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I am interested in looking at germline copy number variations in individuals that are at high risk of developing cancer. Are there any databases where I can look, if a CNV seen in our test case has been seen/reported earlier in a patient with cancer? Thanks.

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  • $\begingroup$ Could you please edit your question and give us a few more details about what you need, exactly? $\endgroup$ – terdon May 7 '19 at 16:57
  • $\begingroup$ Hi @terdon, I have edited my question. Hope it clarifies the question. Thanks. $\endgroup$ – Aprasad May 7 '19 at 17:07
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You can find CNV (and other structural variant) information in:

  • DECIPHER

    DECIPHER is used by the clinical community to share and compare phenotypic and genotypic data. The DECIPHER database contains data from 29603 patients who have given consent for broad data-sharing; DECIPHER also supports more limited sharing via consortia. Have a look at the numbers.

    Anyone can browse publicly-available patient data on DECIPHER and request to be put in contact with the responsible clinician. Why? Because sharing benefits everyone.

  • ExAC

    The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a wide variety of large-scale sequencing projects, and to make summary data available for the wider scientific community.

    The data set provided on this website spans 60,706 unrelated individuals sequenced as part of various disease-specific and population genetic studies. The ExAC Principal Investigators and groups that have contributed data to the current release are listed here.

    ExAC has included CNV calls since August 2016.

  • ClinVar

    ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data.

  • Database of Genomic Variants

    The objective of the Database of Genomic Variants is to provide a comprehensive summary of structural variation in the human genome. We define structural variation as genomic alterations that involve segments of DNA that are larger than 50bp. The content of the database is only representing structural variation identified in healthy control samples.

    The Database of Genomic Variants provides a useful catalog of control data for studies aiming to correlate genomic variation with phenotypic data. The database is continuously updated with new data from peer reviewed research studies. We always welcome suggestions and comments regarding the database from the research community.

Information from all of these is also displayed in the Structural Variant browser of VarSome*. While you can't search by patient status, so you can't use VarSome to know the clinical history of any sample with the CNV, you can at least look up a specific gene and see the structural variants listed for it. For example, for TP53, you would see:

varsome structural variant genome browser


* Disclaimer: I work for the company behind VarSome.

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  • $\begingroup$ Thanks @terdon. I have been currently using these websites. So, good to hear this. I have also used Varsome and I think it is a nice tool. $\endgroup$ – Aprasad May 7 '19 at 17:34

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