How To Search Disease-Causing Chromosomal Structure Variation?

Question

[Ma_Ko]

Hi all, is there any other useful databases for chromosomal variation? I would like to know the useful database that recoreds disease-causing variations which mapped by using STS markers and so on (not microarrays).

Followings are useful links. Any help would be great thanks.

• dbVar http://www.ncbi.nlm.nih.gov/dbvar/
• CHOP (The Copy Number Variation project at the Children's Hospital of Philadelphia) http://cnv.chop.edu
• DGV (Database of Genomic Variants) http://projects.tcag.ca/variation
• DECIPHER https://decipher.sanger.ac.uk/
• ECARUCA http://agserver01.azn.nl:8080/ecaruca/ecaruca.jsp

Answer 1

[Pierre Lindenbaum]

You can use NCBI ELink to map from the diseases in OMIM to UniSTS. For example, to map the STS linked to the 'LYNCH SYNDROME I' ( omim:120435 ) : http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=omim&db=unists&id=120435

Result:

<eLinkResult>

    <LinkSet>
        <DbFrom>omim</DbFrom>
        <IdList>
            <Id>120435</Id>
        </IdList>
        <LinkSetDb>

            <DbTo>unists</DbTo>
            <LinkName>omim_unists</LinkName>
            <Link>
                <Id>64072</Id>
            </Link>
            <Link>
                <Id>888</Id>

            </Link>
        </LinkSetDb>
    </LinkSet>
</eLinkResult>

both sts (64072 and 888) are unists: 64072 = D2S123

[Ma_Ko]

Great! Thank you for nice example. Combining ELINK and UCSC genome browser (BED) seems to be sufficient and useful!

[Hanif Khalak]

Does this give you a list of CNVs/SVs that were discovered using STSs, or just the STS ids mapped to genes corresponding to OMIM entries?

[Pierre Lindenbaum]

it's the second case

Answer 2

[Malachi Griffith]

The following review article does a nice job of summarizing online resources for structural variation:

Sneddon TP, Church DM. Online resources for genomic structural variation. Methods Mol Biol. 2012;838:273-89. PubMed PMID: 22228017.