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

2. HapMap Phase II Dataset Release #21a, January 2007 (NCBI build 35) 3.8 M genotyped SNPs => 1 SNP/700 bp International HapMap Consortium (2007). Nature 449:851-861 # polymorphic SNPs/kb in consensus dataset

3. Goals of This Tutorial 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 –Add custom tracks of association data –Create publication-quality images Generate customized extracts of the entire data set Download the entire data set in bulk This tutorial will show you how to:

4. Finding HapMap SNPs in a Region of Interest Find the TCF7L2 gene Identify the characterized SNPs in the region View the patterns of LD (NCBI b35) Pick tag SNPs (NCBI b35) Download the region in Haploview format Upload your own annotations & superimpose on the HapMap Make a customized image for publication View GWA hits & OMIM annotations in the region (NCBI b36)

5. HapMap Glossary LD (linkage disequilibrium): For a pair of SNP alleles, it’s a measure of d eviation from random association (which assumes no recombination). Measured by D’, r 2, LOD Phased haplotypes: Estimated distribution of SNP alleles. Alleles transmitted from Mom are in same chromosome haplotype, while Dad’s form the paternal haplotype. Tag SNPs: Minimum SNP set to identify a haplotype. r 2 = 1 indicates SNPs are redundant, so either one “tags” the other. Questions?help@hapmap.org

6. 1: Surf to the HapMap Browser 1a. Go to www.hapmap.org 1b. Select “HapMap Genome Browser B35” ncbi B35: full dataset (includes LD patterns) ncbi B36: latest, new tracks (e.g., GWA hits)

7. 2: Search for TCF7L2 2. Type search term – “ TCF7L2 ” Search for a gene name, a chromosome band, or a phrase like “insulin receptor”

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

9. 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

10. 4: Turn on LD & Haplotype Tracks 4b: Press “Update Image” 4a: Scroll down to the “Tracks” section. Turn on the LD Plot and Haplotype Display tracks. These sections allow you to adjust the display and to superimpose your own data on the HapMap

11. 5: View variation patterns Triangle plot shows LD values using r 2 or D’/LOD scores in one or more HapMap population Phased haplotype track shows all 120 chromosomes with alleles colored yellow and blue

12. 7: Adjust Track Settings (on the spot) 7b. Adjust population and display settings & press “Configure” 7a. Click on question mark preceding track name

13. 7: Adjust Track Settings (cont) Select the analysis track to adjust and press “Configure”

14. 8: Turn on Tag SNP Track 8: Activate the “tag SNP Picker” and press “Update Image”

15. 9: Adjust tag SNP picker Tag SNPs are selected on the fly as you navigate around the genome 9a: Click on question mark behind “tag SNP Picker” Alternatively, you may select “Annotate tag SNP Picker” and press “Configure…”

16. 9: Adjust tag SNP picker (cont) Select population Select tagging algorithm and parameters [optional] upload list of SNPs to be included, excluded, or design scores 9b: Press “Configure” to save changes

17. 10: Generate Reports 10: Select the desired “Download” option and press “Go” or “Configure” Available Downloads: Individual Genotypes Population Allele & Genotype frequencies Pairwise LD values Tag SNPs

18. 10: Generate Reports (cont) The Genotype download format can be saved to disk or loaded directly into Haploview

19. 10: Generate Reports (cont) The tag SNP download is the same as you get from TAGGER …

20. 11: Create your own tracks 11: 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

21. 11: 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. Formatted data for the T2DM association results (score is -LOG10 of p-value)

22. 11: Create your own tracks (cont)

23. Make edits on your own browser window by clicking on “Edit File…” 11: Create your own tracks (cont)

25. 12: Create Image for Publication 12a. 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.

26. Can view file in Firefox, but use other programs (Adobe Illustrator or Inkscape) to convert to other formats and/or edit 12b. Click on “View SVG Image in new browser window” 12c. Save generate file with “.svg” extensions 12: Image for Publication (cont)

27. Inskape is free and lets you edit and convert to other formats (many journals prefer EPS) 12: Image for Publication (cont)

28. 13: View GWA hits 13a. Go to www.hapmap.org 13b. Select “HapMap Genome Browser B36”

29. 13: View GWA hits (cont) 13c. Type search term - “FTO” Default tracks for B36 include GWA hits, OMIM predicted associations, and Reactome pathways

30. 14: Read PubMed abstracts for GWA hits 14a: Mouse over a GWA hit to learn more about the association 14b: Click on the GWA hit to see the study’s PubMed abstract

31. Use HapMart to Generate Extracts of the HapMap Dataset Find all HapMap characterized SNPs that: 1.Have a MAF > 0.20 in the Yoruban population panel (YRI) 2.Cause a nonsynonymous amino acid change

32. 1. Go to hapmart.hapmap.org 1. From www.hapmap.org click on “HapMart”www.hapmap.org

33. 2. Select data source and population of interest 2a. Choose Yoruba population or “All Populations” 2b. Press “Next” Use schema menu to select dataset

34. 3. Select the desired filters 3a. Check “Allele Frequency Filter” and select MAF >= 0.2 3b. Select “SNPs found in Exons – non synonymous coding SNPs” 3c. Press “Next”

35. 4. Select output fields 4b. Select the fields to include in the report. 4c. Press “Export” The summary shows active filters and # SNPs to be output Options at the bottom let you select text or Excel format 4a. Choose among several pages of fields

36. 5. Download report

37. Bulk downloads: Download the Complete Data Download the entire HapMap data set to your own computer

38. 1.Surf to www.hapmap.orgwww.hapmap.org 1. From www.hapmap.org, click on “Bulk Data Download”www.hapmap.org Or directly click on “Data”

39. 2. Choose the Data Type Raw genotypes & frequencies Analytic results HapMap Samples Protocols & assay design Your own copy of the HapMap Browser 2. Select “Genotypes” * Data also available via FTP ftp://www.hapmap.org

40. 3. Choose the dataset of interest Available Genotype Datasets: Non-redundant: QC+ filtered & redundant data removed Filtered-redundant: QC+ filtered; duplicated data not removed Unfiltered-redundant: Includes assays that failed QC 3. Select latest build, fwd_strand orientation, and “non-redundant” fwd_strand => same as NCBI reference assembly rs_strand => same as in dbSNP

41. 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

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