This might not be a specific bioinformatics question. But, as I was starting a paper I was wondering if there is a "Best practice" for finding all genes SNPs, etc. related to a disease or phenotype. Basically I wanted to create a list containing all known genes and SNPs related to nephrotoxicity in children undergoing treatment for ALL (acute lymphoblastic leukemia) and the papers that these findings were published in.
Maybe there is a nicer method than manually searching through various databases and then curating the findings. Well, I just wanted to hear from others what their general methods were and go 2 databases, etc.
Thanks for your comments.
1 answer
Apart from curious suggestion, you can automatically retrieve disease-associated SNPs from the GWAS catalog by R package, gwasrapidd
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I don't know about best practices, but the other day I was looking for all snps that have been associated with diabetes. This seemed to give me a good starting point:
https://www.ebi.ac.uk/gwas/