MSI

Module: molecular

Module Contents

  1. msi
    1.CENTER_NO
    2.PERSON_ID
    3.MSI_TEST_LAB
    4.COLLECTION_CID
    5.TEST_TISSUE
    6.TUMOR_NO
    7.POLYP_NO
    8.BLOCK_SPEC_CID
    9.NUC_ACID_CID_TUMOR
    10.NUC_ACID_CID_NORMAL
    11.METASTASIS
    12.MSI_DETECTION_METHOD
    13.MSI_ACTC
    14.MSI_BAT25
    15.MSI_BAT26
    16.MSI_BAT34C4
    17.MSI_BAT40
    18.MSI_D5S346
    19.MSI_D10S197
    20.MSI_D17S250
    21.MSI_D18S55
    22.MSI_D2S123
    23.MSI_MYCL

1 CENTER_NO number (2,0) Required:true
Center identification number.
Allowable Values
11 Sinai Health Systems (formerly Cancer Care Ontario)
12 Cedars-Sinai & Cleveland Clinic (formerly USC Consortium)
13 University of Melbourne
14 University of Hawaii Cancer Center
15 Mayo Clinic
16 Fred Hutch, Seattle
17 UCSF: University of California at San Franscisco (formerly CPIC, originally Northern California (NCCC))


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

3 MSI_TEST_LAB number (1,0) Required:true
Code for type of lab that did the MSI testing.
Allowable Values
1 CFR Lab
2 Clinical Lab


4 COLLECTION_CID string (30) Required:true
Identifier used internally by centers to denote a unique surgical event.

5 TEST_TISSUE number (1,0) Required:true
Tissue on which test was performed.
Allowable Values
1 Cancer
2 Contiguous (Adjacent) adenoma
3 Colon Polyp
4 Gastric polyp
5 Sebaceous 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 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 -9, -1 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 NUC_ACID_CID_TUMOR string (40) Required:true
Center's unique identifier for the tumor DNA used in this MSI test. Each DNA extraction has a unique identifier.

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

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


12 MSI_DETECTION_METHOD number (2,0) Required:true
MSI Testing method.
Allowable Values
1 PCR non-radiolabeled
2 PCR radiolabeled
3 Fluorescent PCR capillary electrophoresis
4 Fluorescent PCR slab gel electrophoresis
5 Silver-stained gel electrophoresis
-13 Not tested: Quantity of DNA or tissue not sufficient
-15 Method not specified


13 MSI_ACTC number (2,0) Required:true
MSI test result at ACTC locus
Allowable Values
1 Stable
2 Unstable
6 Equivocal (Inconclusive)
7 Stable - Normal DNA not used in test
8 Unstable - Normal DNA not used in test
9 Equivocal (Inconclusive) - Normal DNA not used in test
-11 No Amplification
-12 Not tested, reason not specified
-13 Quantity of DNA or tissue not sufficient
-14 Tested, outcome not specified
-15 Unknown if tested


14 MSI_BAT25 number (2,0) Required:true
MSI test result at BAT25 locus
Allowable Values
1 Stable
2 Unstable
6 Equivocal (Inconclusive)
7 Stable - Normal DNA not used in test
8 Unstable - Normal DNA not used in test
9 Equivocal (Inconclusive) - Normal DNA not used in test
-11 No Amplification
-12 Not tested, reason not specified
-13 Quantity of DNA or tissue not sufficient
-14 Tested, outcome not specified
-15 Unknown if tested


15 MSI_BAT26 number (2,0) Required:true
MSI test result at BAT26 locus
Allowable Values
1 Stable
2 Unstable
6 Equivocal (Inconclusive)
7 Stable - Normal DNA not used in test
8 Unstable - Normal DNA not used in test
9 Equivocal (Inconclusive) - Normal DNA not used in test
-11 No Amplification
-12 Not tested, reason not specified
-13 Quantity of DNA or tissue not sufficient
-14 Tested, outcome not specified
-15 Unknown if tested


16 MSI_BAT34C4 number (2,0) Required:true
MSI test result at BATC34C4 locus
Allowable Values
1 Stable
2 Unstable
6 Equivocal (Inconclusive)
7 Stable - Normal DNA not used in test
8 Unstable - Normal DNA not used in test
9 Equivocal (Inconclusive) - Normal DNA not used in test
-11 No Amplification
-12 Not tested, reason not specified
-13 Quantity of DNA or tissue not sufficient
-14 Tested, outcome not specified
-15 Unknown if tested


17 MSI_BAT40 number (2,0) Required:true
MSI test result at BAT40 locus
Allowable Values
1 Stable
2 Unstable
6 Equivocal (Inconclusive)
7 Stable - Normal DNA not used in test
8 Unstable - Normal DNA not used in test
9 Equivocal (Inconclusive) - Normal DNA not used in test
-11 No Amplification
-12 Not tested, reason not specified
-13 Quantity of DNA or tissue not sufficient
-14 Tested, outcome not specified
-15 Unknown if tested


18 MSI_D5S346 number (2,0) Required:true
MSI test result at D5S346 locus
Allowable Values
1 Stable
2 Unstable
6 Equivocal (Inconclusive)
7 Stable - Normal DNA not used in test
8 Unstable - Normal DNA not used in test
9 Equivocal (Inconclusive) - Normal DNA not used in test
-11 No Amplification
-12 Not tested, reason not specified
-13 Quantity of DNA or tissue not sufficient
-14 Tested, outcome not specified
-15 Unknown if tested


19 MSI_D10S197 number (2,0) Required:true
MSI test result at D10S197 locus
Allowable Values
1 Stable
2 Unstable
6 Equivocal (Inconclusive)
7 Stable - Normal DNA not used in test
8 Unstable - Normal DNA not used in test
9 Equivocal (Inconclusive) - Normal DNA not used in test
-11 No Amplification
-12 Not tested, reason not specified
-13 Quantity of DNA or tissue not sufficient
-14 Tested, outcome not specified
-15 Unknown if tested


20 MSI_D17S250 number (2,0) Required:true
MSI test result at D17S250 locus
Allowable Values
1 Stable
2 Unstable
6 Equivocal (Inconclusive)
7 Stable - Normal DNA not used in test
8 Unstable - Normal DNA not used in test
9 Equivocal (Inconclusive) - Normal DNA not used in test
-11 No Amplification
-12 Not tested, reason not specified
-13 Quantity of DNA or tissue not sufficient
-14 Tested, outcome not specified
-15 Unknown if tested


21 MSI_D18S55 number (2,0) Required:true
MSI test result at D18S55 locus
Allowable Values
1 Stable
2 Unstable
6 Equivocal (Inconclusive)
7 Stable - Normal DNA not used in test
8 Unstable - Normal DNA not used in test
9 Equivocal (Inconclusive) - Normal DNA not used in test
-11 No Amplification
-12 Not tested, reason not specified
-13 Quantity of DNA or tissue not sufficient
-14 Tested, outcome not specified
-15 Unknown if tested


22 MSI_D2S123 number (2,0) Required:true
MSI test result at D2S123 locus
Allowable Values
1 Stable
2 Unstable
6 Equivocal (Inconclusive)
7 Stable - Normal DNA not used in test
8 Unstable - Normal DNA not used in test
9 Equivocal (Inconclusive) - Normal DNA not used in test
-11 No Amplification
-12 Not tested, reason not specified
-13 Quantity of DNA or tissue not sufficient
-14 Tested, outcome not specified
-15 Unknown if tested


23 MSI_MYCL number (2,0) Required:true
MSI test result at MyCL locus
Allowable Values
1 Stable
2 Unstable
6 Equivocal (Inconclusive)
7 Stable - Normal DNA not used in test
8 Unstable - Normal DNA not used in test
9 Equivocal (Inconclusive) - Normal DNA not used in test
-11 No Amplification
-12 Not tested, reason not specified
-13 Quantity of DNA or tissue not sufficient
-14 Tested, outcome not specified
-15 Unknown if tested