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

2. GAD The Genetic Association Database Materials prepared by: Mary Mangan, Ph.D. www.openhelix.com Version 2

3. Copyright OpenHelix. No use or reproduction without express written consent3 GAD Agenda Introduction and Credits Basic Search Advanced Search Other Features Summary Exercises GAD: http://geneticassociationdb.nih.gov/

4. Copyright OpenHelix. No use or reproduction without express written consent4 Introduction GAD Genetic Association Database Associates human genes with diseases See the big picture first, via tables See the specifics next, via detailed records Extensive links to other databases Integrated with UCSC Genome Browser Help curate & add new records Developed by Kevin Becker & team at NIH

5. Copyright OpenHelix. No use or reproduction without express written consent5 What is Genetic Association? Healthy PopulationDiseased Population Genetic Association: between allele G and the disease. A A A A A G G G G

6. Copyright OpenHelix. No use or reproduction without express written consent6 Complex Diseases have Complex Associations Healthy PopulationDiseased Population Genetic Association: [ allele G + allele T + smoking ] and the disease G T ++ G T ++ G T ++ G T + G C ++ A T ++

7. Copyright OpenHelix. No use or reproduction without express written consent7 What about OMIM? Wealth of information Text-based narrative Just hard to visualize alleles and polymorphisms environmental factors genes

8. Copyright OpenHelix. No use or reproduction without express written consent8 GAD Data 1. Incorporates OMIM - reformats text  tables 3. Curates additional data - from less common journals - genetic associations of lower significance - negative data - user-submitted reports 2. Multiple phenotype levels Disease Class Broad Phenotype MeSH Term Narrow Disease Molecular Phenotype 4. Standardizes molecular nomenclature - official gene symbols - official polymorphisms

9. Copyright OpenHelix. No use or reproduction without express written consent9 GAD Preview Tables Preview the big picture first...... then select an individual record for details Record

10. Copyright OpenHelix. No use or reproduction without express written consent10 GAD Homepage PMID: 15118671 Feedback PMC: 2822734

11. Copyright OpenHelix. No use or reproduction without express written consent11 GAD Agenda Introduction and Credits Basic Search Advanced Search Other Features Summary Exercises GAD: http://geneticassociationdb.nih.gov/

12. Copyright OpenHelix. No use or reproduction without express written consent12 GAD Views click

13. Copyright OpenHelix. No use or reproduction without express written consent13 Gene View, part 1 Data Column official gene symbol Data Columns icon links unique genetic association

14. Copyright OpenHelix. No use or reproduction without express written consent14 Links and Field Descriptions Field Descriptions Explains each data field

15. Copyright OpenHelix. No use or reproduction without express written consent15 Gene View, part 2 SCROLL to see more... Genetic Association? Disease Class

16. Copyright OpenHelix. No use or reproduction without express written consent16 A2M Detailed Record More links

17. Copyright OpenHelix. No use or reproduction without express written consent17 Disease View Disease data highlighted click to open Disease View for CAD

18. Copyright OpenHelix. No use or reproduction without express written consent18 Coronary Artery Disease View SCROLL to see more...

19. Copyright OpenHelix. No use or reproduction without express written consent19 Chromosome View

20. Copyright OpenHelix. No use or reproduction without express written consent20 Environmental Factor and Gene Interaction View environmental factors

21. Copyright OpenHelix. No use or reproduction without express written consent21 Simple Search click HMOX1 TIP: always use official gene nomenclature!

22. Copyright OpenHelix. No use or reproduction without express written consent22 HMOX1 Gene View Total records

23. Copyright OpenHelix. No use or reproduction without express written consent23 HMOX1 Positive Data Only from “total” to just “positive” all Y TIP: just be sure to Reset for next query

24. Copyright OpenHelix. No use or reproduction without express written consent24 GAD Agenda Introduction and Credits Basic Search Advanced Search Other Features Summary Exercises GAD: http://geneticassociationdb.nih.gov/

25. Copyright OpenHelix. No use or reproduction without express written consent25 Advanced Search SCROLL for over 60 field options IMPORTANT: GAD remembers the last query you did. If last query was Disease-related, then you get a Disease-restricted query page click “Reset”

26. Copyright OpenHelix. No use or reproduction without express written consent26 Advanced Query Example prostate cancer Japanese smoking click scroll

27. Copyright OpenHelix. No use or reproduction without express written consent27 Batch Search pick-list paste in gene list

28. Copyright OpenHelix. No use or reproduction without express written consent28 Batch Search Results Disease Classes (see “Links” for abbreviations) TotalIMM NEURPSY

29. Copyright OpenHelix. No use or reproduction without express written consent29 Analyzing Large Gene Sets Disease Classes Immune Inflammation Neurological

30. Copyright OpenHelix. No use or reproduction without express written consent30 GAD Agenda Introduction and Credits Basic Search Advanced Search Other Features Summary Exercises GAD: http://geneticassociationdb.nih.gov/

31. Copyright OpenHelix. No use or reproduction without express written consent31 Add a Record

32. Copyright OpenHelix. No use or reproduction without express written consent32 Become an Expert

33. Copyright OpenHelix. No use or reproduction without express written consent33 Download GAD

34. Copyright OpenHelix. No use or reproduction without express written consent34 GAD Track on UCSC Browser turn GAD track on to see data integrated with browser

35. Copyright OpenHelix. No use or reproduction without express written consent35 GAD Agenda Introduction and Credits Basic Search Advanced Search Other Features Summary Exercises GAD: http://geneticassociationdb.nih.gov/

36. Copyright OpenHelix. No use or reproduction without express written consent36 GAD Summary Tables Record

37. Copyright OpenHelix. No use or reproduction without express written consent37 GAD: View from Different Perspectives DiseaseGene Polymorphism Reference Environmental Factor ALL Scroll...

38. Copyright OpenHelix. No use or reproduction without express written consent38 GAD: Searches Basic keyword reference gene disease Multiple Options input gene list Batch Query

39. Copyright OpenHelix. No use or reproduction without express written consent39 GAD: Other Features Add recordsBecome an Expert GAD on UCSC Browser Download GAD

40. Copyright OpenHelix. No use or reproduction without express written consent40 GAD Agenda Introduction and Credits Basic Search Advanced Search Other Features Summary Exercises GAD: http://geneticassociationdb.nih.gov/

41. Copyright OpenHelix. No use or reproduction without express written consent41