Biostars

What’s The Answer? (consumer genomics help)

This week’s highlighted questions are part of a larger “meta” thing that I keep musing about. Recently, independently, these questions showed up at the Biostar site.  Interesting convergence of questions from the public, I thought. Although some folks wading into recreational genomics have some biology or computational background, so many of the ones coming from genealogy or from a family’s eager adoption of testing all the relatives of this may not. They probably don’t know what a reference genome is. They won’t get the plug-in idea. They don’t know what the right questions are. I think this is just the tip of an iceberg.


Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Thursdays we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.


Question: Reverse gene lookup from SNP

I’ve exported my 23andme results, and the resulting spreadsheet contains only the rs# and genotype. I would also like an extra column that lists the genes that these particular SNP’s belong to where applicable.

I realize it’s easy to find rs#s given a gene, but how do you find a gene that an rs# belongs to, if indeed it does belong to a gene? Is there an automated way to do this? Thanks.

mass2

And:

Question: Is it possible to load export files from AncestryDNA into IGB?

See title. There’s not a lot more than that to say :) Thanks.

drmoose94

People are wanting help getting their consumer data into the tools. These are probably more advanced consumers, but more and more this will become an issue. And I hadn’t seen the tool providers doing support or outreach for that until I saw this answer from Nowlan at IGB.

One of the optional plug-ins for IGB converts raw 23andMe SNP data into a BED file for viewing. AncestryDNA data is quite similar to 23andMe data, so we could add a new plug-in to convert AncestryDNA as well.

I can imagine there’s some hesitation, lest people make some bad conclusions from some possible interpretations. But there’s also opportunity here to get people interested in genomics in new ways. But the level of support they need is very different. Their questions are coming, though. Just yesterday this was in the searches to this blog:

23andme_question

I’ve seen this kind of thing before, too, and I assume all genomics bloggers are seeing stuff like that. I keep thinking someone will do some kind of consumer browser, too, and I’m still not seeing that. I really think it’s time now. I continue to dream of genomics outreach that is like “extension” services that agricultural schools in the US have. Their mission is to roll out appropriate tech and info to the practitioners–farmers and the public. I wish the Precision Medicine initiatives had something like that. But I haven’t seen any talk of it.