1. GVS: Genome Variation Server Materials prepared by: Warren C. Lathe, PhD www.openhelix.com Updated: Q2 2010 Version 2

2. Copyright OpenHelix. No use or reproduction without express written consent2 GVS Agenda Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises Genome Variation Server: http://gvs.gs.washington.edu/GVS/

3. Copyright OpenHelix. No use or reproduction without express written consent3 Genome Variation Server at SeattleSNPs http://pga.gs.washington.edu/ The Genome Variation Server: a project of SeattleSNPs

4. Copyright OpenHelix. No use or reproduction without express written consent4 Access to Genome Variation Server http://pga.gs.washington.edu/ access GVS

5. Copyright OpenHelix. No use or reproduction without express written consent5 GVS Information Information about GVS and contact email http://gvs.gs.washington.edu/GVS/

6. Copyright OpenHelix. No use or reproduction without express written consent6 Four Steps to Results Choose Data Source (population) Set Parameters View Results Search Method

7. Copyright OpenHelix. No use or reproduction without express written consent7 GVS Agenda: Search Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises Genome Variation Server: http://gvs.gs.washington.edu/GVS/

8. Copyright OpenHelix. No use or reproduction without express written consent8 Search Strategies Search Entire Database Search Project Genes Upload Data

9. Copyright OpenHelix. No use or reproduction without express written consent9 Search: Chromosome Location Choose chromosome and specific location

10. Copyright OpenHelix. No use or reproduction without express written consent10 Search: Gene Name Gene name (HUGO) and upstream or downstream sequence if wanted

11. Copyright OpenHelix. No use or reproduction without express written consent11 Search: Gene ID Gene ID (NCBI) and upstream or downstream sequence if needed

12. Copyright OpenHelix. No use or reproduction without express written consent12 Search: Gene ID http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene Gene IDs at Entrez Gene site abo

13. Copyright OpenHelix. No use or reproduction without express written consent13 Search: rs ID rs ID (NCBI) and upstream or downstream sequence

14. Copyright OpenHelix. No use or reproduction without express written consent14 Search: rs ID http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp rs IDs found at Entrez SNP site

15. Copyright OpenHelix. No use or reproduction without express written consent15 Search: Browse Chromosomes Clicking gene symbol to open next steps Browse to location

16. Copyright OpenHelix. No use or reproduction without express written consent16 Search: PGA or EGP Genes Choose gene from menu, next steps are on the same page

17. Copyright OpenHelix. No use or reproduction without express written consent17 Search: Upload Own Data Upload your own data file

18. Copyright OpenHelix. No use or reproduction without express written consent18 Search: Upload Own Data File Format SeattleSNPs “prettybase” format: http://pga.gs.washington.edu/data_download.html Upload File

19. Copyright OpenHelix. No use or reproduction without express written consent19 Refining Search Link returns to search page to expand and refine search

20. Copyright OpenHelix. No use or reproduction without express written consent20 Changing Map Location Click icon to open interactive map of the region of your search Browse to new location, click gene symbol to modify search

21. Copyright OpenHelix. No use or reproduction without express written consent21 GVS Agenda: Populations Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises Genome Variation Server: http://gvs.gs.washington.edu/GVS/

22. Copyright OpenHelix. No use or reproduction without express written consent22 Choose Population Data Source Select population Data merging

23. Copyright OpenHelix. No use or reproduction without express written consent23 Choose Population: Links to Information Link to dbSNP population record Link to dbSNP submitter record

24. Copyright OpenHelix. No use or reproduction without express written consent24 GVS Agenda: Parameters Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises Genome Variation Server: http://gvs.gs.washington.edu/GVS/

25. Copyright OpenHelix. No use or reproduction without express written consent25 Parameters: Help Section Links to help section

26. Copyright OpenHelix. No use or reproduction without express written consent26 Parameters: Merge Populations Merge Population Samples MultiPop

27. Copyright OpenHelix. No use or reproduction without express written consent27 Parameters: Sorting Data Sort data by position or ID

28. Copyright OpenHelix. No use or reproduction without express written consent28 Parameters: Table or Text Display data in a variety of formats

29. Copyright OpenHelix. No use or reproduction without express written consent29 Parameters: SNP Filtering, Clustering, Colors FilterClusterTag SNPsPlot Color

30. Copyright OpenHelix. No use or reproduction without express written consent30 GVS Agenda: Analysis Results Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises Genome Variation Server: http://gvs.gs.washington.edu/GVS/

31. Copyright OpenHelix. No use or reproduction without express written consent31 Choose Display Results Four analysis choices to display Display

32. Copyright OpenHelix. No use or reproduction without express written consent32 Display Genotypes Parameters SNPs Individuals Data Color-coded SNP ID, population sample & alleles Table Graphical

33. Copyright OpenHelix. No use or reproduction without express written consent33 Display Tag SNPs Parameters Data SNPs clustered by r-squared LD values Individuals SNPs bin

34. Copyright OpenHelix. No use or reproduction without express written consent34 Display Linkage Disequilibrium Parameters Data R-squared values for all pairs of SNPs LD Plot

35. Copyright OpenHelix. No use or reproduction without express written consent35 Display SNPs Summary Summary of SNP data Link to dbSNP Link to UCSC Genome Browser Add data columns Interactive Map Column Descriptions

36. Copyright OpenHelix. No use or reproduction without express written consent36 GVS Agenda: Merging Populations Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises Genome Variation Server: http://gvs.gs.washington.edu/GVS/

37. Copyright OpenHelix. No use or reproduction without express written consent37 Merging Populations & Tag SNPs: Example Click gene name http://gvs.gs.washington.edu/GVS/ Click Search “Determine tag SNPs for genotyping variations with a minor allele frequency of greater than 20% in the ABO gene for both the PGA European & PGA African populations.”

38. Copyright OpenHelix. No use or reproduction without express written consent38 Choosing Two Populations Data Sets

39. Copyright OpenHelix. No use or reproduction without express written consent39 Merging Populations Display Tag SNPs

40. Copyright OpenHelix. No use or reproduction without express written consent40 TagSNPs Results (Multiple Populations) Open Table

41. Copyright OpenHelix. No use or reproduction without express written consent41 Population 1 Tag SNPs Open Table

42. Copyright OpenHelix. No use or reproduction without express written consent42 Population 2 Tag SNPs Open Table

43. Copyright OpenHelix. No use or reproduction without express written consent43 Graphic Display of Population 1 Tag SNPs Open Graphic

44. Copyright OpenHelix. No use or reproduction without express written consent44 Merging Option A Error: No Common Individuals Display Tag SNPs

45. Copyright OpenHelix. No use or reproduction without express written consent45 Populations with Common Individuals

46. Copyright OpenHelix. No use or reproduction without express written consent46 Merging Option: Common Individuals Display Tag SNPs

47. Copyright OpenHelix. No use or reproduction without express written consent47 Results: Tag SNPs Open Table

48. Copyright OpenHelix. No use or reproduction without express written consent48 GVS Agenda: Summary Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises Genome Variation Server: http://gvs.gs.washington.edu/GVS/

49. Copyright OpenHelix. No use or reproduction without express written consent49 Genome Variation Server http://pga.gs.washington.edu/ The Genome Variation Server is a project of SeattleSNPs access GVS

50. Copyright OpenHelix. No use or reproduction without express written consent50 Eight Search Possibilities

51. Copyright OpenHelix. No use or reproduction without express written consent51 Several Data Sources to Choose Select population

52. Copyright OpenHelix. No use or reproduction without express written consent52 Limit and Refine Results Filter Cluster Tag SNPs Plot Color Output Merge

53. Copyright OpenHelix. No use or reproduction without express written consent53 Analysis Display

54. Copyright OpenHelix. No use or reproduction without express written consent54 Genome Variation Server

55. Copyright OpenHelix. No use or reproduction without express written consent55 GVS Agenda: Summary Introduction Search (step 1) Populations (step 2) Parameters (step 3) Analysis Results (step 4) Example: Merging Populations Summary Exercises Genome Variation Server: http://gvs.gs.washington.edu/GVS/

56. Copyright OpenHelix. No use or reproduction without express written consent56