1. Copyright OpenHelix. No use or reproduction without express written consent1

2. HapMap A resource of Human SNP and haplotype data Materials prepared by: Warren C. Lathe III, Ph.D www.openhelix.com Updated: Q2 2010 Version_4.0

3. Copyright OpenHelix. No use or reproduction without express written consent3 Agenda for HapMap Introduction and Credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap: http://www.hapmap.org

4. Copyright OpenHelix. No use or reproduction without express written consent4 HapMap Introduction http://www.hapmap.org Started in 2002 Variations in 270 people 4 populations Yoruba in Ibadan, Nigeria (abbreviation: YRI) Japanese in Tokyo, Japan (abbreviation: JPT) Han Chinese in Beijing, China (abbreviation: CHB) CEPH (Utah residents with ancestry from northern and western Europe) (abbreviation: CEU) Over 4 million unique genotyped SNPs

5. Copyright OpenHelix. No use or reproduction without express written consent5 HapMap Introduction www.hapmap.org/whatishapmap.html About the project Participant details Participating groups and funding agencies

6. Copyright OpenHelix. No use or reproduction without express written consent6 HapMap Credits http://www.hapmap.com/groups.html 24 institutions 6 countries 10 funding agencies

7. Copyright OpenHelix. No use or reproduction without express written consent7 HapMap Publications The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861. 2007. Publications The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320. 2005. Original Recent

8. Copyright OpenHelix. No use or reproduction without express written consent8 HapMap Introduction Project Information Data Useful links Data browser Bulk download

9. Copyright OpenHelix. No use or reproduction without express written consent9 Agenda for HapMap Introduction and credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap: http://www.hapmap.org

10. Copyright OpenHelix. No use or reproduction without express written consent10 HapMap Browser Start Type “clock” Choose data source Click search clock

11. Copyright OpenHelix. No use or reproduction without express written consent11 HapMap Browser Location LocationExamples

12. Copyright OpenHelix. No use or reproduction without express written consent12 Browser Search Type search term Select data set View & download Scroll & zoom

13. Copyright OpenHelix. No use or reproduction without express written consent13 Region Overview Overview of chromosome & statistics Yellow line is location viewed in details section Region of chromosome & statistics

14. Copyright OpenHelix. No use or reproduction without express written consent14 Details Variation details Gene structure

15. Copyright OpenHelix. No use or reproduction without express written consent15 Data Tracks Available Data types & annotation tracks to add to details view

16. Copyright OpenHelix. No use or reproduction without express written consent16 Display Settings Change image width Highlight settings Key and track positions

17. Copyright OpenHelix. No use or reproduction without express written consent17 Add Your Own Tracks Help

18. Copyright OpenHelix. No use or reproduction without express written consent18 Agenda for HapMap Introduction and credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap: http://www.hapmap.org

19. Copyright OpenHelix. No use or reproduction without express written consent19 Linkage Disequilibrium (LD) Plots, Example LD plots show linkage disequilibrium between two chromosomal segments

20. Copyright OpenHelix. No use or reproduction without express written consent20 Tag SNPs, Example AACACGCA…TTCGGGGTC…AGTCGACCG AACACGCA…TTCGAGGTC…AGTCAACCG AACATGCA…TTCGGGGTC…AGTCAACCG AACACGCA…TTCGGGGTC…AGTCGACCG Variable positions and alleles from individuals C T C A A A G C A C G G T T C A G G C A T T G A T T G A G C A A C A G T A A T A C C C G A T C T G T G A T A C T G G T G T C G A T T C T G C G G T T G A G A C A haplotype l haplotype 2 haplotype 3 haplotype 4 These variable positions are inherited together or linked: haplotypes A/G C/A/TC/G Some positions can be used to predict haplotype: tag SNPs G, T, C

21. Copyright OpenHelix. No use or reproduction without express written consent21 Location Help links Type in search term or location Choose data source Click search

22. Copyright OpenHelix. No use or reproduction without express written consent22 Overview & Details Overview of location & data details

23. Copyright OpenHelix. No use or reproduction without express written consent23 Adding & Configuring Annotation Reports & Analysis to add data to details Configure

24. Copyright OpenHelix. No use or reproduction without express written consent24 Adding & Configuring Annotation Click Configure Choose rsquare for LD property

25. Copyright OpenHelix. No use or reproduction without express written consent25 LD Plot in Details Section Linkage disequilibrium plot

26. Copyright OpenHelix. No use or reproduction without express written consent26 Zooming In: Add Detail Zooming in allows you to view more detailed data and information

27. Copyright OpenHelix. No use or reproduction without express written consent27 Zooming In: Add Detail SNPs reference sequences & alleles show up in zoomed view

28. Copyright OpenHelix. No use or reproduction without express written consent28 Zooming In Further: More Detail Zoom to 20kbp

29. Copyright OpenHelix. No use or reproduction without express written consent29 Further Zoom & Link Out Click gene Click SNP Zooming further shows more detailed information such as allele frequencies SNP “rs” reference number

30. Copyright OpenHelix. No use or reproduction without express written consent30 Configuring Tracks Configure tracks

31. Copyright OpenHelix. No use or reproduction without express written consent31 Adding Data with Tracks LD Plot added Update image Add 3-frames Add tag SNPs

32. Copyright OpenHelix. No use or reproduction without express written consent32 Added Tracks tag SNPs 3-frames

33. Copyright OpenHelix. No use or reproduction without express written consent33 Changing Tracks within Browser Window “?” Configuration menu Click track and drag Move track to new position

34. Copyright OpenHelix. No use or reproduction without express written consent34 Two Places to Add Analysis Add LD plot in tracks section Add tag SNPs in tracks section Add tag SNPs with Reports & Analysis menu Click Configure Add LD plot with Reports & Analysis menu

35. Copyright OpenHelix. No use or reproduction without express written consent35 Agenda for HapMap Introduction and credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap: http://www.hapmap.org

36. Copyright OpenHelix. No use or reproduction without express written consent36 HapMart Access HapMart

37. Copyright OpenHelix. No use or reproduction without express written consent37 HapMart Searches Three Steps: Start Filter Output

38. Copyright OpenHelix. No use or reproduction without express written consent38 Click next HapMap Start Choose schema/release Choose population dataset Choose data to search

39. Copyright OpenHelix. No use or reproduction without express written consent39 HapMart Filters “Start” choices appear on right side Filter data for specific requirements

40. Copyright OpenHelix. No use or reproduction without express written consent40 Selecting HapMart Filters Choose minor allele frequency Choose SNP type Choose chromosomal location Gene & ENCODE filters

41. Copyright OpenHelix. No use or reproduction without express written consent41 Selecting HapMart Filters Click next Choose another dataset

42. Copyright OpenHelix. No use or reproduction without express written consent42 HapMart Output Page “filter” choices appear on right side Choose data attributes

43. Copyright OpenHelix. No use or reproduction without express written consent43 HapMart Output SNP details Allele frequency Genotype Genotype frequency Genotype count Choose output format, file compression & saved location

44. Copyright OpenHelix. No use or reproduction without express written consent44 Output Options Output format Download to desktop or show in browser Compress file Click export

45. Copyright OpenHelix. No use or reproduction without express written consent45 HapMart Export

46. Copyright OpenHelix. No use or reproduction without express written consent46 Agenda for HapMap Introduction and credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap: http://www.hapmap.org

47. Copyright OpenHelix. No use or reproduction without express written consent47 HaploView Software Download Help & download

48. Copyright OpenHelix. No use or reproduction without express written consent48 HaploView Help & Download Download link

49. Copyright OpenHelix. No use or reproduction without express written consent49 HaploView Download Data Configure Download genotype data

50. Copyright OpenHelix. No use or reproduction without express written consent50 HaploView Data Download Click “Go” Choose population Open directly in Haploview or save to disk Choose strand

51. Copyright OpenHelix. No use or reproduction without express written consent51 Click Choose Format HaploView Data Views Upload file Set parameters Click dumped_region

52. Copyright OpenHelix. No use or reproduction without express written consent52 Viewing HaploView Uploaded Data Four types of analysis: LD, haplotypes, markers, tag SNPs

53. Copyright OpenHelix. No use or reproduction without express written consent53 Agenda for HapMap Introduction and credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap: http://www.hapmap.org

54. Copyright OpenHelix. No use or reproduction without express written consent54 HapMap Project and Tools

55. Copyright OpenHelix. No use or reproduction without express written consent55 Other Repositories GVS: http://gvs.gs.washington.org/GVS SeattleSNPs: http://pga.gs.washington.org Ensembl Genome Browser: http://www.ensembl.org UCSC Genome Browser: http://genome.ucsc.edu http://genome.ucsc.edu dbSNP http://www.ncbi.nlm.nih.gov/SNP/

56. Copyright OpenHelix. No use or reproduction without express written consent56 Additional Data to View SNPedia: http://www.snpedia.comhttp://www.snpedia.com MutaGeneSys: http://magnet.c2b2.columbia.edu/mutagenesys/ http://magnet.c2b2.columbia.edu/mutagenesys/ Load and view these data sets on the HapMap GBrowser http://snpedia.blogspot.com/ 2007/12/gbrowse-snpedia.html

57. Copyright OpenHelix. No use or reproduction without express written consent57 Agenda for HapMap Introduction and credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap: http://www.hapmap.org

58. Copyright OpenHelix. No use or reproduction without express written consent58