Module: molecular

Module Contents

  1. genomics
    1.CENTER_NO (*PK)
    2.PERSON_ID
    3.GENOMIC_CID (*PK)
    4.GENE
    5.VARIANT_ORIGIN
    6.SOURCE_NUC_ACID
    7.NUC_ACID_CID
    8.DETECTION_METHOD
    9.GENOMIC_REGION_TESTED
    10.TEST_RESULT
    11.VARIANT_NAME_RESULT
    12.EXON_NO
    13.INTRON_NO
    14.OTHER_REGION
    15.NUC_POS_START
    16.NUC_POS_END
    17.NUCLEOTIDE_FROM
    18.NUCLEOTIDE_TO
    19.DELETE_SEQ
    20.INSERT_SEQ
    21.TYPE_VARIANT
    22.CODON
    23.AA_FROM
    24.AA_TO
    25.CONSEQUENCE
    26.ZYGOSITY
    27.SEVERITY
    28.INSIGHT_SEVERITY
    29.LAB_ID
    30.LAB_OTHER_TEXT
    31.DATE_TEST

1CENTER_NO (*PK)number (2,0)Required:true
Center identification number. * CENTER_NO & GENOMIC_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.

3GENOMIC_CID (*PK)string (40)Required:true
Center identifier for the test. *CENTER_NO & GENOMIC_CID are the primary key for the table.

4GENEnumber (1,0)Required:true
Gene on which testing has been performed.
Allowable Values
1MLH1
2MSH2
3MSH6
4MUTYH
5PMS2
6BRAF
7KRAS
8EPCAM


5VARIANT_ORIGINnumber (1,0)Required:true
Describes if the variant was tested as an acquired or a germline variant.
Allowable Values
1Presumed somatic
2Known somatic
3Germline

Error Description
If GENE is in (6,7) AND SOURCE_NUC_ACID is in (7,8), then VARIANT_ORIGIN = 1
If GENE is in (6,7) AND SOURCE_NUC_ACID is not in (7,8), then VARIANT_ORIGIN = 3

6SOURCE_NUC_ACIDnumber (1,0)Required:true
Specifies source of tissue used for testing
Allowable Values
1blood
2Mouth wash/saliva
3lymphoblastoid cells
4normal fresh frozen tissue
5other non-tumour tissue
6polyp
7tumour (paraffin embedded tumour- PET)
8tumor- fresh frozen
9unknown/private lab


7NUC_ACID_CIDstring (12)Required:true
Identifier used internally by centers for a single extraction on which the test was carried out

Error Description
If SOURCE_NUC_ACID=9, then NUC_ACID_CID must be -9

8DETECTION_METHODnumber (2,0)Required:true
Germline or somatic DNA testing method. (Mass Spec = Sequenom MassARRAY system, MALDI-TOF)
Allowable Values
1DNA Sequencing
10DHPLC (Denaturing High Performance Liquid Chromatography)
11Phase 1 protocol DHPLC+SEQ (MLH1 and MSH2)
1212 SNP panel genotyping by Mass Spec
1312 SNP panel genotyping, dHPLC with sequencing (MUTYH)
149 SNP panel genotyping by Mass Spec
159 SNP panel genotyping with sequencing (MUTYH)
16PTT
17SSCP
18Fluorescent ASP (BRAF)
19HRM with sequencing (KRAS)
33Sequencing from Conversion Analysis
99Unknown/private genetic test results


9GENOMIC_REGION_TESTEDstring (100)Required:true
Indicates what part(s) of the gene or specific mutation or other genomic region(s) was TESTED

10TEST_RESULTnumber (1,0)Required:true
Result of the test carried out and this is at the test level (e.g. entire gene sequencing or MSH2 exon 2 etc.). This is NOT at person level or at variant level.
Allowable Values
1Change detected
2No change detected
3Test failed
9Equivocal


11VARIANT_NAME_RESULTstring (100)Required:false
Proper variant name using Human Genomic Variant Society (HGVS) nomenclature.

Error Description
If TEST_RESULT is not 1 or 9 then VARIANT_NAME_RESULT must be null
If TEST_RESULT is 1 and DETECTION_METHOD is not 10, then VARIANT_NAME_RESULT must not be null

12EXON_NOnumber (2,0)Required:false
Number of exon containing variant. In the case the variant spans more than one exon, then this field should indicate the first exon affected by the variant.
Allowable Values
1 to 99Range

Error Description
If TEST_RESULT is not 1 or 9 and DETECTION_METHOD is not 10, then EXON_NO must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then EXON_NO must be null
If DETECTION_METHOD = 10 AND CENTER_NO = 11 then must EXON_NO be null
If INTRON_NO is null AND OTHER_REGION is null and TEST_RESULT = 1 AND LAB_ID not in(998,999), then EXON_NO must not be NULL

13INTRON_NOnumber (2,0)Required:false
Number of intron containing variant. In the case the variant spans more than one intron, then this field should indicate the first intron affected by the variant
Allowable Values
1 to 99Range

Error Description
If TEST_RESULT is not 1, INTRON_NO then must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then INTRON_NO must be null
If DETECTION_METHOD = 10 AND CENTER_NO = 11 then INTRON_NO must be null
If EXON_NO is null AND OTHER_REGION is null and TEST_RESULT = 1 AND LAB_ID not in(998,999), then INTRON_NO must not be NULL

14OTHER_REGIONnumber (1,0)Required:false
Region, other than coding exon and intron, containing the variant.
Allowable Values
15 UTR
23 UTR
3Other

Error Description
If TEST_RESULT is not 1 or 9, then OTHER_REGION must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then OTHER_REGION must be null
If DETECTION_METHOD = 10 AND CENTER_NO = 11 then must OTHER_REGION be null
If EXON_NO is null AND INTRON_NO is null and TEST_RESULT = 1 AND LAB_ID not in(998,999), then OTHER_REGION must not be NULL

15NUC_POS_STARTstring (20)Required:false
For exonic mutations, the numeric value of the nucleotide first affected by the mutation relative to the reference sequence. For intronic mutations, the numeric value of the first affected nucleotide relative to the exon number; a (-) indicates the number of nucleotides upstream (5) of the exon, and a (+) indicates the number of nucleotides downstream (3) from the exon. The 5 UTR and 3 UTR are considered to be part of the first andlLast Exon respectively but have special notation here. Positions in the 5-UTR have (-) sign. Positions in the 3-UTR have (*) sign.

Error Description
If TEST_RESULT is not 1 or 9, then NUC_POS_START must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then NUC_POS_START must be null
If TEST_RESULT=1 and LAB_ID not in(998,999), then NUC_POS_START must not be null
If NUC_POS_START is not null AND if OTHER_REGION = 1, then NUC_POS_START must begin with (-)
If NUC_POS_START is not null AND TYPE_VARIANT = 3 (substitution) AND EXON_NO is not null AND OTHER_REGION is null, then NUC_POS_START must not begin with (+,-)
If NUC_POS_START is not null AND If TYPE_VARIANT = 3 (substitution) AND INTRON_NO is not null AND OTHER_REGION is null then NUC_POS_START must begin with in (+, -)
If NUC_POS_START is not null AND If TYPE_VARIANT = 3 (substitution) AND INTRON_NO is not null AND OTHER_REGION is null then NUC_POS_START must begin with in (+, -)
If NUC_POS_START is not null AND if TYPE_VARIANT = 3, then NUC_POS_START = NUC_POS_END
If NUC_POS_START is not null AND if TYPE_VARIANT not in (1,3,9), then NUC_POS_START must not equal NUC_POS_END

16NUC_POS_ENDstring (20)Required:false
For exonic mutations, the numeric value of the nucleotide last affected by the mutation relative to the reference sequence. For intronic mutations, the numeric value of the first affected nucleotide relative to the exon number; a (-) indicates the number of nucleotides upstream (5) of the exon, and a (+) indicates the number of nucleotides downstream (3) from the exon. The 5 UTR and 3 UTR are considered to be part of the first andlLast Exon respectively but have special notation here. Positions in the 5-UTR have (-) sign. Positions in the 3-UTR have (*) sign

Error Description
If TEST_RESULT is not 1 or 9, then NUC_POS_END must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then NUC_POS_END must be null
If TEST_RESULT=1 and LAB_ID not in(998,999), then NUC_POS_END must not be null
If NUC_POS_END is not null AND if OTHER_REGION = 1, then must begin with (-)
If NUC_POS_END is not null AND If TYPE_VARIANT = 3 (substitution) AND EXON_NO is not null AND OTHER_REGION is null, then NUC_POS_END must not begin with (+,-)
If NUC_POS_END is not null AND If TYPE_VARIANT = 3 (substitution) AND INTRON_NO is not null AND OTHER_REGION is null then NUC_POS_END must begin with in (+, -)
If NUC_POS_END is not null AND if TYPE_VARIANT = 3, then NUC_POS_START = NUC_POS_END
If NUC_POS_END is not null and TYPE_VARIANT not in (1,3,9), then NUC_POS_START must not equal NUC_POS_END

17NUCLEOTIDE_FROMstring (1)Required:false
Expected nucleotide with respect to the reference sequence.
Allowable Values
AAdenine
CCytosine
GGuanine
TThymidine

Error Description
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then NUCLEOTIDE_FROM must be null

18NUCLEOTIDE_TOstring (1)Required:false
Observed (mutated) nucleotide.
Allowable Values
AAdenine
CCytosine
GGuanine
TThymidine

Error Description
If TEST_RESULT is not 1 or 9, then NUCLEOTIDE_TO must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then NUCLEOTIDE_TO must be null

19DELETE_SEQstring (50)Required:false
Deletion nucleotide sequence

Error Description
If TEST_RESULT is not 1, then NUCLEOTIDE_TO must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then NUCLEOTIDE_TO must be null
If TEST_RESULT=1 and TYPE_VARIANT in (1,7), then NUCLEOTIDE_TO must not be null

20INSERT_SEQstring (50)Required:false
Insertion nucleotide sequence

Error Description
If TEST_RESULT is not 1, then INSERT_SEQ must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then INSERT_SEQ must be null
If TEST_RESULT=1 and TYPE_VARIANT in (2,4,7), then INSERT_SEQ must not be null

21TYPE_VARIANTnumber (1,0)Required:false
Type of genetic change
Allowable Values
1Deletion
2Insertion
3Substitution
4Duplication
5Translocation
6Inversion
7Complex Rearrangement
9Uncertain

Error Description
If TEST_RESULT is not 1 or 9, then TYPE_VARIANT must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then TYPE_VARIANT must be null
If TEST_RESULT is 1 and LAB_ID is not 998 or 999, then TYPE_VARIANT must not be null
If VARIANT_NAME_RESULT is null, AND LAB_ID is not 998 or 999 then TYPE VARIANT must not be null

22CODONnumber (4,0)Required:false
Numeric location of first mutated amino acid of reference sequence. A numeric value of 1 to the total number of codons on the reference sequence
Allowable Values
1 to 9999Range

Error Description
If TEST_RESULT is not 1, then CODON must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then CODON must be null
If TEST_RESULT=1 and EXON_NO=null, then CODON must be null
If TEST_RESULT=1 AND EXON_NO is not null AND TYPE_VARIANT =3 , then CODON must not be null

23AA_FROMstring (1)Required:false
Wild type amino acid value of first affected amino acid on reference sequence
Allowable Values
AAla
CCys
DAsp
EGlu
FPhe
GGly
HHis
IIle
KLys
LLeu
MMet
NAsn
PPro
QGln
RArg
SSer
TThr
VVal
WTrp
YTyr
XStop

Error Description
If TEST_RESULT is not 1, then AA_FROM must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then AA_FROM must be null
If TEST_RESULT=1 and EXON_NO=null, then AA_FROM must be null
If TEST_RESULT=1 AND EXON_NO is not null AND TYPE_VARIANT =3 , then AA_FROM must not be null

24AA_TOstring (1)Required:false
Expressed amino acid value of last affected amino acid on reference sequence
Allowable Values
AAla
CCys
DAsp
EGlu
FPhe
GGly
HHis
IIle
KLys
LLeu
MMet
NAsn
PPro
QGln
RArg
SSer
TThr
VVal
WTrp
YTyr
XStop

Error Description
If TEST_RESULT is not 1, then AA_TO must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then AA_TO must be null
If TEST_RESULT=1 and CODON=null, then AA_TO must be null
If TEST_RESULT=1 AND EXON_NO is not null AND TYPE_VARIANT =3 , then AA_TO must be not null

25CONSEQUENCEnumber (2,0)Required:false
Category of mutation- defining outcome of the variant
Allowable Values
1Missense
2Premature termination
4Aberrant splicing
7Nonstop
8Other
99Uncertain

Error Description
If TEST_RESULT is not 1 or 9, then CONSEQUENCE must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then CONSEQUENCE must be null
If TEST_RESULT is 1, then CONSEQUENCE must NOT be null

26ZYGOSITYnumber (1,0)Required:false
Indicates the heterozygote/homozygote state of a variation, regardless of whether it is a polymorphism, unclassified variant or well established mutation.
Allowable Values
1Homozygous wildtype
2Heterozygous
3Homozygous change
9 unknown

Error Description
If VARIANT_ORIGIN does not equal 3 (germline), then ZYGOSITY must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then ZYGOSITY must be null
If VARIANT_ORIGIN = 3 and TEST_RESULT = 3 (failed), then ZYGOSITY must be null
If VARIANT_ORIGIN = 3 and TEST_RESULT not equals 3, then ZYGOSITY must be not null
If VARIANT_ORIGIN = 3 and TEST_RESULT=9, then ZYGOSITY must be 9

27SEVERITYnumber (1,0)Required:false
Type of mutation
Allowable Values
1Deleterious
2Polymorphism, assumed neutral
3Unclassified variant
4Unclassified variant, possibly pathogenic. DNA missense alteration with corresponding loss of expression by tumor IHC; alternatively, missense alteration that cosegregates with the disease in family.

Error Description
If TEST_RESULT is not 1 or 9, then SEVERITY must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then SEVERITY must be null
If VARIANT_ORIGIN in (1,2) AND TEST_RESULT = 1, then SEVERITY must be null

28INSIGHT_SEVERITYnumber (1,0)Required:false
This will be the 5-point severity code which InSiGHT use.
Allowable Values
5Pathogenic
4Likely Pathogenic
3Unclassified
2Likely Neutral
1Neutral
9Unknown

Error Description
If TEST_RESULT is not 1 or 9, then INSIGHT_SEVERITY must be null
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then INSIGHT_SEVERITY must be null
If TEST_RESULT=1 and SEVERITY=null, INSIGHT_SEVERITY then must be null
If GENE in (6,7), then INSIGHT_SEVERITY must be null

29LAB_IDnumber (3,0)Required:true
Lab or individual who performed the testing.
Allowable Values
119 Graham Casey
125 Steve Gallinger
128 Peter Laird
129 Joanne Young
141 Steve Thibodeau
228 Robert Haile
300 Dan Buchanan
301 Karen Makar
998 Other (specify, free text)
999 Unknown


30LAB_OTHER_TEXTstring (50)Required:false
Name of other/private lab
31DATE_TESTstring (8)Required:false
Date on which test was performed. Format: YYYYMMDD
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:
2002Minimum year

Error Description
Minimum year 2002