My background is in computer science, and I have a method which may be able to relate a disease to its expression in DNA. I wish to test this out. Are there any free data sets which contains raw DNA data and the diseases associated with this DNA?
Many thanks,
Jack
Hi Jack,
You may look at the SRA database at NCBI that archive sequence reads from high throughpout platform. Also, the GEO database at NCBI may contain some dataset you may be interested in. Both database are publicly available.
Good luck
Nick
@Nicolas Vodovar. Many thanks for your fast reply, both databases seem extremely useful, however they are slightly overwhelming as genetic data mining is not my area. I should have been more specific in my question. I am looking for some sort of benchmarking data set (as described above) which is used to compare genetic mining techniques.
Hi Jack,
I would suggest you Disgenet (http://www.disgenet.org/). I am sure you will find something usefull. Also OMIM may help you.
I do not understand what "format" should have the data you are searching for: NGS data, association gene-disease, microarray, etc
Good work
Erika
Hello Jack,
Check the attached website, hope you will find the dataset.
Regards.
http://202.97.205.78/diseasemeth/download.html
Jack: Great question, though unfortunately there isn't yet a great answer.
First, what sort of DNA are you looking for: whole genome, whole exome, variant call sets relative to a reference sequence, etc.? Genome In A Bottle (http://jimb.stanford.edu/giab) is the go-to resource for benchmarking genome variant calls, but doesn't have much in the way of genotype-phenotype data based on samples with known diseases. Still, it's a great place to start.
dbGaP has lots of DNA+phenotype of data (https://www.ncbi.nlm.nih.gov/gap) but no standard sets used as reference, since access is controlled (and difficult). Coriell has DNA & cell lines from patients with known diseases but is not open source and you would need to have it sequenced (e.g. https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=NA11254&Product=DNA).
The Cancer Genomics Hub has tons of data for a variety of cancers, but would likely take a bit of wrangling to get it in the format you need https://wiki.nci.nih.gov/display/TCGA/Cancer+Genomics+Hub
The GA4GH (http://genomicsandhealth.org/) is working to create infrastructure to enable better clinical genome data sharing of the sort you are looking for, but there's still a ways to go.
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