Module: molecular

Module Contents

  1. mlpa
    1.CENTER_NO (*PK)
    2.PERSON_ID
    3.GENE
    4.NUC_ACID_CID (*PK)
    5.MLPA_DATE_TESTED
    6.MLPA_INVEST_ID
    7.MLPA_DETECTION_METHOD
    8.MLPA_RESULT
    9.MLPA_RESULT_SUB
    10.MLPA_EXON_FROM
    11.MLPA_EXON_TO
    12.MLPA_OTHER_TEST_COMMENT
    13.GENOMIC_REGION_TESTED
    14.VARIANT_NAME

1CENTER_NO (*PK)number (2,0)Required:true
Center identification number. *CENTER_NO & NUC_ACID CID are the primary key for the table.
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.

3GENEstring (20)Required:true
Gene on which testing has been performed.
Allowable Values
BRCA1
BRCA2
MLH1
MSH2
MSH6
PMS2
EPCAM


4NUC_ACID_CID (*PK)string (40)Required:true
Identifier used internally by centers for a nucleic acid sample from a single extraction. *CENTER_NO & NUC_ACID_CID are the primary key for the table.
5MLPA_DATE_TESTEDstring (8)Required:true
Date of test.
Date Value Check
The date must follow to the following format:

Format YYYYMMDD. Must consist of valid date.
Components of date should be right justified and zero filled.
MM = 01 - 12, 88, 99
DD = 01 - 31, 88, 99
YYYY = Minimum year - system date year, 8888, 9999
Use 88, 8888 for not currently known, in progress to obtain information.
Use 99, 9999 for not known.
If century is known, but year is unknown then give an estimate of year or code YYYY = 9999.
If MM = 99 then DD must = 99.
If century is known, but year is unknown then give an estimate of year or code YYYY = 9999.
If YYYY = 9999 then MM and DD must = 99.

The following special parameters are used:
1700Minimum year



6MLPA_INVEST_IDnumber (1,0)Required:true
Laboratory investigator conducting the tests on samples.
Allowable Values
1Dr. Steve Thibodeau
2Dr. Melissa Southey
3GMP Genetics (Corporation)
4Joanne Young
5Clinical Laboratory
6Dan Buchanan


7MLPA_DETECTION_METHODnumber (1,0)Required:false
Testing method.
Allowable Values
1Multiplex ligation-dependent probe amplification (MLPA)
2Conversion analysis


8MLPA_RESULTnumber (1,0)Required:true
Summary of test findings.
Allowable Values
0Failed test
1Negative (no deletion or duplication)
2Deletion
3Duplication
4Equivocal


9MLPA_RESULT_SUBnumber (2,0)Required:false
Additional specific findings of test.
Allowable Values
0Failed test
1Confirmed by second MLPA test only
2Confirmed by Southern blot
3Confirmatory test not done for positive result
4Confirmed by other method or other information
5Deletion artifact. DNA sequence change under primer found by sequencing (scored as negative)
6Deletion artifact. Results not consistent, normal on repeat (scored as negative)
7Deletion artifact. Southern did not confirm deletion
8Deletion artifact. Sequencing and/or Southern not done to determine cause for discordant result (assumed to be negative based on analysis of other similar cases)
9Deletion artifact, Other
10Duplication artifact. Results not consistent, normal on MLPA repeat (scored as negative)
11Duplication artifact. Southern did not confirm duplication
12Duplication artifact. Sequencing and/or Southern not done to determine cause for discordant result (assumed to be negative based on analysis of other similar cases)
13Duplication artifact, Other
14Equivocal. Single exon deletion, unclear whether artifact; Southern could not be performed
15Equivocal. Multiple exons deleted, not enough sample to repeat test
16Equivocal. Single exon duplication, unclear whether artifact; Southern could not be performed
17Equivocal. Multiple exons duplicated, not enough sample to repeat test
-7NA One assay only for negative result

Error Description
If MLPA_RESULT = 0, then MLPA_RESULT_SUB = 0
If MLPA_RESULT=1 then MLPA_RESULT_SUB must be in (-7,1,2) or in range 4-13
If MLPA_RESULT is 2 or 3, then MLPA_RESULT_SUB must be in range 1-4
If MLPA_RESULT=4, then MLPA_RESULT_SUB must be in range 14-17

10MLPA_EXON_FROMnumber (10,0)Required:false
Starting exon in range.
Allowable Values
1 to 9999999999 or -7Range
-7NA: Negative result or failed test Otherwise number of starting exon.

Error Description
If MLPA_RESULT is in (0,1), then MLPA_EXON_FROM must be -7
If MLPA_RESULT is in (2,3,4), then MLPA_EXON_FROM must not be -7
If GENE = MLH1 then MLPA_EXON_FROM must be -7 or in range 1-19
If GENE = MSH2 then MLPA_EXON_FROM must be -7 or in range 1-16
If GENE = MSH6 then MLPA_EXON_FROM must be -7 or in range 1-10
If GENE = PMS2 then MLPA_EXON_FROM must be -7 or in range 1-15

11MLPA_EXON_TOnumber (10,0)Required:false
Ending exon in range.
Allowable Values
1 to 9999999999 or -7Range
-7NA: Negative result or failed test Otherwise number of starting exon.

Error Description
If MLPA_RESULT is 0 or 1, then MLPA_EXON_TO must be -7
If MLPA_RESULT is in (2,3,4), then MLPA_EXON_TO must not be -7
If GENE = MLH1 then MLPA_EXON_TO must be -7 or in range 1-19
If GENE = MSH2 then MLPA_EXON_TO must be -7 or in range 1-16
If GENE = MSH6 then MLPA_EXON_TO must be -7 or in range 1-10
If GENE = PMS2 then MLPA_EXON_TO must be -7 or in range 1-15

12MLPA_OTHER_TEST_COMMENTstring (400)Required:false
Text field containing comments regarding other test findings.

13GENOMIC_REGION_TESTEDstring (100)Required:false
Indicates what part(s) of the gene or other genomic region(s) was tested.

14VARIANT_NAMEstring (100)Required:false
Proper variant name using HGVS nomenclature.