1. Resources at HapMap.Org HapMap3 Tutorial Marcela K. Tello-Ruiz Cold Spring Harbor Laboratory

2. HapMap Project Phase 1Phase 2Phase 3 Samples & POP panels 269 samples (4 panels) 270 samples (4 panels) 1,115 samples (11 panels) Genotyping centers HapMap International Consortium PerlegenBroad & Sanger Unique QC+ SNPs 1.1 M3.8 M (phase I+II) 1.6 M (Affy 6.0 & Illumina 1M) ReferenceNature (2005) 437:p1299 Nature (2007) 449:p851 Draft Rel. 1 (May 2008)

3. Phase 3 Samples * Population is made of family trios

4. Phase 3 11 panels & 1,115 samples –558/557 males/females –924/191 founders/non-founders Platforms: –Illumina Human 1M (Sanger) –Affymetrix SNP 6.0 (Broad) EXCLUDED from QC+ data set: –Samples with low completeness, and SNPs with low call rate in each pop (< 80%) and not in HWE (p < 0.001) –Overall false positive rate: ~ 3.2% Data merged with PLINK (concordance over 249,889 overlapping SNPs = 0.9931) Alleles on the (+/fwd) strand of NCBI b36

5. Phase 3: Draft Release 1 samplesQC+ SNPspoly QC+ SNPs 71 ASW1,632,1861,536,247 162 CEU1,634,0201,403,896 82 CHB1,637,6721,311,113 70 CHD1,619,2031,270,600 83 GIH1,631,0601,391,578 82 JPT1,637,6101,272,736 83 LWK1,631,6881,507,520 71 MEX1,614,8921,430,334 171 MKK1,621,4271,525,239 77 TSI1,629,9571,393,925 163 YRI1,634,6661,484,416

6. Goals of This Tutorial Find HapMap3 SNPs near a gene or region of interest (ROI) –Visualize allele frequencies in HapMap3 populations –Download SNP genotypes in ROI for use in Haploview 4.1 –Identify GWA hits in the vicinity of ROI & visualize in the context of all chromosomes (karyogram) –Add custom data onto the GWAs karyogram –Add custom tracks of association data onto ROI –Create publication-quality images (these are optional, and ghow advanced features This tutorial will show you how to:

7. 1: Surf to the HapMap Browser 1b. Select “ HapMap phase 3 ” 1a. Go to www.hapmap.org

8. 2: Search for TCF7L2 2. Type search term – “ TCF7L2 ” Search for a gene name, a chromosome band, or a phrase like “ insulin receptor ”

9. 3: Examine Region Region view puts your ROI in genomic context Chromosome-wide summary data is shown in overview Default tracks show HapMap genotyped SNPs, refGenes with exon/intron splicing patterns, etc. 3: This exonic region has many typed SNPs. Click on ruler to re-center image.

10. 3: Examine Region (cont) As you zoom in further, the display changes to include more detail Use the Scroll/Zoom buttons and menu to change position & magnification 3: Mouse over a SNP to see allele frequency table Click to go to SNP details page

11. 4: Generate Text Reports 4: Select the desired “ Download ” option and press “ Go ” or “ Configure ” Available phase 3 downloads: - Individual genotypes - Population allele & genotype frequencies

12. 4: Generate Reports (cont) The Genotype download format can be saved to disk or loaded directly into Haploview v4.1

13. 5: Find GWA hits 5a: Scroll down to turn on GWA studies tracks in overview & region panels 5b: Find GWA hits in nearby region. Click on a GWA hit to re-center

14. 5: Find GWA hits (cont) 5c: Mouse over & click on GWA hit for more info

15. 6: Examine GWA hits in entire genome 6: From www.hapmap.org, select “ Karyogram ”www.hapmap.org

16. 6: Custom GWA hits in karyogram Detailed help on the format is under the “Help” link 6: Follow these instructions to upload your own GWA data

17. 7: Create your own tracks 7: Upload example file: TCF7L2_annotations.txt Example: Interested in T2DM genetics Create file with custom annotations from http://www.broad.mit.edu/diabetes and superimpose on the HapMap Detailed help on the format is under the “Help” link

18. 7: Create your own tracks (cont) Save as a text file! Some SNPs were typed (known platform) and others were imputed. Format data for both typed & imputed SNPs. Scores allow you to display data in quantitative form, such as XY plots

19. 7: Create your own tracks (cont) Remember to point your browser to the location of your annotations (TCF7L2 gene in this case).

20. Make edits on your own browser window by clicking on “Edit File…” 7: Create your own tracks (cont)

22. 8: Create Image for Publication 8a. Click on “ High-res Image ” Click on the +/- sign to hide/show a section Mouse over a track until a cross appears. Click on track name to drag track up or down.

23. Can view file in Firefox, but use other programs (Adobe Illustrator or Inkscape) to convert to other formats and/or edit 8b. Click on “View SVG Image in new browser window” 8c. Save generated file with “.svg” extensions 8: Image for Publication (cont)

24. Inkscape is free and lets you edit and convert to other formats (many journals prefer EPS) 8: Image for Publication (cont)

25. Further Information HapMap Publications & Guidelines http://hapmap.cshl.org/publications.html.en Past tutorials & user’s guide to HapMap.org http://www.hapmap.org/tutorials.html.en Questions? help@hapmap.org

26. HapMap DCC Present Members (CSHL) Lincoln Stein Marcela K. Tello-Ruiz Zhenyuan Lu Wei Zhao HapMap DCC Former Members Lalitha Krishnan Albert Vernon Smith Gudmundur Thorisson Fiona Cunningham