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

1 CENTER_NO (*PK) number (2,0) Required:true
Center identification number. *CENTER_NO & NUC_ACID CID are the primary key for the table.
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 GENE string (20) Required:true
Gene on which testing has been performed.
Allowable Values
BRCA1  
BRCA2  
MLH1  
MSH2  
MSH6  
PMS2  
EPCAM  


4 NUC_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.

5 MLPA_DATE_TESTED string (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:
1700 Minimum year


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


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


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


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


10 MLPA_EXON_FROM number (10,0) Required:false
Starting exon in range.
Allowable Values
1 to 9999999999 or -7 Range
   
-7 NA: 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


11 MLPA_EXON_TO number (10,0) Required:false
Ending exon in range.
Allowable Values
1 to 9999999999 or -7 Range
   
-7 NA: 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


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

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

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