LOVD & ITHANET: Synergies and plans under GG2020 - Carsten W Lederer
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A look at how LOVD and ITHANET can work together for the benefit of GG2020
![The Cyprus
Institute of
Neurology
and Genetics
Key Characteristics
LOVD
LOVD-localised HBB variant database already with data form >7000
individuals (>18.500 variants)
Standardised entry of variant-related data
Sequence variants, including large (gene-spanning) indels
Individual and clinical data
Support for SSL-access
Cooperativity
Batch import, including NGS import with automated gene/transcript setup
ITHANET/IthaGenes
Complementary web environment for target group(s)
Seamlessly “disease-specific” (disease-specific, rather than locus-specific)
Visualisation of sequence context
Map display
Visualisation of epidemiology
Contributor/publication-specific display: comparison of findings and trends
Integration and formatted display of multimedia content
CE-HPLC
[e-Education content]
Genotype-phenotype database
www.lovd.nl
www.ithanet.eu](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)
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LOVD & ITHANET: Synergies and plans under GG2020 - Carsten W Lederer
- 1. The Cyprus Institute of Neurology and Genetics LOVD & ITHANET – Synergies and Plans under GG2020 Carsten W. Lederer The Cyprus Institute of Neurology and Genetics The Cyprus School of Molecular Medicine Lederer@cing.ac.cy http://www. relationology.co.uk UNESCO Headquarters Paris, France 30 – 31st May 2016 Human Variome Project Consortium 6th Biennial Meeting GG2020 Fringe Meeting
- 2. The Cyprus Institute of Neurology and Genetics Key Characteristics LOVD LOVD-localised HBB variant database already with data form >7000 individuals (>18.500 variants) Standardised entry of variant-related data Sequence variants, including large (gene-spanning) indels Individual and clinical data Support for SSL-access Cooperativity Batch import, including NGS import with automated gene/transcript setup ITHANET/IthaGenes Complementary web environment for target group(s) Seamlessly “disease-specific” (disease-specific, rather than locus-specific) Visualisation of sequence context Map display Visualisation of epidemiology Contributor/publication-specific display: comparison of findings and trends Integration and formatted display of multimedia content CE-HPLC [e-Education content] Genotype-phenotype database www.lovd.nl www.ithanet.eu
- 3. The Cyprus Institute of Neurology and Genetics Synergies for GG2020 LOVD Familiar interface Secure and stable data entry point Training of partners for all LOVD-based databases ITHANET Content customisation Meta-analyses Visualisations (Maps, HPLC, other) [Statistical analyses (Summary data)] Interactive tools [Prediction of disease severity] [Suggestion of underlying variants] http://http://www.condenaststore.com/
- 4. The Cyprus Institute of Neurology and Genetics The Envisaged Database Molecular per gene as standard Which variants to include? – All Which genes to include? – All?! Which non-molecular data to include? – All??? Consider the human aspect of medical data entry Fields left blank for many entries become worthless or ? Spartan? Lucullan?
- 5. The Cyprus Institute of Neurology and Genetics Local LOVD Installation in Cyprus
- 6. The Cyprus Institute of Neurology and Genetics Current ITHANET Genotype- Phenotype Database
- 7. The Cyprus Institute of Neurology and Genetics Current ITHANET Genotype- Phenotype Database
- 8. The Cyprus Institute of Neurology and Genetics Suggested Fields
- 9. The Cyprus Institute of Neurology and Genetics Suggested Fields
- 10. The Cyprus Institute of Neurology and Genetics Suggested Fields
- 11. The Cyprus Institute of Neurology and Genetics Suggested Fields
- 12. The Cyprus Institute of Neurology and Genetics Suggested Fields
- 13. The Cyprus Institute of Neurology and Genetics Suggested Fields
- 14. The Cyprus Institute of Neurology and Genetics What next? G6PD-deficiency data fields pending. Decision on required and optional fields. Decision on how to integrate LOVD and the ITHANET Portal Decision on collection strategy (personnel/online/offline). Addressing the elephant that is (NOT) in the room. Your input pending and essential! Digital Registries https://en.wikipedia.org/wiki/Elephant_in_the_room
- 15. The Cyprus Institute of Neurology and Genetics Global Globin 2020 Challenge It is good you are here! 15 Barabasi & Bonabeau 2003 PMID12701331
- 16. The Cyprus Institute of Neurology and Genetics This project has received funding from the European Union’s Sixth and Seventh Framework Programmes for research, technological development and demonstration under grant agreement nos. 26539 (ITHANET) and 306201 (ThalaMoSS) and from the Cypriot Government as core funding and through the Research Promotion Foundation of Cyprus. Acknowledgements CING & ITHANET Marina Kleanthous Petros Kountouris Pavlos Fanis Coralea Stephanou Xenia Feleki GG2020 Helen Robinson Zilfalil bin Alwi Raj Ramesar LOVD Johan T. den Dunnen All our collaborators and patients! 16
Editor's Notes
- Notes for Ithanet/LOVD talk Provision of complementary environment and content for the target group Combination of multiple loci: not LSDB, but DSDB Provision of additional components that are not part of LOVD Maps As indicated by Petros for the fine-mapping and additional information on health care provision etc. Ithaphen All genes in Ithagenes Multiple examinations Categories We want staff HPLC data Visualisations and annotation of sequence context Plans for GG2020 ?Registries? Transfer of mutations, only, not problematic GG2020 as networking motivation GenPhen with individual data problematic (but essential) – has to be resolved How to receive data Web interface for individual entry. LOVD? Batch upload by file format (XML; JSON). LOVD? Receipt of summary data for IthaMap Storage of summary data Visualisation of epidemiology [BioRad portal for genotype-phenotype]
- Personal data GG2020ID Sex Date of birth Country of residence Ethnic group Referring Centre Diagnosis Date or age at diagnosis Type of diagnosis: neonatal screening, other screening, complication Status idem + add item deceased Beta locus Alpha locus Genotype idem Treatment Penicillin therapy no, yes date of initiation ; date of termination Folic acid no, yes date of initiation ; date of termination Hydroxyurea no, yes date of initiation ; date of termination other specify History of transfusion : no yes date unspecified General Clinical Examination Date Age ? (=date of birth - date) Blood pressure Height Weight Jaundice Splenomegaly Splenectomy no yes date Leg ulcers no yes date unspecified Pain crises no yes date (multiple entry or #/yr) unspecified History of acute chest syndrome ACS no yes date (multiple entry) unspecified Cholelithiasis no yes date unspecified Cholecystectomy no yes date unspecified Priapism no yes date unspecified inappropriate Neurovascular disease no yes date unspecified Hip injury no yes date unspecified Fertility : Children General Biomarkers Date Haematology CBC including reticulocytes
- Personal data GG2020ID Sex Date of birth Country of residence Ethnic group Referring Centre Diagnosis Date or age at diagnosis Type of diagnosis: neonatal screening, other screening, complication Status idem + add item deceased Beta locus Alpha locus Genotype idem Treatment Penicillin therapy no, yes date of initiation ; date of termination Folic acid no, yes date of initiation ; date of termination Hydroxyurea no, yes date of initiation ; date of termination other specify History of transfusion : no yes date unspecified General Clinical Examination Date Age ? (=date of birth - date) Blood pressure Height Weight Jaundice Splenomegaly Splenectomy no yes date Leg ulcers no yes date unspecified Pain crises no yes date (multiple entry or #/yr) unspecified History of acute chest syndrome ACS no yes date (multiple entry) unspecified Cholelithiasis no yes date unspecified Cholecystectomy no yes date unspecified Priapism no yes date unspecified inappropriate Neurovascular disease no yes date unspecified Hip injury no yes date unspecified Fertility : Children General Biomarkers Date Haematology CBC including reticulocytes
- Personal data GG2020ID Sex Date of birth Country of residence Ethnic group Referring Centre Diagnosis Date or age at diagnosis Type of diagnosis: neonatal screening, other screening, complication Status idem + add item deceased Beta locus Alpha locus Genotype idem Treatment Penicillin therapy no, yes date of initiation ; date of termination Folic acid no, yes date of initiation ; date of termination Hydroxyurea no, yes date of initiation ; date of termination other specify History of transfusion : no yes date unspecified General Clinical Examination Date Age ? (=date of birth - date) Blood pressure Height Weight Jaundice Splenomegaly Splenectomy no yes date Leg ulcers no yes date unspecified Pain crises no yes date (multiple entry or #/yr) unspecified History of acute chest syndrome ACS no yes date (multiple entry) unspecified Cholelithiasis no yes date unspecified Cholecystectomy no yes date unspecified Priapism no yes date unspecified inappropriate Neurovascular disease no yes date unspecified Hip injury no yes date unspecified Fertility : Children General Biomarkers Date Haematology CBC including reticulocytes
- Personal data GG2020ID Sex Date of birth Country of residence Ethnic group Referring Centre Diagnosis Date or age at diagnosis Type of diagnosis: neonatal screening, other screening, complication Status idem + add item deceased Beta locus Alpha locus Genotype idem Treatment Penicillin therapy no, yes date of initiation ; date of termination Folic acid no, yes date of initiation ; date of termination Hydroxyurea no, yes date of initiation ; date of termination other specify History of transfusion : no yes date unspecified General Clinical Examination Date Age ? (=date of birth - date) Blood pressure Height Weight Jaundice Splenomegaly Splenectomy no yes date Leg ulcers no yes date unspecified Pain crises no yes date (multiple entry or #/yr) unspecified History of acute chest syndrome ACS no yes date (multiple entry) unspecified Cholelithiasis no yes date unspecified Cholecystectomy no yes date unspecified Priapism no yes date unspecified inappropriate Neurovascular disease no yes date unspecified Hip injury no yes date unspecified Fertility : Children General Biomarkers Date Haematology CBC including reticulocytes
- Personal data GG2020ID Sex Date of birth Country of residence Ethnic group Referring Centre Diagnosis Date or age at diagnosis Type of diagnosis: neonatal screening, other screening, complication Status idem + add item deceased Beta locus Alpha locus Genotype idem Treatment Penicillin therapy no, yes date of initiation ; date of termination Folic acid no, yes date of initiation ; date of termination Hydroxyurea no, yes date of initiation ; date of termination other specify History of transfusion : no yes date unspecified General Clinical Examination Date Age ? (=date of birth - date) Blood pressure Height Weight Jaundice Splenomegaly Splenectomy no yes date Leg ulcers no yes date unspecified Pain crises no yes date (multiple entry or #/yr) unspecified History of acute chest syndrome ACS no yes date (multiple entry) unspecified Cholelithiasis no yes date unspecified Cholecystectomy no yes date unspecified Priapism no yes date unspecified inappropriate Neurovascular disease no yes date unspecified Hip injury no yes date unspecified Fertility : Children General Biomarkers Date Haematology CBC including reticulocytes
- Personal data GG2020ID Sex Date of birth Country of residence Ethnic group Referring Centre Diagnosis Date or age at diagnosis Type of diagnosis: neonatal screening, other screening, complication Status idem + add item deceased Beta locus Alpha locus Genotype idem Treatment Penicillin therapy no, yes date of initiation ; date of termination Folic acid no, yes date of initiation ; date of termination Hydroxyurea no, yes date of initiation ; date of termination other specify History of transfusion : no yes date unspecified General Clinical Examination Date Age ? (=date of birth - date) Blood pressure Height Weight Jaundice Splenomegaly Splenectomy no yes date Leg ulcers no yes date unspecified Pain crises no yes date (multiple entry or #/yr) unspecified History of acute chest syndrome ACS no yes date (multiple entry) unspecified Cholelithiasis no yes date unspecified Cholecystectomy no yes date unspecified Priapism no yes date unspecified inappropriate Neurovascular disease no yes date unspecified Hip injury no yes date unspecified Fertility : Children General Biomarkers Date Haematology CBC including reticulocytes
- Personal data GG2020ID Sex Date of birth Country of residence Ethnic group Referring Centre Diagnosis Date or age at diagnosis Type of diagnosis: neonatal screening, other screening, complication Status idem + add item deceased Beta locus Alpha locus Genotype idem Treatment Penicillin therapy no, yes date of initiation ; date of termination Folic acid no, yes date of initiation ; date of termination Hydroxyurea no, yes date of initiation ; date of termination other specify History of transfusion : no yes date unspecified General Clinical Examination Date Age ? (=date of birth - date) Blood pressure Height Weight Jaundice Splenomegaly Splenectomy no yes date Leg ulcers no yes date unspecified Pain crises no yes date (multiple entry or #/yr) unspecified History of acute chest syndrome ACS no yes date (multiple entry) unspecified Cholelithiasis no yes date unspecified Cholecystectomy no yes date unspecified Priapism no yes date unspecified inappropriate Neurovascular disease no yes date unspecified Hip injury no yes date unspecified Fertility : Children General Biomarkers Date Haematology CBC including reticulocytes