HLA Genetics Consortium Meeting, December 14-15, 2010.

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Presentation transcript:

HLA Genetics Consortium Meeting, December 14-15, 2010

HLA region genomics consortium Representation and Use of Clinical Data in Immport David Karp, M.D., Ph.D. Richard Scheuermann, Ph.D.

HLA Genetics Consortium Meeting, December 14-15, 2010 General Thoughts Regarding Clinical Data  Please make sure any prospectively collected data used consent forms that take data sharing into account.  Other researchers  NIH  De-identified  No Protected Healthcare Information is displayed. E.g., dates are converted to study times  Genetic data such as SNP haplotypes or frequencies are not part of the Semi-Public Workspace.

HLA Genetics Consortium Meeting, December 14-15, 2010 Current Data Submission Process  Study Design Study Design Templates  Case Report Form Data Clinical Data Templates Define Load files (one load file per database table) Mapping of CRF Data to Templates  Experiment Data Submission Experiment Templates

HLA Genetics Consortium Meeting, December 14-15, 2010 Levels of Clinical Data  Simple – Subject demographics and phenotype  Can use built-in data submission templates (Excel)  Complex – Clinical measurements, time course  Vital signs  CBC  Chemistry  Serologies  Response to vaccination  Pulmonary function tests  BASDI, BASFI, Rodnan Skin Score, etc.

HLA Genetics Consortium Meeting, December 14-15, 2010 Submitting Clinical Data  Investigator controls data during loading  Give BISC team (Meagan Kong, Ph.D.) a data dictionary, protocol, and database schema  We create map from your data to our data model  You generate the load file  More time-consuming on your part  Investigator gives data to BISC for loading  BISC team creates data maps and load files  Investigator can then validate the data integrity  Neither method is easy to do incrementally – best to have all data loaded at once

HLA Genetics Consortium Meeting, December 14-15, 2010 Standard Subject Templates

HLA Genetics Consortium Meeting, December 14-15, 2010 ImmPort Data Templates

HLA Genetics Consortium Meeting, December 14-15, 2010 Current Data Submission Data Submission Task Assignment User with CRO Support User without CRO Support Study DesignUserBISC CRF Data MappingBISC Load File GenerationUserBISC Load Data into DatabaseBISC Experimental DataUser Data ValidationUser

HLA Genetics Consortium Meeting, December 14-15, 2010 Content of Study Design Workbook Study Interventional Parameters Observational Parameters Inclusion Exclusion Arm or Cohort Period Event Plan Visit Plan Visit to Arm Event Panel Event Panel components Site Study Personnel Subject Measure Definitions Outcome Measure Definitions Glossary

HLA Genetics Consortium Meeting, December 14-15, 2010 Cartoon Representation of ImmPort Study Schema

HLA Genetics Consortium Meeting, December 14-15, 2010 Study Design Workbook Study Arm or Cohort Period Event Plan Visit Plan

HLA Genetics Consortium Meeting, December 14-15, 2010 Study Design Workbook Observational parameters Interventional Parameters Subject Measure Definitions Dropdown Menus Comments

HLA Genetics Consortium Meeting, December 14-15, 2010 Case Report Form Data Submission  Why is mapping of CRF study data to clinical data templates needed? 1. Studies tailor their assessment and lab test data sets to the specific needs of the study 2. BISC needed a generic representation of assessments and lab tests 3. The mapping process shows how the study specific data is fitted into the generalized BISC framework

HLA Genetics Consortium Meeting, December 14-15, 2010 Case Report Form Data Templates Content Biosampling (e.g., Blood draw) Substance Merge (e.g., Medication) Assessment (e.g., Medical History) Lab test Reference Range Adverse Event Early Termination Protocol Deviation Actual Visit Subject Measure Results Lab Test (panel ) Derived Results Arm or Cohort to Subject Biosampling to Biological Samples Study to Protocol

HLA Genetics Consortium Meeting, December 14-15, 2010 Case Report Form Data Templates Assessment (e.g., Medical History, Family History, Vital Signs) Biosampling Lab Test

HLA Genetics Consortium Meeting, December 14-15, 2010 Case Report Form Data Submission Mapping File Generation

HLA Genetics Consortium Meeting, December 14-15, 2010 Experiment (Mechanistic Assay) SUBJECT Name Description … BIOLOGICAL SAMPLE Name Description … EXPERIMENT_SAMPLE Name Description … EXPERIMENT Name Description … PROTOCOL Name Description … Assay Results Name Description … REAGENT Name Description …

HLA Genetics Consortium Meeting, December 14-15, 2010

Tube 33 Population 2 Lymphocyte Region

HLA Genetics Consortium Meeting, December 14-15, 2010 ImmPort Clinical Data  ImmPort currently has a wealth of experimental data in the personal workspaces of investigators  Use of data in the Semi-Public Workspaces offers an exciting ability to collaborate, generate hypotheses, and share data  Structured data models are necessary to use complex clinical research data  Mapping data to make it useful for translational and clinical studies is time-consuming – work with us early!