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.
|Rows 1, 4:||Show the date that the original primary and secondary tumor tissue samples were collected. BESTDY is the actual study day of the start of the observation relative to the sponsor-defined RFSTDTC in Demographics (DM).|
|Rows 2, 5:|
Show that a specimen from the tumor tissue sample was retrieved from an archived sample for testing. The date the archived sample was retrieved was represented in BESTDTC.
|Rows 3, 6:||After the slides were assessed by hematoxylin and eosin (H&E) staining for sufficient amount of tumor specimen, DNA was then extracted from the original tumor samples for genetic testing.|
Shows a blood sample was taken on the day the secondary tumor tissue was collected.
|1||PACA015||BE||1700||1||300067||COLLECTING||COLLECTING||TUMOR TISSUE||PANCREAS, HEAD||1||SCREENING||2008-05-05||-300||PRIMARY|
|2||PACA015||BE||1700||2||300067||ARCHIVE RETRIEVING||ARCHIVE RETRIEVING||TUMOR TISSUE||1||SCREENING||2009-05-05||-9|
|4||PACA015||BE||1700||4||400081||COLLECTING||COLLECTING||TUMOR TISSUE||LUNG, RIGHT LOWER LOBE||1||SCREENING||2009-04-30||-15|
|5||PACA015||BE||1700||5||400081||ARCHIVE RETRIEVING||ARCHIVE RETRIEVING||TUMOR TISSUE||1||SCREENING||2009-05-05||-9|
BE NSV Metadata
|BETTSORI||Tumor Tissue Origin||text|
Non-standard Record Qualifier
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.
|1||PACA015||BS||1700||1||300067-1||TUMCECE||Tumor Cells/Total Cells||25||%||25||25||%||TUMOR TISSUE||HEMATOXYLIN AND EOSIN STAIN||1||SCREENING||2008-05-05|
|2||PACA015||BS||1700||2||400081-1||TUMCECE||Tumor Cells/Total Cells||32||%||32||32||%||TUMOR TISSUE||HEMATOXYLIN AND EOSIN STAIN||1||SCREENING||2009-04-30|
The RELREC dataset shows the relationship between the BE and BS datasets.