Creation

1
Creation Maintenance of Helixa web based
database of medical genetics laboratories for
geneticists

• P Tarczy-Hornoch, Maxine Covington, Joseph
  Edwards, Paul Shannon, Sherrilynne Fuller,
  Roberta Pagon
• Biomedical Informatics, Genetics, Neonatology,
• University of Washington
• Seattle WA

2
Outline

• Statement of the problem
• Database content and design
• User view of Helix
• Administrative view of Helix
• Results
• Conclusion

3
The Problem

• Genetics professionals need to quickly find up to
  date information on availability of state of the
  art genetic testing to diagnose, counsel and
  manage patients with genetic disorders
• As we elucidate the genetic basis of common
  diseases it is no longer just geneticists

4
Information Overload in Genetics

• Human Genome Project
• 100,000-120,000 genes
• 100-10000 mutations/gene
• New genes daily new diseases weekly
• Hard to keep up!
• Explosion of genetic testing
• Burgeoning decentralized genetic testing industry
  
• Genetic testing for 111 diseases in 93 and 625
  in 98
• We need a Yellow Pages of genetic testing
  availability

5
Helix and GeneClinics

• Helix database Yellow pages of genetic testing
• Free, searchable directory of available genetic
  testing
• Restricted to healthcare providers
• 93-96 stand alone FoxPro database,
• 97- WWW accessible/maintained Informix database
• healthlinks.washington.edu/helix
• GeneClinics Users manual for genetic testing
• under construction
• expert authored, peer reviewed knowledge base
• XML, Java, OODB

6
Why a User Manual of Genetic Testing?

• But outside the scrupulous environs of a
  scientific study there are no regulations on how
  tests should be performed, or patients informed.
  Myriad Genetics of Salt Lake City, Utah, will
  check a blood sample for all known BRCA
  mutations, for 2500
• The Economist, May 24, 1997 (p78)
• JAMA 19972771467-74

7
Outline

• Statement of the problem
• Database content and design
• User view of Helix
• Administrative view of Helix
• Results
• Conclusion

8
Helix Content

• Seeks to answer questions such as How do I test
  my patient for neurofibromatosis? What do I need
  to send to whom where?
• Content provided by laboratories ranging from
  small university research labs to large
  commercial clinical labs
• Database maintained at the University of
  Washington by Helix staff
• Continually updated via Java applets
• Long term plan is for distributed curation by
  data owners

9
Helix Clinical and Research Testing

• Clinical Research
• disease name
• OMIM, GeneClinics
• gene/locus/product
• laboratory
• director
• contact information
• test methodology
  research description
• prenatal availability
  research
  citation(s)
• clinical citation(s)

last update
10
Helix Database Design
Informix RDMS Java maintenance C/JDBC bridge C
CGI reports
11
Helix - Links Nomenclature

• Gene Locus OMIM
• plus also links to HGMD
• Gene Product SWISS-PROT
• Gene Symbol HUGO/GDB
• Human Gene Nomenclature Committee
• Phenotype GeneClinics, OMIM, others
• very fluid nomenclature
• changes as our understanding of genotypic basis
  of phenotype change

12
New Genotype/phenotype Schema
13
Outline

• Statement of the problem
• Database content and design
• User view of Helix
• Administrative view of Helix
• Results
• Conclusion

14
Helix User Search Options

• Disease name
• Gene, locus, product
• Primary clinical feature (phenotype)
• OMIM number
• Geographical region
• Laboratory
• Laboratory director name

15
(No Transcript)
16
(No Transcript)
17
(No Transcript)
18
(No Transcript)
19
(No Transcript)
20
(No Transcript)
21
(No Transcript)
22
(No Transcript)
23
(No Transcript)
24
Outline

• Statement of the problem
• Database content and design
• User view of Helix
• Administrative view of Helix
• Results
• Conclusion

25
Main Helix Administration Java Panel
26
User Panel
27
Pick List Maintenance Panel
28
(No Transcript)
29
Report Panel
30
Outline

• Statement of the problem
• Database content and design
• User view of Helix
• Administrative view of Helix
• Results
• Conclusion

31
Growth of Helix Over Time
32
Helix - Searches/Day
InternetAccess
33
Helix - Use by Occupation
34
Helix - Laboratory Test Menus
Total Clinical Research 625 300 325
35
1998 Helix User Survey
E-mail survey, 15 response Results should be
considered qualitative Respondents demographics
no different than non-respondents
36
Outline

• Statement of the problem
• Database content and design
• User view of Helix
• Administrative view of Helix
• Results
• Conclusion

37
Conclusions (I)

• The rapid adoption of Helix Internet access by
  the genetics community demonstrates the
  feasibility and viability of delivering
  dynamically changing medical reference
  information via the Web
• The Java database maintenance tools demonstrate
  the technical feasibility of distributed platform
  independent curation of a complex clinical
  reference database

38
Conclusions (II)

• Linkages to other genomic databases are made
  possible by our use of standardized genomic
  nomenclatures
• We plan to test distributed curation of Helix
• We plan to implement in Helix our new GeneClinics
  genotype-phenotype design to accommodate the
  rapid evolution of our understanding of
  genotype/phenotype particularly for complex
  (multi-gene) diseases
• We plan to populate the GeneClinics knowledge
  base based on Helix usage analysis

39
Helix Collaborators Funding

• Funding NLM 92-99 MCH 97-00
• Medical Director RA Pagon MD
• Project Manager ML Covington
• Educators N Hanson MS
• W Neufeld-Kaiser MS
• Informatics P Tarczy-Hornoch MD
• J Edwards PhD
• Sherrilynne Fuller PhD
• Paul Shannon
• Assistants GM Grohs
• A Hughes
• Advisory Board 11 Members