Bioinformatics

myKaryoView v2: Navigate Your Own Genome!


Following on the release of a Nature article on the rise of genome bloggers, in which Manuel Corpas’ Blog is linked, I would like to take this opportunity to announce the release of myKaryoView v2, an open source visualization software for personal genomics. Combining Rafael Jimenez’s and my own efforts, we have significantly augmented myKaryoView’s capabilities to allow users to visualize their personal genomes.

Visualization of one’s own personal genome is done via Bernat Gel’s easyDAS tool. This tool converts files with biological annotations into a DAS source. DAS sources can be thought of as tracks in a genome browser. The beauty of DAS is that it does not require any data to be stored locally and, as long as the reference coordinates are the same, any kind of biological features can be easily integrated.

Exploring My Own Genome With myKaryoView

23andMe analyses results report that I have a 28.1% risk of developing prostate cancer as opposed to a 17.8% average risk in males. This risk is calculated analysing the genotypes of 12 SNPs. The SNP marker rs10993994 shows the greatest risk among the 12 reported markers, a 1.3 increased odds. This SNP is located in 10q11, near the MSMB gene and the found allele (T) has been shown to affect its expression levels, decreasing its cancer suppressor function [1].

Having no history of prostate cancer in close relatives, I wanted to find more information about this SNP in order to confirm results. My whole genome profile, containing > 570,000 SNPs, was downloaded from 23andMe and a DAS source was created using easyDAS. The resulting data source was held privately in my newly created easyDAS account. Once easyDAS creates a new DAS source, the data is available through a URL. I pasted the URL for my genome data into the myKaryoView interface, selecting all accompanying tracks to be shown in its zoom view.

I typed the ‘MSMB’ gene myKaryoView’s query search box and once results were returned,  I zoomed out to have a better overview of my 10q11 chromosome region, shown below.

Visualization of MSMB region with myKaryoView

My genomic profile is the bottom track with SNPs in green. The top track in purple corresponds to genes involved in mendelian inheritance diseases (taken from OMIM), in red all existing genes, blue and green normal CNV regions and in yellow somatic mutations found in cancer (from the COSMIC database). I clicked on the gene and SNPs feature bars to find further information. Clicking on the MSMB gene feature, I found that this gene’s start position is 51219559, only 57 bp after the rs10993994 SNP position. The track with yellow features (COSMIC) also contained four reported mutations for MSMB (MSMB:ENST00000358559), indicative of the involvement of this gene in cancer, but all of them within the genes exons, i.e. not outside the gene. Following MSMB’s link to OMIM revealed also its implication in prostate cancer.

By seeing all these data sources in myKaryoView I feel more confident with the validity of 23andMe’s reported risk. It is true that all the sources visualized in myKaryoView can be found if searched for in the Internet. The merit of this tool is, I think, that it provides a one stop shop for a first step in analyzing original data sources for one’s personal genomic results.

About myKaryoView

myKaryoView is a web tool for visualization of genomic data specifically designed for direct-to-consumer genomic tests that uses publicly available data distributed throughout the Internet. It does not require data to be locally held and it is capable of rendering any feature as long as it conforms to a standard protocol named DAS. Configuration and addition of sources in myKaryoView can be done through the interface. myKaryoView should be considered a prototype and not a finalized tool. Here offer a proof of principle of myKaryoView’s ability to display personal genomics data with 23andMe genome data sources. Prior to publication, please acknowledge Rafael Jimenez and Manuel Corpas if using myKaryoView.

[1] Proc Natl Acad Sci U S A. 2009 May 12;106(19):7933-8. Epub 2009 Apr 21.

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