Module: molecular

Module Contents

  1. braf_kras
    1.CENTER_NO (*PK)
    2.SOMATIC_CID (*PK)
    3.PERSON_ID
    4.TUMOR_NO
    5.POLYP_NO
    6.GENE
    7.VARIANT_ORIGIN
    8.SOURCE_NUC_ACID
    9.NUC_ACID_CID
    10.DETECTION_METHOD
    11.GENOMIC_REGION_TESTED
    12.TEST_RESULT
    13.VARIANT_NAME_RESULT
    14.EXON_NO
    15.NUC_POS_START
    16.NUC_POS_END
    17.NUCLEOTIDE_FROM
    18.NUCLEOTIDE_TO
    19.TYPE_VARIANT
    20.CODON
    21.AA_FROM
    22.AA_TO
    23.CONSEQUENCE
    24.LAB_ID
    25.LAB_OTHER_TEXT
    26.DATE_TEST

1 CENTER_NO (*PK) number(2,0) Required:TRUE
Center identification number. *CENTER_NO & SOMATIC_CID are the primary key for the table.
Allowable Values
11 Cancer Care Ontario - Colon
12 USC Consortium - Colon
13 University of Melbourne - Colon
14 Cancer Research Center of Hawaii - Colon
15 Mayo Clinic - Colon
16 Fred Hutchinson, Seattle - Colon
17 Northern California (NCCC) - Colon


2 SOMATIC_CID (*PK) String (40) Required:TRUE
Centre identifier for the test. *CENTER_NO & SOMATIC_CID are the primary key for the table.

3 PERSON_ID string (12) Required:TRUE
Number that uniquely identifies an individual.

4 TUMOR_NO number (2,0) Required:TRUE
Number labelling the tumor of the individual. Numbers are not necessarily sequential.
Allowable Values
-9 NA/Out of scope: Tissue is not cancer or contiguous adenoma.
-15 Information Unknown


5 POLYP_NO number (2,0) Required:TRUE
Sequential number over range of 1 to 99 to distinguish a polyp removed on a particular date.
Allowable Values
-9 NA/Out of scope: Tissue is not a polyp.
-1 Polyp has MSI/IHC result but center is currently unable to locate polyp pathology information


6 GENE number (1,0) Required:TRUE
Gene on which testing has been performed.
Allowable Values
6 BRAF
7 KRAS


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

Error Description
If GENE in (6,7) AND SOURCE_NUC_ACID (5,6,7,8), then VARIANT_ORIGIN must equal 1


8 SOURCE_NUC_ACID number (1,0) Required:TRUE
Specifies source of tissue used for testing
Allowable Values
4 normal fresh frozen tissue
5 other non-tumour tissue
6 polyp
7 tumour (paraffin embedded tumour- PET)
8 tumor- fresh frozen
9 unknown/private lab


9 NUC_ACID_CID string (15) Required:TRUE
Identifier used internally by centers for a single extraction on which the test was carried out
Allowable Values
   
-9 unknown

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


10 DETECTION_METHOD number (2,0) Required:TRUE
Somatic DNA testing method.
(Mass Spec = Sequenom MassARRAY system, MALDI-TOF)
Allowable Values
1 DNA Sequencing
18 Fluorescent ASP (BRAF)
19 HRM with sequencing (KRAS)
40 SYBR real time PCR assay
99 Unknown/private genetic test results


11 GENOMIC_REGION_TESTED string (30) Required:TRUE
Indicates what part(s) of the gene or specific mutation or other genomic region(s) was TESTED
Allowable Values
BRAF c.1799T>A p.Val600Glu  
KRAS codons 12 and 13 (g.10537--g.10647)  
KRAS codon 61  


12 TEST_RESULT number (1,0) Required:TRUE
Result of the test carried out and this is at the test level. This is NOT at person level.
Allowable Values
1 Change detected
2 No change detected
3 Test failed
9 Equivocal


13 VARIANT_NAME_RESULT string (30) Required:FALSE
Proper variant name using Human Genomic Variant Society (HGVS) nomenclature.
Allowable Values
BRAF c.1799T>A p.V600E  
KRAS c.34G>A  
KRAS c.34G>C  
KRAS c.34G>T  
KRAS c.35G>A  
KRAS c.35G>C  
KRAS c.35G>T  
KRAS c.37G>A  
KRAS c.37G>C  
KRAS c.37G>T  
KRAS c.38G>A  
KRAS c.38G>T  

Error Description
If TEST_RESULT does not equal 1, then VARIANT_NAME_RESULT must be null
If TEST_RESULT=1, then VARIANT_NAME_RESULT must not be null


14 EXON_NO number (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
2 KRAS
15 BRAF

Error Description
If TEST_RESULT does not equal 1, then EXON_NO must be null
If INTRON_NO is null AND OTHER_REGION is null AND LAB_ID not in(998,999), then EXON_NO must not be NULL


15 NUC_POS_START string (20) Required:false
For exonic mutations, the numeric value of the nucleotide first affected by the mutation relative to the reference sequence.

Error Description
If TEST_RESULT does not equal 1, 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 TYPE_VARIANT =3, then NUC_POS_START must equal NUC_POS_END
If TYPE_VARIANT does not equal 3, then NUC_POS_START must not equal NUC_POS_END


16 NUC_POS_END string (20) Required:false
For exonic mutations, the numeric value of the nucleotide last affected by the mutation relative to the reference sequence.

Error Description
If TEST_RESULT does not equal 1, 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 TYPE_VARIANT =3, then NUC_POS_END must equal NUC_POS_START
If TYPE_VARIANT <> 3, then NUC_POS_END must not NUC_POS_START


17 NUCLEOTIDE_FROM string (1) Required:false
Expected nucleotide with respect to the reference sequence.
Allowable Values
A Adenine
C Cytosine
G Guanine
T Thymidine

Error Description
If TEST_RESULT does not equal 1, then NUCLEOTIDE_FROM must be null


18 NUCLEOTIDE_TO string (1) Required:FALSE
Observed (mutated) nucleotide.
Allowable Values
A Adenine
C Cytosine
G Guanine
T Thymidine

Error Description
If TEST_RESULT does not equal 1, then NUCLEOTIDE_TO must be null


19 TYPE_VARIANT number (1,0) Required:false
Type of genetic change
Allowable Values
3 Substitution
9 Uncertain

Error Description
If TEST_RESULT does not equal 1, then TYPE_VARIANT must be null
If TEST_RESULT=1, then TYPE_VARIANT must be in (3,9)


20 CODON number (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

Error Description
If TEST_RESULT does not equal 1, then CODON must be null
If TEST_RESULT=1 AND EXON_NO does not equal null AND TYPE_VARIANT =3 , then CODON must be not null


21 AA_FROM string (1) Required:FALSE
Wild type amino acid value of first affected amino acid on reference sequence
Allowable Values
A Ala
C Cys
D Asp
E Glu
F Phe
G Gly
H His
I Ile
K Lys
L Leu
M Met
N Asn
P Pro
Q Gln
R Arg
S Ser
T Thr
V Val
W Trp
Y Tyr
X Stop

Error Description
If TEST_RESULT does not equal 1, then AA_FROM must be null
If TEST_RESULT=1 AND CODON is not null AND TYPE_VARIANT =3 , then AA_FROM must not be null


22 AA_TO string (1) Required:FALSE
Expressed amino acid value of last affected amino acid on reference sequence
Allowable Values
A Ala
C Cys
D Asp
E Glu
F Phe
G Gly
H His
I Ile
K Lys
L Leu
M Met
N Asn
P Pro
Q Gln
R Arg
S Ser
T Thr
V Val
W Trp
Y Tyr
X Stop

Error Description
If TEST_RESULT does not equal 1, then AA_TO must be null
If TEST_RESULT=1 AND CODON is not null AND TYPE_VARIANT =3 , then AA_TO must not be null


23 CONSEQUENCE number (1,0) Required:FALSE
Category of mutation- defining outcome of the variant
Allowable Values
1 Missense
2 Premature termination
9 Uncertain

Error Description
If TEST_RESULT does not equal 1, then CONSEQUENCE must be null
If TEST_RESULT=1, then CONSEQUNCE must be not null


24 LAB_ID number (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


25 LAB_OTHER_TEXT string (30) Required:false
Name of other/private lab

26 DATE_TEST string (8) Required:TRUE
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:
YYYYMMDD :  
MM 01 - 12, 88, 99
DD 01 - 31, 88, 99
YYYY 2002 - system year, 8888, 9999