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Where can I find a vcf file with individuals in it, that have a specific disease?

I built a tool for PRS - Calculation and interpretation for my thesis, and in order to evaluate it, I need a .vcf file from one (or many) individuals with a certain disease (ideally: Hypertension, Breast cancer, Lung cancer or Type 2 Diabetes).

Does anybody have any ideas where I can find data like that?

phenotype vcf
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updated by edu123updates • edu123updates • written by Patrick • Patrick

3 answers

human data often comes with restrictions on access due to privacy. the uk biobank and nih all of us require applying for access for example

you can access certain types of data freely on certain types of patients however in other circumstances

for example, here are somatic mutations from the TCGA (the cancer genome atlas) in vcf format. this is just the somatic mutations called with various tools. cnv calls, gene expression, and other things are also available with uncontrolled access for bam/cram/germline vcf require controlled access https://portal.gdc.cancer.gov/repository?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22content%22%3A%7B%22field%22%3A%22cases.case_id%22%2C%22value%22%3A%5B%22set_id%3AkNa6uowBB1xFKettIGZf%22%5D%7D%2C%22op%22%3A%22IN%22%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_format%22%2C%22value%22%3A%5B%22vcf%22%5D%7D%7D%5D%7D

there is also the 1000 genomes dataset, which is a fully open repository of human sequencing data with no controlled access (which is quite unique)! the clinical data available with the 1000 genomes is limited but it has been analyzed in some papers, for example https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135193 and it has full unrestricted access to bam/cram/vcf (including germline/ancestry info) at https://www.internationalgenome.org/data that said, you may be going out on a limb trying to clinically characterize the 1000 genomes project

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written by cmdcolin cmdcolin

Thanks for your detailed answer.

I tried the link you send from TCGA, but when trying to download something, I am required to to sign in as a researcher which I am not.

However, I found a website called openSNP where people can upload their raw data from companies like 23andme, along with some phenotype descriptions. I think you can convert these into vcf files as well Although it's probably not as detailed and accurate as data from the other, more official sources, I think it may suffice for my purposes.

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written by Patrick • Patrick

you're right, those are controlled. I added a filter for all the uncontrolled files here https://portal.gdc.cancer.gov/repository?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22content%22%3A%7B%22field%22%3A%22cases.case_id%22%2C%22value%22%3A%5B%22set_id%3AkNa6uowBB1xFKettIGZf%22%5D%7D%2C%22op%22%3A%22IN%22%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.access%22%2C%22value%22%3A%5B%22open%22%5D%7D%7D%5D%7D it includes genotyping arrays which might be able to be converted to VCF potentially. openSNP looks good also

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written by cmdcolin cmdcolin

I would recommend trying the NIAID Data Ecosystem because you can search simultaneously across numerous existing repositories. I just briefly tried using the advanced search tool to find datasets with 'SNP' as the Topic Category and 'lung cancer' anywhere else in the record and got 72 results: https://data.niaid.nih.gov/search?q=topicCategory.name%3A%22snp%22+AND+%22lung+cancer%22

These look like mostly xlsx files but you should be able to convert them. You could also try other combinations of search/filters to get something else or narrow it down to your specific parameters.

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written by ehaag • ehaag

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