosis and developmental delay in the chick embryo in vivo. Our evidence suggests a pathophysiological link between TDP-43 and ALS.

There was a Boston Globe story about a couple of brothers in my area who were struggling with this disease. One brother had ALS and was fighting to survive, the other was fighting like crazy to find help his brother and find a cure. They did a movie that was shown on PBS, some of you may have seen it.

What would you do if you were 29 years old and found out that you only had a few years to live? The story of the remarkable events set in motion when one family confronted a disease that would transform their lives.

A subsequent story in the Globe reported that Stephen died.

Continue reading

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

Continue reading