Module: derived

Module Contents

  1. d_MSI_IHC_PK_IHC

1PERSON_IDstring (12)Required:true
Number that Uniquely Identifies an Individual.

2COLLECTION_CIDstring (40)Required:true
The label assigned by the center to all tissue associated with a single surgical event - resection or biopsy/endoscopy procedure.


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

3TEST_TISSUEnumber (1,0)Required:true
Type of tissue tested.

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
1Cancer
2Contiguous (Adjacent) adenoma
3Colon Polyp
4Gastric polyp
5Sebatious adenoma


4TUMOR_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
1 to 99 or -9, -15Range
-9NA/Out of scope: Tissue does not currently have a TUMOR_NO and is not cancer or contiguous adenoma
-15Information Unknown


5POLYP_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
1 to 99 or -9, -1Range
-9NA/Out of scope. Tissue is not a polyp.
-1Polyp has IHC/MSI result but center is currently unable to locate polyp pathology information. Center review to obtain this information is currently underway.


6BLOCK_SPEC_CIDstring (40)Required:true
Unique local identifier used at a center to uniquely identify a block tissue specimen.
Allowable Values
-15 Information Unknown


7IHC_STATUS_TISSUEnumber(1,0)Required:true
IHC status of tissue from tested block.

Expression is absent if any of IHC_MLH1, IHC_MSH2, IHC_MSH6, IHC_PMS2 equal either 0 or 4. Expression is normal if at least one of them equals 1 or 2 and none equal 0 or 4.
Allowable Values
-8 No data transmitted from centers
-7 NA/Out of scope: None of IHC_MLH1, IHC_MSH2, IHC_MSH6, IHC_PMS2 recorded values 0,1,2,4.
1 Normal MMR protein expression
2 Absence of MMR protein expression


8MSI_STATUS_TISSUEnumber(1,0)Required:true
MSI status of tissue from tested block.

The maximum of MSI_STATUS_DNA over all DNA extractions from a given tissue-block combination.
Allowable Values
-8 No data transmitted from centers
-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


9MSIIHC_STATUS_TISSUEnumber(1,0)Required:true
MMR status considering all MSI DNA extractions and IHC results on that tissue/block combination.

MSIIHC_STATUS_TISSUE has a value for each tissue that has an MSI and/or IHC result within a given block.
MSIIHC_STATUS_TISSUE is defective 2 if MSI_STATUS_TISSUE is high and IHC_STATUS_TISSUE is absent.
MSIIHC_STATUS_TISSUE is defective 1 if it does not qualify as defective 2 and MSI_STATUS_TISSUE is high or IHC_STATUS_TISSUE is absent.
MSIIHC_STATUS_TISSUE is proficient 2 if MSI_STATUS_TISSUE is stable or low and IHC_STATUS_TISSUE is normal.
MSIIHC_STATUS_TISSUE is proficient 1 if it does not qualify as proficient 2 or as defective, and MSI_STATUS_TISSUE is stable or low or IHC_STATUS_TISSUE is normal.
MSIIHC_STATUS_TISSUE otherwise equals -7, corresponding to both MSI_STATUS_TISSUE and IHC_STATUS_TISSUE equaling -7 or one them equaling -7 with no record available to merge to on the other table.
Allowable Values
-8 No data transmitted from centers
-7 NA/Out of Scope - Both source variables out of scope
1 Proficient MMR 1
2 Proficient MMR 2
3 Defective MMR 1
4 Defective MMR 2