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

2. dbGaP The Database of Genotypes and Phenotypes Materials prepared by: Cynthia Perreault-Micale, Ph.D. Dorothy S. Reilly, Ph.D. www.openhelix.com Updated: Q4 2010 Version 2

3. Copyright OpenHelix. No use or reproduction without express written consent3 NCBI dbGaP Agenda Introduction & Credits Basic Searching & Browsing Report Types Analysis Reports Advanced Searching Summary Exercises dbGaP: www.ncbi.nlm.nih.gov/gapwww.ncbi.nlm.nih.gov/gap

4. http://www.ncbi.nlm.nih.gov/gap Copyright OpenHelix. No use or reproduction without express written consent4 Many Contribute dbGaP Studies Launched Dec. 2006 Major contributors include: National Eye Institute’s Age Related Eye Disease Study, The Genetic Association Information Network (GAIN), & many more!

5. Copyright OpenHelix. No use or reproduction without express written consent5 Data Content & Organization Many types of studies are included 2 types of access - open & controlled Open access: studies, documents, variables, analyses Controlled access: de- identified phenotypes & genotypes for individual study subjects Specific authorization process for controlled access requests

6. Copyright OpenHelix. No use or reproduction without express written consent6 Multiple Data Types - Stable Identifiers phs = Studies phd = study Documents phv = phenotypic Variables pha = genotype-phenotype Analyses pht = dataseTs Study number phs000007.v1.p1 “v” data version “p” participant set version Unique identifiers assigned These numbers increase when data changes

7. Copyright OpenHelix. No use or reproduction without express written consent7 Citing a Study in dbGaP BMC Medical Genetics 8:S7, 2007 http://www.pubmedcentral.nih.gov/ articlerender.fcgi?tool=pubmed&pu bmedid=17903306 URL with unique study ID number

8. Copyright OpenHelix. No use or reproduction without express written consent8 dbGaP Homepage Resources http://www.ncbi.nlm.nih.gov/gap Important Links Getting Started Access to dbGaP Data Tutorial, Overview, FAQs & Submission instructions Apply for Controlled Access, FTP site, Browse Studies RSS Feed, Conduct Codes, Security Procedures & Contact Us Start Searches & Help

9. Copyright OpenHelix. No use or reproduction without express written consent9 dbGaP Homepage Additional Resources List of Latest Studies Getting Started Contact Categorized list of NCBI resources Popular resources Featured resources NCBI information Additional access Genetics & Medicine

10. Copyright OpenHelix. No use or reproduction without express written consent10 NCBI Homepage - The Interlinked Entrez Network http://www.ncbi.nlm.nih.gov dbGaP All Databases dbGaP results An Entrez Global Query - results in all databases

11. Copyright OpenHelix. No use or reproduction without express written consent11 Results Utilize Many Handy Entrez Features Many helpful tools & links Search box & menu Display Settings Categorized results For more information about Entrez search functions: OpenHelix Entrez Overview tutorial (www.openhelix.com)www.openhelix.com NCBI Entrez documentation (http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpentrez&part=EntrezHelp; http://www.ncbi.nlm.nih.gov/Entrez/tutor.html) http://www.ncbi.nlm.nih.gov/Entrez/tutor.html

12. Copyright OpenHelix. No use or reproduction without express written consent12 dbGaP Credits Nature Genetics 39:1181, 2007 http://www.nature.com/ng/journal/v39/n10/full/ng1007-1181.html Nature Genetics 39:1045, 2007 http://www.nature.com/ng/journal/v39/n9/full/ng2127.html Many additional sources of information Click FAQ link on homepage

13. Copyright OpenHelix. No use or reproduction without express written consent13 NCBI dbGaP Agenda Introduction & Credits Basic Searching & Browsing Report Types Analysis Reports Advanced Searching Summary Exercises dbGaP: www.ncbi.nlm.nih.gov/gapwww.ncbi.nlm.nih.gov/gap

14. Copyright OpenHelix. No use or reproduction without express written consent14 Accessing Studies from dbGaP Homepage http://www.ncbi.nlm.nih.gov/gap List All Studies Browse All Studies

15. Copyright OpenHelix. No use or reproduction without express written consent15 Browsing Studies from dbGaP Homepage Result tabs Choose how many items per page Click to return to homepage Next page of results Click Apply

16. Copyright OpenHelix. No use or reproduction without express written consent16 Browsing Studies - Study Information Colored icons indicate Variable, Document & Analysis Reports available

17. Copyright OpenHelix. No use or reproduction without express written consent17 Browsing Studies - More Study Information Many types of studies A variety of study types: Exome Sequencing, Family, Single Patient, Longitudinal, and more. Parent-Offspring trios: Data are collected from parent- parent-offspring sets. Case-Control Studies: Identify individuals with a disease of interest and a control group without the disease. The frequency or levels of an attribute [eg, specific genotype] are compared between these groups.

18. Copyright OpenHelix. No use or reproduction without express written consent18 Browsing Studies - Right Side Options Filters inactive Find related data Recent activity Handy Links

19. Copyright OpenHelix. No use or reproduction without express written consent19 Browsing Other Record Types

20. http://www.ncbi.nlm.nih.gov/gap Copyright OpenHelix. No use or reproduction without express written consent20 Basic Searching from Homepage prostate cancer Our basic search example: prostate cancer

21. Copyright OpenHelix. No use or reproduction without express written consent21 Basic Search Results Number of results & access by record type Search term

22. Copyright OpenHelix. No use or reproduction without express written consent22 NCBI dbGaP Agenda Introduction & Credits Basic Searching & Browsing Report Types Analysis Reports Advanced Searching Summary Exercises dbGaP: www.ncbi.nlm.nih.gov/gapwww.ncbi.nlm.nih.gov/gap

23. Copyright OpenHelix. No use or reproduction without express written consent23 Study Report Access phs000130 phs = Studies Search Results: Enter Study ID phs000130 Click here

24. Copyright OpenHelix. No use or reproduction without express written consent24 Study Report NIDDK IBD Genetics Consortium Crohn’s Disease Genome-Wide Association Study Accession: phs000130.v1.p1 We will enlarge each section next auth. data access req. study name, #, navigation tabs Search within study, Associated Substudies, if available description auth. access data public data (FTP) criteria, molecular history, publications diseases (MeSH) study attribution

25. Copyright OpenHelix. No use or reproduction without express written consent25 Study Report: Description Linked Logos May also see study version history Navigation tabs Study type & number of participants

26. Copyright OpenHelix. No use or reproduction without express written consent26 Study Report: Data Access Authorized access data - rules for this study Public data - FTP

27. Copyright OpenHelix. No use or reproduction without express written consent27 Study Report: Criteria & Molecular

28. Copyright OpenHelix. No use or reproduction without express written consent28 Study Report: Study History & Publications

29. Copyright OpenHelix. No use or reproduction without express written consent29 Study Report: Diseases, Attribution, Access Research Use Statements

30. Copyright OpenHelix. No use or reproduction without express written consent30 Sample Variable Report phv = phenotypic Variables Access Click here

31. Copyright OpenHelix. No use or reproduction without express written consent31 Sample Document Report phd = study Documents Navigation Document Name & Accession Search Study Name & Accession

32. Copyright OpenHelix. No use or reproduction without express written consent32 Associated Datasets Name & Accession Similar organization pht = dataseTs Description Dataset type Dataset Summary

33. Copyright OpenHelix. No use or reproduction without express written consent33 NCBI dbGaP Agenda Introduction & Credits Basic Searching & Browsing Report Types Analysis Reports Advanced Searching Summary Exercises dbGaP: www.ncbi.nlm.nih.gov/gapwww.ncbi.nlm.nih.gov/gap

34. Analysis Methods Copyright OpenHelix. No use or reproduction without express written consent34 Sample Analysis Report Analysis Plots http://gmed.bu.edu/about/index.html “Please note that all associations... are considered "candidate associations" pending replication in additional studies.” Details Publications pha001340.1 Enter ID into homepage search box pha = genotype-phenotype Analyses Study version history Browser

35. Copyright OpenHelix. No use or reproduction without express written consent35 Analysis Report & Genome Browser dbSNP homepage: http://www.ncbi.nlm.nih.gov/projects/SNP/ Click here

36. Copyright OpenHelix. No use or reproduction without express written consent36 Analysis Browser zoom scroll Controls NCBI Service Utility menu: SNP Genotype, Entrez SNP, Sequence Viewer, Map Viewer HTML view to maximize, print or save Toggle expanded or compacted Close that data track Highlight top ten SNP hits

37. Copyright OpenHelix. No use or reproduction without express written consent37 Analysis Browser - More Features Other buttons allow you to close particular windows Mouse over many items for tool tips & links

38. Copyright OpenHelix. No use or reproduction without express written consent38 Browse SNPs sample size, P-value rank allele freq., call rate Link to dbSNP record Scroll over Mouse over bin to see SNP record highlighted GWAS catalog page # in bin = # markers tested, + for 10 or more

39. Copyright OpenHelix. No use or reproduction without express written consent39 Analysis Browser - Customizing Your Display We will remove the GWAS Catalog Chromosome 3 SNP Bins reference track & highlight the top ten SNPs on the Sequence Viewer Click here One reference track removed Top ten SNPs highlighted

40. Copyright OpenHelix. No use or reproduction without express written consent40 NCBI dbGaP Agenda Introduction & Credits Basic Searching & Browsing Report Types Analysis Reports Advanced Searching Summary Exercises dbGaP: www.ncbi.nlm.nih.gov/gapwww.ncbi.nlm.nih.gov/gap

41. Copyright OpenHelix. No use or reproduction without express written consent41 Advanced Searching TIPS Use the Boolean operators AND, OR and NOT. They must be capitalized. Words can be truncated with * (asterisk): fibro* Add quotes, as in “fibroblast growth factor”, for complete phrase, exact word order (Use with caution, can be TOO restrictive)

42. http://www.ncbi.nlm.nih.gov/gap Copyright OpenHelix. No use or reproduction without express written consent42 Advanced Search Example heart rate AND exercise Our advanced search example: heart rate AND exercise

43. Copyright OpenHelix. No use or reproduction without express written consent43 Search Results: Heart Rate AND Exercise Limits: exclude or include specific types of records Advanced search: similar functions, & several more Click to open the dbGaP Advanced Search form

44. Copyright OpenHelix. No use or reproduction without express written consent44 dbGaP Advanced Search Form Limits, Search Details, Help Back to homepage Search History Search Builder Help  Multiple easy options in a single query form

45. Copyright OpenHelix. No use or reproduction without express written consent45 dbGaP Advanced Search - Search Builder Click Search or Preview Term added to Search box Click here heart rate Choose Boolean  Repeat steps as many times as needed to build query  We will add the term “AND exercise[Variable]” Search Builder

46. Copyright OpenHelix. No use or reproduction without express written consent46 dbGaP Advanced Search - Search Builder Results  Query: (heart rate[Variable]) AND exercise[Variable]

47. Copyright OpenHelix. No use or reproduction without express written consent47 dbGaP Advanced Search - Search History Search History Most Recent Queries Click to access Combine, view, delete or save previous searches #1 AND #2 Click Search or Preview

48.  Click here to learn more about My NCBI Copyright OpenHelix. No use or reproduction without express written consent48 Saving Searches in My NCBI Register & log in to My NCBI Click here to save search in My NCBI About My NCBI Save

49. Copyright OpenHelix. No use or reproduction without express written consent49 NCBI dbGaP Agenda Introduction & Credits Basic Searching & Browsing Report Types Analysis Reports Advanced Searching Summary Exercises dbGaP: www.ncbi.nlm.nih.gov/gapwww.ncbi.nlm.nih.gov/gap

50. Copyright OpenHelix. No use or reproduction without express written consent50 Summary of NCBI’s dbGaP Many groups contribute data http://www.ncbi.nlm.nih.gov/gap

51. Copyright OpenHelix. No use or reproduction without express written consent51 Data Organized into Uniform Report Types Stable identifiers assigned Genome browser provided

52. Copyright OpenHelix. No use or reproduction without express written consent52 NCBI dbGaP Agenda Introduction & Credits Basic Searching & Browsing Report Types Analysis Reports Advanced Searching Summary Exercises dbGaP: www.ncbi.nlm.nih.gov/gapwww.ncbi.nlm.nih.gov/gap

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