Germline CNV Databases for Healthy and/or Cancer Patients

Question

[tohc]

Hello,

I have been working with TCGA's Copy Number Variation Data and have been primarily interested in germline copy number variation.

I was wondering if there are any sets of "healthy" germline copy number variation datasets as well as additional cancer germline copy number datasets?

COSMIC seems to hold somatic CNV data.

Any help would be appreciated.

Thanks, Chris

Answer 1

[Kevin Blighe]

The one that has been around for as long as I can remember is Database of Genomic Variants. I recall there being criticism of it years ago, but I am sure that they have refined the database multiple times since then as large scale sequencing projects have concluded and methods improved.

Answer 2

[Garan]

You could try the Genome In A Bottle reference SV calls v0.6. They are for the HG002 (NA24385 PGP Ashkenazim Jewish Son) genome so shouldn't contain any rare pathogenic CNVs/SVs, but should have common SVs across the genome ("Healthy " germline copy number variation).

ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6

Quite a few groups have called CNVs/ SVs on the UK Biobank genotyping data from microarrays. Not sure if this is public yet (one of our local collaborators has a set), but a number of papers have been published off this data. This would be SVs for around 500,000 mainly healthy UK participants. When the Exome / Genome sequencing is complete on this cohort there should be a great resource for healthy CNVs.

Not directly related but an example of how a group involved in Cancer research is proposing to use the UK Biobank data. https://www.ukbiobank.ac.uk/2018/11/identification-of-functional-germline-variants-in-childhood-cancers/?platform=hootsuite