Meeting summary and thoughts
Garry Cutting, MD
McKusick Nathans Institute of Genetic Medicine
Johns Hopkins
sharing data ·...
Kudos
Scientific Programme Committee
Richard G. H. Cotton (Melbourne, Australia)
Raymond Dalgleish (Leicester, United King...
And finish on time
Don’t be boring
Annotating variation in the human genome
• The challenge
• Potential solutions
The Cambridge Wine Blogger
http://cambridge...
Stylianos Antonarakis, Session VIII
Rapid increase in the number of genes
associated with mendelian phenotypes
Source: OMIM
Years
Numberofgenes
Number of variants reported per gene in the
Leiden Open Variation Database (LOVD)
Variants from LOVD databases version 2.0...
• Increasing number of genes associated
with mendelian disease
• Increasing number of variants per gene
Perfect Storm of V...
Interpretive gap: Difference between
rate of variant discovery and rate of
variant annotation
Variants identified
Interpre...
Quantifying the interpretive gap
CFTR
137 for OMIM, 1301 for HGMD, 345 for LOVD
HBA1
HBB
Gene matched counts of variants p...
Christopher Cassa, Session X
Stylianos Antonarakis, Session VIII
Thomy de Ravel, Session II
Nik Nor Liza Nik Hassan, Session II
Raj Ramesar, Session III
Dwomoa Adu, Session III
Enock Matovu, Session III
Stylianos Antonarakis, Session VIII
Ted Kalbfleisch, Session IV
Moris Swertz, Session IV
Stylianos Antonarakis, Session VIII
Peter Taschner, Session V
Raymond Dalgleish, Session V
Ada Hamosh, Session V
Stylianos Antonarakis, Session VIII
Hoan Nyugen, Session VIII
Tuuli Lappalainen, Session VIII
Variant Annotation Projects
• INSiGHT: International Society for Gastrointestinal
Hereditary Tumors
– Mismatch repair gene...
Maurizio Genuardi, Session IX
Finlay Macrae, Session IX
Christopher Cassa, Session X
Standards Development &
Recommended Systems
• HGVS variation nomenclature
• Mutalyzer
• LOVD
• VarioML
• Variation Ontolog...
Summary
Thank you for attending HVP5
sharing data · reducing disease
an NGO Official Partner of UNESCO
HVP5: Meeting summary and thoughts - Garry Cutting
HVP5: Meeting summary and thoughts - Garry Cutting
HVP5: Meeting summary and thoughts - Garry Cutting
HVP5: Meeting summary and thoughts - Garry Cutting
HVP5: Meeting summary and thoughts - Garry Cutting
HVP5: Meeting summary and thoughts - Garry Cutting
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HVP5: Meeting summary and thoughts - Garry Cutting

  1. 1. Meeting summary and thoughts Garry Cutting, MD McKusick Nathans Institute of Genetic Medicine Johns Hopkins sharing data · reducing disease an NGO Official Partner of UNESCO
  2. 2. Kudos Scientific Programme Committee Richard G. H. Cotton (Melbourne, Australia) Raymond Dalgleish (Leicester, United Kingdom) Johan T. den Dunnen (Leiden, Netherlands) Marc Greenblatt (Burlington, VT, United States) Aida Falcon de Vargas (Caracas, Venezuela) Finlay Macrae (Melbourne, Australia) Martina Witsch-Baumgartner (Innsbruck, Austria) Organising Secretariat Rania Horaitis, ICO Heather Howard, ICO Helen Robinson , ICO Timothy Smith, ICO Casimiro Vizzini, UNESCO
  3. 3. And finish on time Don’t be boring
  4. 4. Annotating variation in the human genome • The challenge • Potential solutions The Cambridge Wine Blogger http://cambridgewineblogger.blogspot.com/2011/06/on- breadth-vs-depth-in-tasting.html
  5. 5. Stylianos Antonarakis, Session VIII
  6. 6. Rapid increase in the number of genes associated with mendelian phenotypes Source: OMIM Years Numberofgenes
  7. 7. Number of variants reported per gene in the Leiden Open Variation Database (LOVD) Variants from LOVD databases version 2.0-24 or higher and with properly configured reference sequences were used to extract the number of unique alleles reported per gene. If a gene was present in multiple databases (duplicate instances), the raw data was parsed such that the highest number of variants per a given gene was reported. Data courtesy of Ivo F.A.C. Fokkema and Johan T. den Dunnen. Figures courtesy of Melissa Lee Cutting GR AJHG 2014
  8. 8. • Increasing number of genes associated with mendelian disease • Increasing number of variants per gene Perfect Storm of Variants
  9. 9. Interpretive gap: Difference between rate of variant discovery and rate of variant annotation Variants identified Interpretive gap Annotated Cost of sequencing Time $$ Cutting GR AJHG 2014
  10. 10. Quantifying the interpretive gap CFTR 137 for OMIM, 1301 for HGMD, 345 for LOVD HBA1 HBB Gene matched counts of variants per gene, sorted by length
  11. 11. Christopher Cassa, Session X
  12. 12. Stylianos Antonarakis, Session VIII
  13. 13. Thomy de Ravel, Session II
  14. 14. Nik Nor Liza Nik Hassan, Session II
  15. 15. Raj Ramesar, Session III
  16. 16. Dwomoa Adu, Session III
  17. 17. Enock Matovu, Session III
  18. 18. Stylianos Antonarakis, Session VIII
  19. 19. Ted Kalbfleisch, Session IV
  20. 20. Moris Swertz, Session IV
  21. 21. Stylianos Antonarakis, Session VIII
  22. 22. Peter Taschner, Session V
  23. 23. Raymond Dalgleish, Session V
  24. 24. Ada Hamosh, Session V
  25. 25. Stylianos Antonarakis, Session VIII
  26. 26. Hoan Nyugen, Session VIII
  27. 27. Tuuli Lappalainen, Session VIII
  28. 28. Variant Annotation Projects • INSiGHT: International Society for Gastrointestinal Hereditary Tumors – Mismatch repair genes (Thompson et al Nat Genet 2014) • CFTR2: Clinical and Functional Translation of CFTR – CFTR (Sosnay et al Nat Genet 2013) • ENIGMA :Evidence-based Network for the Interpretation of Germline Mutant Alleles – BRCA 1/2 sharing data · reducing disease an NGO Official Partner of UNESCO
  29. 29. Maurizio Genuardi, Session IX
  30. 30. Finlay Macrae, Session IX
  31. 31. Christopher Cassa, Session X
  32. 32. Standards Development & Recommended Systems • HGVS variation nomenclature • Mutalyzer • LOVD • VarioML • Variation Ontology (VariO) • W01:Disclaimer Statements on G/DSDBs • WG02: Assigning Pathogenicity to a Genetic Variant • WG03 Minimal content for gene variant databases (LSDBS) • WG04 Minimum Content Requirements for HVP Country Nodes • WG05: Variant Database Quality Assessment • WG06: Disease &Phenotype Descriptions in Gene/Disease Specific Databases sharing data · reducing disease an NGO Official Partner of UNESCO
  33. 33. Summary
  34. 34. Thank you for attending HVP5 sharing data · reducing disease an NGO Official Partner of UNESCO

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