Module: molecular

Module Contents

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

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	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	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.

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

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

GENE

number (1,0)

Required:TRUE

Gene on which testing has been performed.

Allowable Values
6	BRAF
7	KRAS

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

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

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

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

GENOMIC_REGION_TESTED

string (30)

Required:TRUE

Indicates what part(s) of the gene or specific mutation or other genomic region(s) was TESTED

TEST_RESULT

number (1,0)

Required:TRUE

Result of the test carried out at the tumor level. This is NOT at person level.

Allowable Values
1	Change detected
2	No change detected
3	Test failed
9	Equivocal

VARIANT_NAME_RESULT

string (30)

Required:FALSE

Proper variant name using Human Genomic Variant Society (HGVS) nomenclature.

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
Error Description
If INTRON_NO is null AND OTHER_REGION is null AND LAB_ID not in(998,999), then EXON_NO must not be NULL
This special value check will pass under the following conditions: EXON_NO in {2,15}

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.

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.

NUCLEOTIDE_FROM

string (1)

Required:false

Expected nucleotide with respect to the reference sequence.

Allowable Values
A	Adenine
C	Cytosine
G	Guanine
T	Thymidine

NUCLEOTIDE_TO

string (1)

Required:FALSE

Observed (mutated) nucleotide.

Allowable Values
A	Adenine
C	Cytosine
G	Guanine
T	Thymidine

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
Error Description
If TEST_RESULT=1, then TYPE_VARIANT must be in (3,9)
This special value check will pass under the following conditions: TYPE_VARIANT in {3,9}

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

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
Error Description
If TEST_RESULT=1 AND CODON is not null AND TYPE_VARIANT =3 , then AA_FROM must not be null
This special value check will pass under the following conditions: AA_FROM in {A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,X}

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
Error Description
If TEST_RESULT=1 AND CODON is not null AND TYPE_VARIANT =3 , then AA_TO must not be null
This special value check will pass under the following conditions: AA_TO in {A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,X}

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
Error Description
If TEST_RESULT=1, then CONSEQUNCE must be not null
This special value check will pass under the following conditions: CONSEQUENCE in {1,2,9 }

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

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:
MM	01 – 12, 88, 99
DD	01 – 31, 88, 99
YYYY	2002 – system year, 8888, 9999