Finding genes associated with a specific SNP using the Genome Browser

Off-the-shelf Infinium Human arrays such as the Omni and CytoSNP arrays have a beadchip type-specific Gene Annotation file associated with them, which can be downloaded from the Illumina website, to help identify genes associated with the SNP probes on the arrays. However, for custom Infinium arrays, Illumina does not provide gene annotation files.

In order to identify what genes the SNP on these chips are associated with, the user can utilize the GenomeStudio GenomeViewer in chromosome browser mode. GenomeViewer displays genomic annotations below the graphic representation of the chromosome. Since the SNP entry in the GenomeStudio project is hotlinked to the Genomeviewer, the user can select any SNP of interest, jump to the GenomeViewer from the SNP entry and view the genomic annotations (ie, genes) associated with the SNP. The all important caveat is that the GenomeViewer must be configured to display the gene annotations based on the same genome build as the the genome build of the manifest which was used to create the GenomeStudio project.

1. Confirm which genome build the manifest is based on. Open the .csv version of the manifest for the array, and refer to the column GenomeBuild, to see which genome build the annotations (Chr and MapInfo column which lists the genome coordinate of the SNPs) in the manifest are based on.

1. Check which genome build is currently active in the Genome Viewer. In order to do this, GenomeStudio must have a project open and active.

Under the Tools menu select Show Genome Viewer

a. Select samples and subcolumns (B Allele Freq and Log R Ratio) of interest, select Add to favorite button, then select OK.

b. To confirm the active genome in chromosome browser, in the Genome Viewer window, under the Edit menu select Preferences...

c. The currently active genome, as well as the default genome at startup, will be displayed in the Preferences window

d. If the Active Genome matches the genome referred to in the manifest, the SNP coordinates should match the active genome, and select Cancel and continue. If the active genome does not match, select the options in the drop-down menus for species and build so that they match the manifest genome. If the needed options for genome do not appear in the menus, consult the GenomeStudio 2008.1 Framework User Guide for instructions on downloading and installing genomes, under the section "Getting Data Files" on page 113.

1. In order to obtain gene information for a particular SNP, first, change the view in Genome Viewer to Chromosome Browser by selecting View=>Chromosome Browser.

** **

1. The view changes, so that there is a window containing the samples and subcolumns in graphical form, with a representation of the chromosome, and below, diagrams of the genes in the region, as well as several tabs with information about any selected gene in the view.

1. Next, switch to the GenomeStudio main window, and in either the SNP Table or Full Data Table, select a SNP of interest and right click on it. In the pop-up menu, select "Jump to IGV" (note - IGV = Illumina Genome Viewer).

1. The active window will immediately switch to the GenomeViewer, and the SNP of interest will appear zoomed in and centered in the Chromosome Browser. Select the zoom out button to gain a wider context; the SNP will stay centered.

1. Note that any genes that are located at the SNP will appear in the pane below. Select the graphic representation of a gene, and it will turn red; information regarding the selected gene will appear in the tabs below.

1. Note that the RefSeq ID is a hot link and selecting it will open up a browser window to the NCBI website associated with that accession number.

Note that any information obtained by this method may be subject to change, and should be confirmed by alternate investigation.

For any feedback or questions regarding this article (Illumina Knowledge Article #3503), contact Illumina Technical Support [email protected].