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Old 01-20-2014, 07:09 AM   #1
ljw1001
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Location: boston

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Default Sample case/control variants for any human phenotypes

Hi,

I'm new to bioinformatics and doing some experimental work in machine learning. I'm looking for sample variant data with the following characteristics:

- human
- ideally vcf format
- samples tagged with phenotypes or marked as case/control for a given phenotype. Alternately, pairs of cancer/normal samples would probably do
- more samples is better

if there are any publicly accessible datasets with these characteristics, it would be super helpful. I've looked at 1000G, but they seem to be all apparently normal, and clinvar, but they seem to collect data about variants, but not individuals. I'm really looking for sets of samples where some are affected and some not, for a given feature.

Thank you!!
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Old 01-20-2014, 09:53 AM   #2
donfreed
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Hi,

It sounds like the ideal data repository for your project would be dbGaP. However, the data is controlled access and might be difficult for your lab to apply for.

If dbGaP is not feasible, then I think the next best place to look would be the NCBI SRA. Although this data may not be ideal.
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Old 01-21-2014, 02:59 AM   #3
ljw1001
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Thanks donfreed.

I think you are right that dbGaP would be perfect and that I won't get access . I will dig more into NCBI_SRA.

If I drop the requirement that the data be human, does that open up any possibilities? Really looking for nextgen samples (hence the VCF preference) with phenotypic features associated, but mice or another species would make for a good proof of concept.
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