What's Your Problem? Open Thread

wyp_q_mark2_thumbnailWelcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.

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15 thoughts on “What's Your Problem? Open Thread

  1. John

    Hi there. I am trying to find ways to use the human SNP data against the human databases so that I can get information on the genes related to diseases and the risks associated with the genomes. I have asked around some people and no one gave me right answer except saying that use data from human HapMap databases or dbSNP’s. Can anyone here explain me how one can compare the SNP data to databases to get info on risks and diseases associated. Its something similar to what personal genomics companies like 23andme and decode and Navigenics are doing. Appreciate your help.
    Thanks.
    John.

  2. Mary

    Hi John–

    It sounds to me like you want more of a catalog of SNPs than an analysis tool, is that right?

    Two things you might find useful for that sort of perusal are:

    NHGRI’s GWAS catalog: http://genome.gov/gwastudies/

    SNPedia: http://www.snpedia.com/index.php/SNPedia

    You can sign up for 23andMe without having them type you. You can look around at some of the information. https://www.23andme.com/

    But if that’s not what you want give me some more details about what you want to accomplish.

  3. John

    Dear mary and Jennifer, thanks for the suggestions. I once again want to make it clear what I am looking for as I think I confused you all. I am looking for databases that I can use to get information from genotyped human SNP data. I have genotyped human snps and now want to know which of them are associated with diseases so that I can find risks associated with that genome. I tried ur suggestions, but they dont do that type of associations. so in a nutshell, I want to know which databases should I use to get info on risk factors associated with the genome, based on affymetrix snp 6.0 human data.

  4. Trey

    John,

    If you are looking for using your own data and determining disease associations from a genotype, perhaps this database: http://www.biomedcentral.com/1471-2350/10/6 in combination with UCSC Genome Graphs: http://genome.ucsc.edu/cgi-bin/hgGenome could help.

    Or you if it’s something a bit more simple, just determining if the SNP data you have is associated with a disease gene, you could upload your own SNP data into the Table Browser (genome.ucsc.edu) and intersect it with the OMIM track. (or I can think of several other intersections/filters like with dbSNP, etc)

  5. John

    Hey Trey, thanks for the info. I will chek them and I am not sure coz I have already looked at both sites before and found no use. I might have overlooked, so will see it one more time. I am assuming that when I submit my data to the database, it gives me output including the diseases associated with the genome submitted? Comment….thanks.

  6. Trey

    I’m not sure exactly what it is you are looking for.

    dbGAP is a database of association studies you can search by disease (and then look at the study for associated variants).
    http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gap

    I suspect that might not be exactly what you are looking for. Unfortunately, I’m not sure a comprehensive database exists like the Navigenics site you just pointed to.. one that is comprehensive, easily searched for snps, disease associations, studies, etc. These all come close, but they take a bit of sleuthing and analysis.

  7. Mary

    You can get some of that data out of the HapMap site. For example, I took the top SNP on that Navigenics page. I used that as a search at HapMap, and then clicked on the resulting SNP. You get this page:
    http://hapmap.org/cgi-perl/snp_details_phase3?name=rs12288738&source=hapmap27_B36&tmpl=snp_details_phase3

    If you had the OMIM track turned on at HapMap you could visualize any OMIM data in that region.

    You might be able to pull that down in tables with BioMart, but I haven’t tried that specifically.

  8. John

    Dear Trey and Mary, the one at hapmap wont tell what diseases or risks associated with the genes or SNP’s present in the genome. If u have data and want to know what are the genes or snps in ur data that are associated with diseases, what would you do? This is what I am looking for….a database that lists diseases associated based on your data submitted.

  9. Jennifer

    Hey John,

    I looked at the Navigenics link you sent & my guess is that it is from an internal database they’ve created by culling public databases & adding in their own proprietary data.

    I’m not sure there is a public database set up just the way you are hoping for, but I did find this article: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=29769

    And you’ve given me a great lead for a Tip of the Week at dbSNP. Keep checking back – I’ll probably get to is soon. And if you do find just what you are looking for, please do share your info!

    Take care.

  10. John

    Jennifer, you are right. There is no public database that does that, but I am looking for the closest option. I will do share if I find something, but meanwhile keep an eye on it.

  11. John

    I guess this was the toughest discussion ever, without any solution so far. BTW, does anyone know how we can find info on tag SNP’s i.e., based on info on tag SNP’s, can we determine the assocaited SNP’s. Is there a list or database on this? Comment on this…..thanks.

  12. Trey

    As far as I can tell and understand from your request, there is no database that does exactly what you want John. With some analysis and searching, you could obtain that data from the databases and tools we’ve given, but I see no databases that give it all out without analysis.

    All of these will give what you want for tag SNPs:
    GVS
    Haploview
    Plink

  13. John

    Thanks a lot Trey. I will see what I can find from search engines. I will also check the links you provided. Thanks….

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