myKaryoView: a light-weight client for visualization of genomic data

Abstract

The Distributed Annotation System (DAS) is a protocol for easy sharing and integration of biological annotations. In order to visualize feature annotations in a genomic context a client is required. Here we present myKaryoView, a simple light-weight DAS tool for visualization of genomic annotation. myKaryoView has been specifically configured to help analyse data derived from personal genomics, although it can also be used as a generic genome browser visualization. Several well-known data sources are provided to facilitate comparison of known genes and normal variation regions. The navigation experience is enhanced by simultaneous rendering of different levels of detail across chromosomes. A simple interface is provided to allow searches for any SNP, gene or chromosomal region. User-defined DAS data sources may also be added when querying the system. We demonstrate myKaryoView capabilities for adding user-defined sources with a set of genetic profiles of family-related individuals downloaded directly from 23andMe. myKaryoView is a web tool for visualization of genomic data specifically designed for direct-to-consumer genomic data that uses publicly available data distributed throughout the Internet. It does not require data to be held locally and it is capable of rendering any feature as long as it conforms to DAS specifications. Configuration and addition of sources to myKaryoView can be done through the interface. Here we show a proof of principle of myKaryoView's ability to display personal genomics data with 23andMe genome data sources. The tool is available at: http://mykaryoview.com.

Figure 1. Searching myKaryoView by SNP.

The rs10993994 SNP was identified in a 23andMe report to contribute most to the disease risk of prostate cancer in a customer, implicated by the MSMB gene. In addition to the customer, 4 additional members of his family uploaded their genotypes into myKaryoView for elucidation of how this particular SNP genotype was inherited. Popup windows for the SNP are shown in this order: son, mother, father and sister. The Type Id field shows their genotype for this position in their genome, TT, CT, CT, CT respectively. The aunt (not shown) has a CC genotype for this position.

Figure 2. Chromosome Location Search.

Searching 15∶20000000,24000000 displays part of the 15q11 chromosomal band in zoom view. All listed DAS sources (gene names, genes involved in disease, cancer mutations and variable regions) were selected, choosing zoom and track visualisation options. The total number of features per track is shown next to the legend in parentheses. Forty five genes lie in selected intervals. Clicking on the ‘Genes Involved in Disease’ legend, a popup window appears providing links to the region in Ensembl and the original raw data that can be easily cut and pasted. The UBE3A gene bar is clicked and another popup window appears with links to further information. Variation 7051 reported by DGV is also clicked.