Module: molecular

Module Contents

    1. ihc


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


2 PERSON_ID string (12) Required:true
Number that Uniquely Identifies an Individual.

3 IHC_TEST_LAB number (1,0) Required:true
Lab that conducted the results
Allowable Values
1 CFR lab
2 Clinical lab


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

5 TEST_TISSUE number (1,0) Required:true
Type of tissue tested.
Allowable Values
1 Cancer
2 Contiguous (Adjacent) adenoma
3 Colon Polyp
4 Gastric polyp
5 Sebatious adenoma


6 TUMOR_NO number (2,0) Required:true
Numbers labeling tumors of the individual. Numbers are not necessarily sequential.
Allowable Values
1 to 99 or -9, -15 Range
   
-9 NA/Out of scope: Tissue does not currently have a TUMOR_NO and is not cancer or contiguous adenoma
-15 Information Unknown


7 POLYP_NO number (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.
Allowable Values
1 to 99 or -1, -9 Range
   
-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.


8 BLOCK_SPEC_CID string (40) Required:true
Unique local identifier used at a center to uniquely identify a block tissue specimen.

9 METASTASIS number (1,0) Required:true
Primary or metastatic tumor.
Allowable Values
1 Primary
2 Metastatasis
-9 Test is not performed on cancerous tissue


10 IHC_MLH1 number (2,0) Required:true
IHC result for MSI test at locus MLH1
Allowable Values
0 Negative - Expression absent and abnormal
1 Positive - Expression present and normal
2 Positive - Technically poor, probably positive
3 Positive - Technically equivocal, not truly interpretable but if forced would be positive
4 Negative - Technically poor, probably negative
5 Negative - Technically equivocal, not truly interpretable but if forced would be negative
7 Heterogeneous tumor - some areas lack expression and some have expression
8 Reduced - expression reduced but not absent
-11 Technical failure
-12 Not tested
-13 Quantity of tissue not sufficient


11 IHC_MSH2 number (2,0) Required:true
IHC result for MSI test at locus MSH2
Allowable Values
0 Negative - Expression absent and abnormal
1 Positive - Expression present and normal
2 Positive - Technically poor, probably positive
3 Positive - Technically equivocal, not truly interpretable but if forced would be positive
4 Negative - Technically poor, probably negative
5 Negative - Technically equivocal, not truly interpretable but if forced would be negative
7 Heterogeneous tumor - some areas lack expression and some have expression
8 Reduced - expression reduced but not absent
-11 Technical failure
-12 Not tested
-13 Quantity of tissue not sufficient


12 IHC_MSH6 number (2,0) Required:true
IHC result for MSI test at locus MSH6
Allowable Values
0 Negative - Expression absent and abnormal
1 Positive - Expression present and normal
2 Positive - Technically poor, probably positive
3 Positive - Technically equivocal, not truly interpretable but if forced would be positive
4 Negative - Technically poor, probably negative
5 Negative - Technically equivocal, not truly interpretable but if forced would be negative
7 Heterogeneous tumor - some areas lack expression and some have expression
8 Reduced - expression reduced but not absent
-11 Technical failure
-12 Not tested
-13 Quantity of tissue not sufficient


13 IHC_PMS2 number (2,0) Required:true
IHC result for MSI test at locus PMS2
Allowable Values
0 Negative - Expression absent and abnormal
1 Positive - Expression present and normal
2 Positive - Technically poor, probably positive
3 Positive - Technically equivocal, not truly interpretable but if forced would be positive
4 Negative - Technically poor, probably negative
5 Negative - Technically equivocal, not truly interpretable but if forced would be negative
7 Heterogeneous tumor - some areas lack expression and some have expression
8 Reduced - expression reduced but not absent
-11 Technical failure
-12 Not tested
-13 Quantity of tissue not sufficient