Updated 10/28/2007 Software to download prior to using HapMap Java- Haploview-

Transcription

1 Updated 10/28/2007 Software to download prior to using HapMap Java- Haploview- Use of HapMap: Find HapMap SNPs near a gene or region of interest (ROI). View patterns of LD in the ROI. Select tag SNPs in the ROI. Download information on the SNPs in ROI for use in Haploview. Generate customized extracts of the entire data set. Download the entire data set in bulk. 1) Got to Website: 2) Select [HapMap Genome Browser- full data set]

2 3) Enter gene in [Landmark Region] box (Hint: Able to search for a gene name, chromosome band or receptor name), then click [Search] [Data Source]: Able to select a different data release. The current release is the default. [Scroll/Zoom]: Able to expand to 20 or 40Kbp to include 5 and 3 promoter and UTR

3 4) [Overview]: Shows chromosome wide summary data [Region]: Shows the region on the DNA and can show copy number variation [Details]: Default tracks show HapMap, Genotyped SNPs, named genes from Entrez genes, and alternative mrna splicing patterns

4 5) Under [Reports and Analysis] window, select [Download SNP Genotype data] and click [Configure].

5 6) Select which population (CEU, CHB, JPT, YRI, JPT + CHB), rs and save to disk and select go and [Save] to computer.

6 7) Open program Haploview: 8) Load HapMap Data 9) Open file you saved from the HapMap 10) Check Markers for MAF (minor allele Frequency) Browsing Linkage Disequilibrium. These markers have passed the default cutoffs. The cutoffs can be adjusted on this page and individual markers can be added or removed to the subsequent analysis by clicking the checkboxes in the "Rating" column. All of the other analyses are carried out only on those markers checked on this pane.

7 11) Linkage Disequilibrium (LD) Plot- The LD display allows you to examine your data in a number of ways. Detailed LD statistics for any comparison can be brought up by right-clicking on any box. Right clicking on a marker number shows its name and minor allele frequency. You can zoom in and out using the zoom option in the Display menu (especially helpful for big datasets). Large datasets also show a mini-map in the lower left corner which is helpful for navigating. The color scheme and marker spacing for the LD display can be adjusted in the "Display" menu. A key for the color schemes is at the far right of the menu bar. LD Display ( Perusing the LD Display The color scheme option (Display menu) allows you to choose among several LD color schemes. The following tables provide details on the color schemes, and a key to the meaning of the currently selected scheme can be dropped down from the "Key" menu in the upper right corner of the screen. Table 1.1. Standard Color Scheme

8 D' < 1 D' = 1 LOD < 2 white blue LOD 2 shades of pink/red bright red Table 1.2. Confidence Bounds Color Scheme Strong Evidence of LD Uninformative Strong Evidence of Recombination dark grey light grey white Table 1.3. r 2 Color Scheme r 2 = 0 white 0 < r 2 < 1 shades of grey r 2 = 1 black Table 1.4. Alternate D'/LOD Color Scheme Low D' High D' Low LOD white shades of pink High LOD white black (r 2 and Alt D'/LOD courtesy of Will Fitzhugh) Table Gamete Color Scheme 4 distinct 2-marker haplotypes white < 4 distinct 2-marker haplotypes black In order to help keep the display uncluttered, D prime values of 1.0 are never shown (the box is empty). These values can be switched on or off with the "Show LD values" option in the Display menu. The zoom option (Display menu) allows you to select one of three zoom modes. The two zoomed out versions can be useful for browsing large datasets. Large datasets also show a "map" in the lower left corner which gives an overview of the D prime display and allows you to navigate quickly. Clicking on an area of the map will cause the main display to jump to that area. This map also shows the currently defined blocks as small black lines across the top. Markers with additional notes (as loaded from the info file) are highlighted (the names are green in the zoomed-in view and the lines from the SNP position to the

9 LD chart are green in the zoomed-out view. Details can be viewed by right clicking on the marker number (as mentioned below). Right clicking on the marker number (or the equivalent space in the zoomed out views) shows the marker name, minor allele frequency and any additional notes specified in the info file. This can be especially helpful in the zoomed out views which do not display marker names. The last such piece of popup information clicked will be shown at the top of the LD plot. This reminder can be dismissed by left clicking anywhere on the LD plot. Right clicking on any pairwise LD comparison will show a more detailed summary of the LD between the two markers in question. This information is also shown at the top of the screen as described above and can be dismissed by left clicking anywhere on the LD plot. Use Chi Squared Distribution: 1) Go to website: 2) X= chi Sq Value say ) Df=1 4) Billelic SNPs 5) If < 0.05, then Not in HWE 6) If > 0.05, OK in HWE