Illustrates Domains
BE
BS
RELSPEC
Illustrates Variables
BEREFID
BESPEC
BETTSORI
BSREFID
BSSPEC
BSMETHOD
REFID
SPEC
PARENT
LEVEL
Content
This is an example of tumor specimen collection and handling in a study. The protocol required that a subject have a specimen from the original primary tumor. If the subject presented with any metastatic disease, a specimen from at least 1 site where the tumor had metastasized was also required. The Biospecimen Events (BE) domain was used to represent the collection of the specimen and the retrieval of any specimen from an archived sample. The sponsor allowed either formalin-fixed paraffin embedded (FFPE) tissue or fresh frozen tissue samples to be used.
BELOC, BELAT, and BEDIR are used to represent the anatomic location where the specimen was extracted. These location variables are populated only when the subject participates in and is directly affected by the event given in BETERM. The NSV BETTSORI (Tumor Tissue Origin) is used to indicate whether the collected sample was extracted from a primary tumor site or a metastatic (secondary) tumor site. Like the location variable, this NSV is used only when the subject participates in and is directly affected by the event given in BETERM. This NSV is not used to represent any actual findings about the specimen.
The sponsor also recorded the event of DNA extraction from each original specimen. This DNA extraction is considered an event which occurred to the biospecimen. BEENDTC is null, but included in the dataset because it is an expected SDTM variable. Note that BEDTC is not included, as explained in Section 1.3, Known Issues.
A challenge when performing molecular tests is the capability of detecting mutations in samples consisting of a mixture of tumor cells and normal cells. The percentage of tumor cells in the sample may impact the interpretation of these tests. Therefore, the sponsor needed to calculate the percentage of tumor cells in each specimen obtained from a tumor sample.
The Biospecimen (BS) dataset contains the details about the characteristics of the specimen; in this case, the tumor cell percentage from each tumor sample. Note that BSDTC is the date the tumor sample was obtained.
The RELSPEC dataset illustrates the relationships between the specimens. A specimen with a LEVEL value of "1" and a blank PARENT value indicates a "collected sample". All other values indicate "derived samples". SPEC shows the specimen type for the sample regardless of whether it is collected or derived.The RELREC dataset shows the relationship between the BE and BS datasets.