Global Specimen Identifiers TBPT Workspace Call 19 July 2010

From 2009 caBIG Life Sciences Objectives Unmet NeedProposed Approach Over the grid, need to be able to identify molecular assays run on a given biospecimen and to link biospecimen annotations to molecular assays Provide globally unique grid IDs for biospecimens and other objects. Next steps: Discuss grid identifier status with caGrid team. Address functional issues with TBPT workspace

Development of GSID service within caTissue Global Specimen identifier service will be developed within caTissue development contract Standalone service Does not require caTissue to use it …but caTissue 2.0 will make use of the GSID service

Existing GSID documents Use cases Service functions Notes from Dec 2009 Face to Face Meeting: GSID_Notes_FIN[1].docx GSID_Notes_FIN[1].docx Frequently Asked Questions

Key projects that will use GSID Cancer Human Biobank (caHUB) The Cancer Genome Atlas (TCGA) To serve caHUB the GSID service needs to be in place by Sept

Use cases

Create Root-Level Specimen Create Root-Level Specimen: A cancer patient volunteers to participate in a clinical trial. When the patient is accepted to the trial, a registered nurse registers the patient. The system automatically requests a new identifier from the specimen identifier service and assigns the grid-unique identifier to identify the patient in the study on the grid. This identifier is stored as a root-level identifier (the identifier has no parent specimen). The root is available to be associated with children any time a specimen is collected from the patient.

Create Child-Level Specimen – New Specimen from a Study Participant New Specimen from a Study Participant: A cancer patient is scheduled for a treatment regimen that involves specimen collection. The researcher schedules a specimen collection through a grid calendar. A grid-unique identifier is automatically created for each sample that is scheduled for collection (with “expected” as a qualifier) and is added to the traceability tree as a child of the patient’s grid-unique identifier. The morning of the scheduled collection, a red-top tube and yellow-top tube are created with the specimen identifiers printed along with the associated bar code directly on the vial. When the patient arrives for the scheduled blood collection, the lab technician collects the specimens in the marked tubes. The technician records the storage conditions of the specimen, which will be associated with the specimen identifier. The technician also changes the status of the specimen from “expected” to “existing.”

Create Child-Level Specimen – Shipping to a New Institution A lab researcher reads a paper published in a peer-reviewed journal and is interested in the results. He designs a study and uses the paper as a reference to the biobank from which he can obtain the required tissue samples. Following institution procedures, the biobank personnel checks with the tissue-use committee to see if the samples can be shipped. Upon approval, the biobank technologist obtains the specimen from storage and takes a portion of the specimen – returning the remainder to storage. The system automatically generates a new identifier for the new portion, making it a child of the original specimen. The technician then places the new identifier on the tube before shipping the specimen.

Shipping to a New Institution using existing identifier A lab researcher reads a paper published in a peer-reviewed journal and is interested in the results. He designs a study and uses the paper as a reference to the biobank from which he can obtain the required tissue samples. Following institution procedures, the biobank personnel checks with the tissue-use committee to see if the samples can be shipped. Upon approval, the biobank technologist updates the inventory record in the grid-enabled specimen management system, indicating the specimen is removed from storage for shipment. The technician ships the specimen using the existing identifier.

Create Child-Level Specimen – Modifying the Specimen A patient with leukemia is registered in a clinical trial has donated a blood sample that has a unique identifier associated with it at the time of the draw. A researcher is interested in a particular gene sequence in cancer patients and has received an aliquot of the blood sample appropriately from a biobank. The researcher logs into caArray and indicates she is creating a DNA extract from the sample. The system automatically generates a grid-unique identifier for the DNA and associates it as a child of the blood specimen. The researcher then adds details of storage conditions for the DNA.

Culling a Specimen A biobank receives a collection of tumor blocks from a breast cancer study. Several slices of the blocks are distributed for research studies, each slice with a unique identifier. After several years, the biobank decides to cull its collection, and the tumor block collection is marked for culling in the specimen management system. The physical specimen is destroyed, and the identifier is marked as “unavailable,” but the traceability tree is maintained.

Search History of Specimen A researcher reads an article and identifies a specimen of interest for an experiment related to her area of research. She orders the specimen from the biobank referenced by the author of the article, but is unable to repeat the experimental results. Suspecting the specimen has not been carefully handled, the researcher contacts the biobank. The biobank tracks the specimen to the patient and is able to locate several other aliquots from the same patient, from a different draw. The researcher agrees that these samples qualify as equivalent for the study and requests a new aliquot. With this sample, she is able to duplicate results.

Service functions

Specimen identification service functions Obtain a set of identifiers which a system may use until further notice. Resolve specimen history i.e. given a specimen id find the ids of all its parents Resolve specimen descendency i.e. given a specimen id find all its children. Resolve specimen distribution/data availability i.e. where was a specimen sent to or where has data been stored on it? It’s really the latter that is important from a caBIG perspective. Register data on a specimen. Track a patient over time and sites Always generate the same id for the same patient

Next steps Definition of GSID service Incorporation of feedback to date caTissue development planning Publish development documents Location to be determined Will be published to caBIG TBPT listserv Provide additional feedback