Question: Best practice for finding all genes SNPs, etc. related to a disease or phenotype
0
gravatar for flight505
4 weeks ago by
flight50570
Denmark/DTU
flight50570 wrote:

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.

snp genome • 111 views
ADD COMMENTlink modified 4 weeks ago by Yean120 • written 4 weeks ago by flight50570

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/

ADD REPLYlink written 4 weeks ago by curious340
2
gravatar for Yean
4 weeks ago by
Yean120
Bangkok
Yean120 wrote:

Apart from curious suggestion, you can automatically retrieve disease-associated SNPs from the GWAS catalog by R package, gwasrapidd

ADD COMMENTlink written 4 weeks ago by Yean120

@Yean Thanks for that suggestion,I am didn't know about gwasrapidd and I guess that there are several other scraping and query tools out there.

I hope that others will post similar suggestions or tools ⚒️.

ADD REPLYlink written 4 weeks ago by flight50570
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