Is there a "consumer" level genome browser?

Question

[Mary]

At the #BioITWorld14 conference last week, this question came up a couple of times. Here it was during John Quackenbush's talk:

"...can you suggest a genome browser that would be good for a consumer?"

Q from the overflow room: can you suggest a genome browser that would be good for a consumer? JQ: No. #BioIT14

— Bio-IT World (@bioitworld) April 29, 2014

A few years back I test drove the Enlis browser (http://www.enlis.com/) and I thought that was a nice one for people who might be new to 23andme data. But that looks to have changed to a more heavy-lifting direction now.

Have you seen a good browser for non-biologist end users? What would you recommend?

[Istvan Albert]

The problem here is with the definition of "consumer level" - and if the definition that one might come up with today would still apply next year.

[Mary]

I talked to the guy who asked that question later. What he does is provide sequence to people who want the data, but he does not want to be responsible for annotations (because FDA). So he is looking for a way for people new to the data to look around, but not overwhelm them with research-type tracks.

[Malachi Griffith]

I suppose that is aim of Illumina's MyGenome App for the iPad. I don't have an iPad and have only played around with it briefly.

Answer 1

[Mary]

In a funny coincidence, as soon as I put up this post, this paper came out. I haven't kicked the tires of this yet, but there is now a tool called The Personal Genome Browser.

The personal genome browser: visualizing functions of genetic variants (paper)

http://www.pgbrowser.org/

[Charles Warden]

The input has to be a .vcf or .gvf file, so one potential limitation is that it won't work with the raw 23andMe data.

Answer 2

[Charles Warden]

As most Biostar readers probably already know, there are some tools for annotations. However, I don't really know of a true browser. Of course, I don't think anything provides the background education like the original 23andMe report, but there are options to connect people to the scientific literature. So, these are what I would probably consider to be the closest option:

1. Promethease / SNPedia (uses raw DTC data format)

   • https://promethease.com
   • https://promethease.com/ondemandlicense

   Blog post describing application to my own data: http://cdwscience.blogspot.com/2011/02/my-23andme-results-getting-free-second.html

2. Interpretome (uses raw 23andMe data format)

   • http://esquilax.stanford.edu/
   • Includes "Lookup" option, which I guess is kind of like a very simple genome browser (although I think even new 23andMe customers can use the "Browse Raw Data" option to look up their genotype at any assayed location based upon position or gene name)

3. Research Databases / General Annotation Tools (requires some reformatting)

   At least for 23andMe, you'll probably have to reformat your data a bit before using popular annotation tools (ANNOVAR, SeattleSNP, Variant Effect Predictor, etc). If the user is at least somewhat comfortable with computers (in order to run things via command line), I've written some scripts to try and make this a tad bit easier (using SeattleSNP and the flat file from the GWAS Catalog):

   Perl scripts for 23andMe data: http://cdwscience.blogspot.com/2012/06/my-23andme-results-getting-free-second.html

   Modification for AncestryDNA data: http://cdwscience.blogspot.com/2013/12/additional-analysis-of-ancestrydna-data.html

[Mary]

Hmm. My first comment to this vanished. I must have hit cancel by accident.

Anyway--I was saying that the great thing about the Enlis browser was that you could just upload your 23andme data really quickly. There was a lightweight but graphically attractive chromosomal browsing aspect. It had annotations for genes, and links to decent sources like OMIM and Genetics Home Reference. I think there was some literature component too. You could also look at your SNPs, and I think you could make little notes to yourself somehow.

The goal is to not require reformatting, scripting, or assuming too much background in genetics.

Seems to me there's a nice niche for this. Maybe it would be a nice student project for someone's course.

Answer 3

[devonEnlis]

Enlis Genome Personal has returned and is available here: https://www.enlis.com/personal_edition.html

Ability to import 23andMe, Ancestry.com, FTDNA.com, VCF, and Complete Genomics

It's definitely more of a premium option compared to other interpretation services, but there is a lot more you can do with it too.