Tumor Specimen Collection and Handling 

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.

be.xpt
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.
Row 7:

Shows a blood sample was taken on the day the secondary tumor tissue was collected.

be.xpt

Row

STUDYID

DOMAIN

USUBJID

BESEQ

BEREFID

BETERM

BEDECOD

BESPECBELOCVISITNUM

VISIT

BESTDTC

BEENDTC

BESTDY
BETTSORI
1PACA015BE17001300067COLLECTINGCOLLECTINGTUMOR TISSUEPANCREAS, HEAD1SCREENING2008-05-05
-300
PRIMARY
2PACA015BE17002300067ARCHIVE RETRIEVINGARCHIVE RETRIEVINGTUMOR  TISSUE
1SCREENING2009-05-05
-9

3PACA015BE17003300067-1DNA EXTRACTING

EXTRACTING

DNA
1SCREENING2009-05-08
-6

4PACA015BE17004400081COLLECTINGCOLLECTINGTUMOR TISSUELUNG, RIGHT LOWER LOBE1SCREENING2009-04-30
-15

METASTATIC 

5PACA015BE17005400081ARCHIVE RETRIEVINGARCHIVE RETRIEVINGTUMOR TISSUE
1SCREENING2009-05-05
-9

6PACA015BE17006400081-1DNA EXTRACTING

EXTRACTING

DNA
1SCREENING2009-05-08
-6

7PACA015BE17007400082COLLECTINGCOLLECTINGBLOOD
1SCREENING2009-04-30
-15

BE NSV Metadata

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.

bs.xpt

bs.xpt

RowSTUDYIDDOMAINUSUBJIDBSSEQBSREFIDBSTESTCDBSTESTBSORRESBSORRESUBSSTRESCBSSTRESNBSSTRESUBSSPECBSMETHODVISITNUMVISITBSDTC
1PACA015BS17001300067-1TUMCECETumor Cells/Total Cells25%2525%TUMOR TISSUEHEMATOXYLIN AND EOSIN STAIN1SCREENING2008-05-05
2PACA015BS17002400081-1TUMCECETumor Cells/Total Cells32%3232%TUMOR TISSUEHEMATOXYLIN AND EOSIN STAIN1SCREENING2009-04-30
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.
relspec.xpt

relspec.xpt

Row

STUDYID

USUBJID

REFID

SPEC

PARENT

LEVEL

1

PACA015

1700

300067

TUMOR TISSUE


1

2

PACA015

1700

300067-1

DNA

300067

2

3

PACA015

1700

400081

TUMOR TISSUE


1

4

PACA015

1700

400081-1

DNA

400081

2

The RELREC dataset shows the relationship between the BE and BS datasets.

relrec.xpt

relrec.xpt

RowSTUDYIDRDOMAINUSUBJIDIDVARIDVARVALRELTYPERELID
1PACA015BE
BEREFID
ONEBE-BS-1
2PACA015BS
BSREFID
ONEBE-BS-1