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

2. Version 1 Copyright OpenHelix. No use or reproduction without express written consent 2 An Online Catalog of Human Genes & Genetic Disorders Materials prepared by: Jennifer Williams, Ph.D. www.openhelix.com OMIM : Online Mendelian Inheritance in Man ® ®

3. Copyright OpenHelix. No use or reproduction without express written consent3 OMIM database: http://omim.org OMIM Agenda Introduction & Credits Basic Search Phenotype Results Gene Results Gene Map Information Advanced Search Additional Features Summary Exercises

4. Copyright OpenHelix. No use or reproduction without express written consent4 OMIM: More than you might think http://www.ncbi.nlm.nih.gov/omim Full-text summaries of a gene or phenotype Clinical Synopsis of Disease New Face of OMIM is at omim.org http://onlinelibrary.wiley.com/doi/10.1002/humu.21466/full

5. Copyright OpenHelix. No use or reproduction without express written consent5 OMIM Homepage & Credits: omim.org http://omim.org

6. click Copyright OpenHelix. No use or reproduction without express written consent6 OMIM Scope and History http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852721/

7. Copyright OpenHelix. No use or reproduction without express written consent7 OMIM Statistics

8. Copyright OpenHelix. No use or reproduction without express written consent8 OMIM Content: Scope of Phenotypes OMIM Focuses On: Single-gene mendelian disease/disorders/phenotypes (including: cystic fibrosis, sickle cell anemia, achondroplasia, phenotypic traits such as hair and eye color, susceptibility to drug reaction as in malignant hyperthermia and warfarin sensitivity, altered reaction to infection such as herpes simplex encephalitis and progression to AIDS in HIV infection, germline susceptibilities to cancer such as BRCA1 and breast/ovarian cancer, etc.) Complex diseases with significant single gene contribution (such as: complement factor H and age related macular degeneration) Descriptions of recurrent deletion and duplication syndromes (e.g., Potocki-Shaffer syndrome, and chromosome 10q26 deletion syndrome)

9. Copyright OpenHelix. No use or reproduction without express written consent9 OMIM Disclaimer NOTE: OMIM is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the OMIM database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions. This tutorial is not a substitute for medical training

10. Copyright OpenHelix. No use or reproduction without express written consent10 OMIM Homepage Tabs Clear, concise documentation from OMIM

11. Copyright OpenHelix. No use or reproduction without express written consent11 OMIM database: http://omim.org OMIM Agenda Introduction & Credits Basic Search Phenotype Results Gene Results Gene Map Information Advanced Search Additional Features Summary Exercises

12. Copyright OpenHelix. No use or reproduction without express written consent12 Basic Search spinocerebellar ataxia examples

13. Basic Search Results Copyright OpenHelix. No use or reproduction without express written consent13 highlight Click to open

14. Clinical Synopses Results Copyright OpenHelix. No use or reproduction without express written consent14

15. Basic Search Results, cont. Copyright OpenHelix. No use or reproduction without express written consent15 Thesaurus options

16. Matching Terms Copyright OpenHelix. No use or reproduction without express written consent16 Matching terms one term

17. Basic Search Results: Links Copyright OpenHelix. No use or reproduction without express written consent17

18. Result Displays: MIM Numbers, etc. Copyright OpenHelix. No use or reproduction without express written consent18 click http://www.omim.org/help/faq#1.2

19. Copyright OpenHelix. No use or reproduction without express written consent19 OMIM database: http://omim.org OMIM Agenda Introduction & Credits Basic Search Phenotype Results Gene Results Gene Map Information Advanced Search Additional Features Summary Exercises

20. Phenotype Entry, Top Copyright OpenHelix. No use or reproduction without express written consent20 Full entry Expandable TOC Expandable links

21. Phenotype Gene Relationships Area Copyright OpenHelix. No use or reproduction without express written consent21 Gene Map Phenotype Entry Gene Entry

22. click Phenotypic Series Copyright OpenHelix. No use or reproduction without express written consent22 Similar phenotypes Phenotypic Series Different genetic locations A quick view of similar phenotypes across the genome

23. click Clinical Synopsis Copyright OpenHelix. No use or reproduction without express written consent23 Clinical Synopsis Provides an overview of the clinical features of a phenotype

24. Associated Gene/Locus Copyright OpenHelix. No use or reproduction without express written consent24 click

25. Copyright OpenHelix. No use or reproduction without express written consent25 OMIM database: http://omim.org OMIM Agenda Introduction & Credits Basic Search Phenotype Results Gene Results Gene Map Information Advanced Search Additional Features Summary Exercises

26. Copyright OpenHelix. No use or reproduction without express written consent26 OMIM Gene Entry Expandable TOC Full entry

27. Copyright OpenHelix. No use or reproduction without express written consent27 Allelic Variation Table View of Allelic Variants Expandable TOC Gene CFTR’s Table View http://www.omim.org/help/faq#1.4

28. Copyright OpenHelix. No use or reproduction without express written consent28 External Links for Genes: Genome by OpenHelix http://openhelix.com/catalog External Links

29. Copyright OpenHelix. No use or reproduction without express written consent29 External Links for Genes: Gene Info Expandable TOC

30. Copyright OpenHelix. No use or reproduction without express written consent30 OMIM database: http://omim.org OMIM Agenda Introduction & Credits Basic Search Phenotype Results Gene Results Gene Map Information Advanced Search Additional Features Summary Exercises

31. Copyright OpenHelix. No use or reproduction without express written consent31 Gene Map Search Easy access to Gene Map search

32. Copyright OpenHelix. No use or reproduction without express written consent32 Gene Map Search Form Example searches: 1p36 kinase CFTR etc. Search tips Search limits

33. Copyright OpenHelix. No use or reproduction without express written consent33 Gene Map Search Results Gene Map Important to Note

34. Copyright OpenHelix. No use or reproduction without express written consent34 OMIM database: http://omim.org OMIM Agenda Introduction & Credits Basic Search Phenotype Results Gene Results Gene Map Information Advanced Search Additional Features Summary Exercises

35. Copyright OpenHelix. No use or reproduction without express written consent35 Advanced Search form click

36. Copyright OpenHelix. No use or reproduction without express written consent36 Advanced Search form Keyword(s) Search limits Display options

37. Copyright OpenHelix. No use or reproduction without express written consent37 Advanced Search form http://omim.org

38. Copyright OpenHelix. No use or reproduction without express written consent38 OMIM database: http://omim.org OMIM Agenda Introduction & Credits Basic Search Phenotype Results Gene Results Gene Map Information Advanced Search Additional Features Summary Exercises

39. Copyright OpenHelix. No use or reproduction without express written consent39 OMIM Homepage Tabs I accept API Help

40. Copyright OpenHelix. No use or reproduction without express written consent40 OMIM Homepage Tabs, cont.

41. Copyright OpenHelix. No use or reproduction without express written consent41 Getting to OMIM from Elsewhere: UCSC Browser http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=omimGene2 OMIM

42. Copyright OpenHelix. No use or reproduction without express written consent42 Get to OMIM from Elsewhere: NCBI and Others http://www.ncbi.nlm.nih.gov/gquery/?term=cftr http://sbkb.org/kb/report_ann.jsp?sid=s1330624928-89&id=1XMI&pid=proteinstructure http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=51930

43. Copyright OpenHelix. No use or reproduction without express written consent43 OMIM App: Access from a Publication http://www.applications.sciverse.com/action/appDetail/298832? Links to OMIM entry http://www.sciencedirect.com/science/article/pii/S0006322311008158

44. Copyright OpenHelix. No use or reproduction without express written consent44 OMIM database: http://omim.org OMIM Agenda Introduction & Credits Basic Search Phenotype Results Gene Results Gene Map Information Advanced Search Additional Features Summary Exercises

45. Copyright OpenHelix. No use or reproduction without express written consent45 OMIM Summary: Scope and History http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852721/ http://onlinelibrary.wiley.com/doi/10.1002/humu.21466/full OMIM = Thousands of Entries

46. Copyright OpenHelix. No use or reproduction without express written consent46 OMIM Summary: Many Entry Points Keyword(s) OMIM SciVerse App to OMIM entry

47. Detailed Entries Gene Map Phenotypic Series Clinical Synopsis Copyright OpenHelix. No use or reproduction without express written consent47 OMIM Summary: Gene, Variant & Phenotype Data

48. Copyright OpenHelix. No use or reproduction without express written consent48 OMIM Summary: Data, cont. Table of Allelic Variants OMIM - Rich Source of Gene and Phenotype Data Links to external sources OMIM database: http://omim.org

49. Copyright OpenHelix. No use or reproduction without express written consent49 OMIM database: http://omim.org OMIM Agenda Introduction & Credits Basic Search Phenotype Results Gene Results Gene Map Information Advanced Search Additional Features Summary Exercises

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