Module: molecular

Module Contents

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

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.

GENE

string (20)

Required:true

Gene on which testing has been performed.

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.

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

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

MLPA_DETECTION_METHOD

number (1,0)

Required:false

Testing method.

Allowable Values
1	Multiplex ligation-dependent probe amplification (MLPA)
2	Conversion analysis

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
5	Inversion

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
Error Description
If MLPA_RESULT=1 then MLPA_RESULT_SUB must be in (-7,1,2) or in range 4-13
Error Description
If MLPA_RESULT is 2 or 3, then MLPA_RESULT_SUB must be in range 1-4
Error Description
If MLPA_RESULT=4, then MLPA_RESULT_SUB must be in range 14-17
This special value check will pass under the following conditions: MLPA_RESULT_SUB in {0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,-7}

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
Error Description
If MLPA_RESULT is in (2,3,4), then MLPA_EXON_FROM must not be -7
Error Description
If GENE = MLH1 then MLPA_EXON_FROM must be -7 or in range 1-19
Error Description
If GENE = MSH2 then MLPA_EXON_FROM must be -7 or in range 1-16
Error Description
If GENE = MSH6 then MLPA_EXON_FROM must be -7 or in range 1-10
Error Description
If GENE = PMS2 then MLPA_EXON_FROM must be -7 or in range 1-15
range check will pass under the following conditions: {MLPA_EXON_FROM>=1 and MLPA_EXON_FROM<=1 } This special value check will pass under the following conditions: MLPA_EXON_FROM in {-7}

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
Error Description
If MLPA_RESULT is in (2,3,4), then MLPA_EXON_TO must not be -7
Error Description
If GENE = MLH1 then MLPA_EXON_TO must be -7 or in range 1-19
Error Description
If GENE = MSH2 then MLPA_EXON_TO must be -7 or in range 1-16
Error Description
If GENE = MSH6 then MLPA_EXON_TO must be -7 or in range 1-10
Error Description
If GENE = PMS2 then MLPA_EXON_TO must be -7 or in range 1-15
range check will pass under the following conditions: {MLPA_EXON_TO>=1 and MLPA_EXON_TO<=1 } This special value check will pass under the following conditions: MLPA_EXON_TO in {-7}

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.