Module: derived

Module Contents

  1. d_MSI_IHC_PK_MSI

1CENTER_NOnumber (2,0)Required:true
Center Identification Number.
Allowable Values
11Cancer Care Ontario - Colon
12USC Consortium - Colon
13University of Melbourne - Colon
14Cancer Research Center of Hawaii - Colon
15Mayo Clinic - Colon
16Fred Hutchinson, Seattle - Colon
17Northern California (NCCC) - Colon


2PERSON_IDstring (12)Required:true
Number that uniquely identifies an individual.

3COLLECTION_CIDstring (30)Required:true
Identifier used internally by centers to denote a unique surgical event.

This data element is typically used to allow aggregation of all materials, such as blocks, from a single surgery.

4TEST_TISSUEnumber (1,0)Required:true
Tissue on which test was performed.

Only values of 1,2,3 link to pathology information.
Although values 2 and 3 may represent the same tissue type, their pathology information is stored in different database tables. Adjacent adenomas are recorded on the Colorect_Malig table and so are associated with a cancer; Colon polyps are recorded on the Polyps table. As a result, the pathology information for each will differ somewhat.
There may be cases where TEST_TISSUE variable has level 2 but the ADJ_ADEN variable of Colorect_Malig table indicates no adjacent adenoma present. In these cases, the TEST_TISSUE value takes precedence and the adjacent adenoma is considered to have been overlooked.
Allowable Values
1 Cancer
2 Contiguous (Adjacent) adenoma
3 Colon polyp
4 Gastric polyp
5 Sebatious adenoma


5TUMOR_NOnumber (2,0)Required:true
Numbers labeling tumors of the individual.

Numbers are not necessarily sequential.
No adjustment is made when a tumor is deleted from the system. Tumor numbers are never reused. PERSON_NO plus TUMOR_NO uniquely identifies each tumor in the central database. The same tumor number from different tables (including tables outside of the biospecimen module) must always refer to the same physical tumor.
Allowable Values
-9 NA/Out of scope: Tissue is not cancer or contiguous adenoma.
-15 Information Unknown


6POLYP_NOnumber (2,0)Required:true
Sequential number over range of 1 to 99 to distinguish a polyp removed on a particular date. The tuple PERSON_ID, DATE_COLLECTED, and POLYP_NO uniquely identify a physical polyp globally within the CFR database.


The colon pathology form has three sets of identical fields for recording information on polyps. The POLYPS table includes corresponding data elements, i.e. POLYP_SITEx, POLYP_TYPEx, POLYP_SIZEx, POLYP_GRADEx, where x is an integer between 1 and 3, inclusive. The physical polyp referenced by x and this data element must be identical.
Polyps are described according to the following rules:
1. The largest polyp is reported first, followed by next largest
2. If size is not indicated, adenomas are reported before hyperplastic polyps
3. Polyps with most severe grade are reported
Not all polyps present in available tissue have an assigned value, as some are not described.
Allowable Values
-9 NA/Out of scope. Tissue is not a polyp.
-1 Polyp has IHC/MSI result but center is currently unable to locate polyp pathology information. Center review to obtain this information is currently underway.


7BLOCK_SPEC_CIDstring (40)Required:true
Unique local identifier used at a center to uniquely identify a block tissue specimen.
Allowable Values
-15 Information Unknown


8NUC_ACID_CID_TUMORstring (40)Required:true
Center's unique identifier for the tumor DNA used in this MSI test. Each DNA extraction has a unique identifier.

Unique Identifier, If this field in not negative, there will be a matching record on the NUC_ACID table that indicates whether remaining tumor DNA from the extraction used for this test is available for distribution to requestors.
If multiple MSI results are provided for the same block and tumor then separate identifiers must be specified.
Allowable Values
- 15 DNA identifying information lost/unknown.
- 14 Center does not keep normal tissue DNA identifying information.
- 13 Quantity of DNA or tissue not sufficient.


9NUC_ACID_CID_NORMALstring (40)Required:true
Center's unique identifier for the normal DNA used in this MSI test. Each DNA extraction has a unique identifier.

Normal DNA may have been extracted from paraffin embedded normal tissue, blood, mouthwash/buccal cells or fresh frozen normal tissue. Paraffin embedded normal tissue is not necessarily associated with the paraffin block from which the tumor DNA is taken.
If this field in not negative, there will be a matching record on the NUC_ACID table that indicates whether remaining normal DNA from the extraction used for this test is available for distribution to requestors.
Allowable Values
- 15 DNA identifying information lost/unknown.
- 14 Center does not keep normal tissue DNA identifying information.
- 13 Quantity of DNA or tissue not sufficient.


10MSI_STATUS_DNAnumber (1,0)Required:true
MSI status of DNA extraction.

For each set of scores with a minimum of 4 of 10 markers (excluding D2S123) that are either stable or unstable (Options 1 and 2 only NOT 7 or 8), the percent unstable among stable and unstable markers is calculated and compared to cutpoints to determine if the results are stable (0% unstable), low (1-29% unstable) or high (30-100% unstable). If only 3 markers are scored but they are all unstable then the status is scored as high.
Allowable Values
-7 NA/Out of scope - Less than 4 marker scores stable or unstable
1 Stable - 0% unstable
2 Low - More than 0% but less than 30% unstable
3 High - At least 30% unstable