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Specimen Model Project: Requirements from Clinical Genomics

Specimen Model Project: Requirements from Clinical Genomics. October 2010 WG meeting. Mukesh Sharma Washington University Medical School St. Louis. Agenda. Scope Requirements represented in specimen CMET Requirements not represented in specimen CMET. Scope.

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Specimen Model Project: Requirements from Clinical Genomics

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  1. Specimen Model Project:Requirements from Clinical Genomics October 2010 WG meeting Mukesh Sharma Washington University Medical School St. Louis

  2. Agenda • Scope • Requirements represented in specimen CMET • Requirements not represented in specimen CMET

  3. Scope • Project will detail specimen collection, procedure(s) done on specimen and specimen storage that will affect the quality of the specimen.

  4. Requirements Represented In Specimen CMET Specimen Handling and Processing • Special handling such as flash freezing • Type of preservatives used and amount. Examples: additives used to preserve RNA/DNA • In the current model, Specimen is associated to Entity Choice Box and Entity is related to ContainerOrAdditive Choice Box. Storage • Type of storage used for collected specimen and any genetic extracted material. Specimen Access • Unique identifiers assigned to all materials (both collected and derived) to help manage access to specimens.

  5. Requirements Represented In Specimen CMET Specimen Type • Whether fluid, tissue, cell or molecular specimen? • Molecular Specimen can be derived from any of the other 3 types of specimens • Cell specimens can be derived from fluid and tissue specimens • In the Specimen model, Natural.code is available to capture type of specimen and DerivedSpecimen class to capture derived specimens Specimen Quantity • Quantity and/or size of specimen collected. • In the Specimen model, Natural class is available to capture this information Specimen Characteristics • Anatomical location/tissue site from where specimens were obtained • In the Specimen model, SpecimenCollectionProcess.targetSiteCode and SpecimenCollectionProcess.approachSiteCode is available to capture this information

  6. Requirements Represented In Specimen CMET Specimen Processing • Sample processing immediately after collection and stored on site. • Requirement includes intermediate processing and specimen types prior to generating genetic material (e.g. PBMC extraction, aliquots, resection) • Will the effectiveTime attribute in the SpecimenCollectionProcess and SpecimenProcessStep capture the information about when the specimen was collected and processed respectively? Specimen Characteristics • RNA/DNA characteristics: e.g. Purity values-A260/A230 and A260/A280, RNA integrity number (RIN) number etc. • Not in the CMET • QC needs to be done by the specimen core lab • Check with O&O if this will be captured by SpecimenProcessStep (QC process step)? • Is the readings of A260/A280 is captured in ObservationEvent?

  7. Requirements Not Represented In Specimen CMET 1. Genetic Consent Form • Linking up with the Genetic Consent Form. • Form signed by the patient to allow genetic/genomic testing and in some cases to permit long-term storage of genetic samples for further research. • Need to know that there is consent; duration that it allows the specimen to be used for (indefinite or restricted to particular duration or protocols). • Consent could be withdrawn and as a result the specimen is pulled out and destroyed. • Suggested Action  • Will add association to the consent class (from CDA model) and add attributes to the consent class to manage specimen (attributes needed are consent active or not -withdrawn consent). • The low priority task/future work would be to design a consent document based on existing documents. • We will review type of consent in various settings (clinical trial, Health Care Enterprise [IHE] organization, other Standard Development Organizations).

  8. Requirements Not Represented In Specimen CMET 2. Specimen Management • SpecimenCollection • Two use cases: • i) Patient comes in and we take 2 or more specimens • ii) Patient comes in and we take 1 specimen • We need to capture the relationship between multiple specimens collected at one time (use case i) • The universal CMET only has one entry point (SpecimenChoice) i.e. all CMETs are starting from Specimen •  Suggested Action  • In the SpecimenChoice Box add the SpecimenCollectionGroup class (especially for use case i)

  9. Requirements Not Represented In Specimen CMET Current Model Proposed Change

  10. Requirements Not Represented In Specimen CMET 3. Transportation • Specimen Sender and Receiver • Capture when specimen was sent to lab and when received by the other lab • Capture information about the transportation vessel etc. • Not currently available in the CMET …..but the note for SpecimenProcessStep class says that it captures event as Specimen Received in lab. This class also captures specimen aliquoting, specimen treatment etc. • Suggested Action • Add a sender and receiver as classes • Classes to have “time stamp” attribute • Other details to capture: site to lab or lab to lab transportation. transportation container, transportation vessel, transportation vehicle etc.

  11. Acknowledgements Austin J. Kreisler and The Clinical Genomics Work group

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