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.
Highlights
Advances in genome sequencing and screening technologies are producing genomic data at an unprecedented scale
In order to extract any meaning from genetic profiles containing single nucleotide polymorphisms (SNPs), copy number variations (CNVs) or specific genomic variants, raw genome data should be analysed in the context of other genes and annotations
Of particular relevance are resources such as HGNC [1] that gives unique and coherent nomenclature for genes, which can be mapped to specific genome coordinates, the On-line Mendelian Inheritance in Man (OMIM) database [2] that characterises genes and syndromes involved in diseases inherited in a Mendelian fashion, the Database of Genomic Variants [3] that collects mostly CNVs reported in normal individuals, or the Database of Somatic Mutations in Cancer (COSMIC) [4]
Summary
Advances in genome sequencing and screening technologies are producing genomic data at an unprecedented scale. Of particular relevance are resources such as HGNC [1] that gives unique and coherent nomenclature for genes, which can be mapped to specific genome coordinates, the On-line Mendelian Inheritance in Man (OMIM) database [2] that characterises genes and syndromes involved in diseases inherited in a Mendelian fashion, the Database of Genomic Variants [3] that collects mostly CNVs reported in normal individuals, or the Database of Somatic Mutations in Cancer (COSMIC) [4] These resources may prove useful when determining the potential genetic origin of specific traits in the person. This process of retrieval of data has to be periodically repeated to make sure that the retrieved information is up-to-date
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