Bioinformatics

Personal Genomic Software: A Review of What Is Available


Readers may have seen that a few previous entries in Manuel Corpas’ Blog have been dedicated to myKaryoView, a personal genome visualization free software. In this post I review some of the software that is currently available for analysis of personal genomes. These are all free third party packages independent from providers such as 23andMe, Navigenics or deCODEme.

Andrew Scheidecker’s Personal Genome Explorer apparently is the first piece of software that was created for analysis of 23andMe personal data. This is a console application that allows 23andme data import, deCODEme data import, SNP database import from SNPedia, analysis of genome based on SNPedia metadata and random genome generation based on population frequency data.

I found that Personal Genome Explorer is a light-weight application that can be easily downloaded and installed. A lot of potential information can be extracted and browsed from a database based on SNPedia data. I tried to upload my own 23andMe chromosome 16 with file extention ‘.txt’ and unfortunately it did not recognize it or gave a clue as to what kind of extension it accepts.

Personal Genome Explorer showing randomly selected SNPs

SNPTips is a firefox plugin extension that allows customers of 23andMe to access their SNP genotype information. SNPTips allows one to hover the mouse cursor over the SNP id in any article text or webpage. Clicking on the SNP icon it creates, a pop up window appears with one’s genotype (i.e. the DNA letters found in your analysis) with links to SNPedia, Google Scholar and dbSNP. I tried to upload my 23andMe chromosome 16 and it worked quickly and neatly. Unfortunately it does not allow simultaneous visualization of more than one personal genome.

Enlis Genome is another tool that can be downloaded as a console. The interface is quite intuitive and it managed to upload my chromosome 16 SNPs in about a couple of minutes. The report it gave back was very neat. However it seemed to provide a very similar kind of information to what is already available to 23andMe customers. The main added value I could find in this tool was that it colated most information provided by a 23andMe’s customer report into a sort of document that can be easily handled. It was unfortunate though that the report concluded I was female. How it infers my gender when I only provided autosome data puzzles me slightly.

 

My results for Enlis Genome uploading my 23andMe chromosome 16.

myKaryoView is to my knowledge the only personal genomics tool that allows navigation and visualization of this genetic data directly as a genome browser. myKaryoView uses the DAS technology, which makes it capable of representing any available DAS source together with one’s genome, such as known genes, OMIM genes, normally variant regions, etc. Currently, adding one’s genome into a DAS source is a process that requires expert knowledge of another tool called easyDAS. Once the DAS source for one’s genome is created, the url where the DAS source genome is located can be added to myKaryoView for exploration via its interface. myKaryoView does not require any download for installation, as it is a web tool, and many personal genomes can be navigated at the same time.

myKaryoView showing my personal genome SNPs in green for a subregion of 10q11.23

The Perfect Tool

If I was able to pick the strengths of each of the reviewed softwares and put them together into one piece I would choose the richness of SNP information from the Personal Genome Explorer, the ease for uploading one’s genome from SNPTips, the reporting capabilities of Enlis Genome and the navigation and visualization capabilities of myKaryoView. Since all of these implementations are already available, the winner of this software “market” will be the one that combines all of these strengths in manner that is easily accessible to lay people. I think 23andMe has a lesson to teach in terms of making accessible to all of us the ability to analyze one’s genome and reporting the relevant information succintly.

Conclusion

Several tools are now available specifically tailored to the analysis and discovery of information related to one’s personal genome. Not a single tool is perfect and to some extent all require some computer and biology knowledge in order to properly operate and understand them. This is clearly not the ideal situation for lay people who are curious to know a bit more about their own personal genome. Certainly if all the strong points of each of the above were combined a much better tool and service to the community could be rendered. Personal genome coders: it’s time to join forces!

5 replies »

  1. Hi Manuel,

    Re: Enlis and gender –
    Obviously, one can not infer gender from only chromosome 16 data. The program was designed around the upload of a complete 23andMe data file. (It’s the lack of Y chromosome data that causes the program to suggest Female)

    As a personal genome browser geared toward consumers, we don’t expect that many will be uploading data from a single chromosome, but with that said it would make more sense to add an “undetermined” gender category.

    All the best,
    Devon

    Like

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s