Module: molecular

Module Contents

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

CENTER_NO (*PK)

number (2,0)

Required:true

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

GENE

number (1,0)

Required:true

Gene on which testing has been performed.

Allowable Values
1	MLH1
2	MSH2
3	MSH6
4	MUTYH
5	PMS2
8	EPCAM
10	APC
11	TP53

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 is in (6,7) AND SOURCE_NUC_ACID is in (7,8), then VARIANT_ORIGIN = 1
Error Description
If GENE is in (6,7) AND SOURCE_NUC_ACID is not in (7,8), then VARIANT_ORIGIN = 3
This special value check will pass under the following conditions: VARIANT_ORIGIN in {1,2,3}

SOURCE_NUC_ACID

number (1,0)

Required:true

Specifies source of tissue used for testing

Allowable Values
1	blood
2	Mouth wash/saliva
3	lymphoblastoid cells
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 (12)

Required:true

Identifier used internally by centers for a single extraction on which the test was carried out

DETECTION_METHOD

number (2,0)

Required:true

Germline or somatic DNA testing method. (Mass Spec = Sequenom MassARRAY system, MALDI-TOF)

Allowable Values
1	DNA Sequencing
10	DHPLC (Denaturing High Performance Liquid Chromatography)
11	Phase 1 protocol DHPLC+SEQ (MLH1 and MSH2)
12	12 SNP panel genotyping by Mass Spec
13	12 SNP panel genotyping, dHPLC with sequencing (MUTYH)
14	9 SNP panel genotyping by Mass Spec
15	9 SNP panel genotyping with sequencing (MUTYH)
16	PTT
17	SSCP
18	Fluorescent ASP (BRAF)
19	HRM with sequencing (KRAS)
33	Sequencing from Conversion Analysis
50	whole exome sequencing
60	whole genome sequencing
70	targeted panel sequencing
99	Unknown/private genetic test results

9	GENOMIC_REGION_TESTED	string (100)	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 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
1	Change detected
2	No change detected
3	Test failed
9	Equivocal

VARIANT_NAME_RESULT

string (100)

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.

INTRON_NO

number (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

OTHER_REGION

number (1,0)

Required:false

Region, other than coding exon and intron, containing the variant.

Allowable Values
1	5 UTR
2	3 UTR
3	Other

Error Description
If TEST_RESULT is not 1 or 9, then OTHER_REGION must be null
Error Description
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then OTHER_REGION must be null
Error Description
If DETECTION_METHOD = 10 AND CENTER_NO = 11 then must OTHER_REGION be null
Error Description
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
This special value check will pass under the following conditions: OTHER_REGION in {1,2,3}

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. 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.

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. 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

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

Error Description
If TEST_RESULT is not 1 or 9, then NUCLEOTIDE_TO must be null
Error Description
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then NUCLEOTIDE_TO must be null
This special value check will pass under the following conditions: NUCLEOTIDE_TO in {A,C,G,T}

DELETE_SEQ

string (50)

Required:false

Deletion nucleotide sequence

INSERT_SEQ

string (50)

Required:false

Insertion nucleotide sequence

TYPE_VARIANT

number (1,0)

Required:false

Type of genetic change

Allowable Values
1	Deletion
2	Insertion
3	Substitution
4	Duplication
5	Translocation
6	Inversion
7	Complex Rearrangement
9	Uncertain

Error Description
If TEST_RESULT is not 1 or 9, then TYPE_VARIANT must be null
Error Description
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then TYPE_VARIANT must be null
Error Description
If TEST_RESULT is 1 and LAB_ID is not 998 or 999, then TYPE_VARIANT must not be null
Error Description
If VARIANT_NAME_RESULT is null, AND LAB_ID is not 998 or 999 then TYPE VARIANT must not be null
This special value check will pass under the following conditions: TYPE_VARIANT in {1,2,3,4,5,6,7,9}

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 is not 1, then AA_FROM must be null
Error Description
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then AA_FROM must be null
Error Description
If TEST_RESULT=1 and EXON_NO=null, then AA_FROM must be null
Error Description
If TEST_RESULT=1 AND EXON_NO 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 is not 1, then AA_TO must be null
Error Description
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then AA_TO must be null
Error Description
If TEST_RESULT=1 and CODON=null, then AA_TO must be null
Error Description
If TEST_RESULT=1 AND EXON_NO is not null AND TYPE_VARIANT =3 , then AA_TO must be not 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 (2,0)

Required:false

Category of mutation- defining outcome of the variant

Allowable Values
1	Missense
2	Premature termination
4	Aberrant splicing
7	Nonstop
8	Other
99	Uncertain

Error Description
If TEST_RESULT is not 1 or 9, then CONSEQUENCE must be null
Error Description
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then CONSEQUENCE must be null
Error Description
If TEST_RESULT is 1, then CONSEQUENCE must NOT be null
This special value check will pass under the following conditions: CONSEQUENCE in {1,2,4,7,8,99}

ZYGOSITY

number (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
1	Homozygous wildtype
2	Heterozygous
3	Homozygous change
9	unknown

Error Description
If VARIANT_ORIGIN does not equal 3 (germline), then ZYGOSITY must be null
Error Description
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then ZYGOSITY must be null
Error Description
If VARIANT_ORIGIN = 3 and TEST_RESULT = 3 (failed), then ZYGOSITY must be null
Error Description
If VARIANT_ORIGIN = 3 and TEST_RESULT not equals 3, then ZYGOSITY must be not null
Error Description
If VARIANT_ORIGIN = 3 and TEST_RESULT=9, then ZYGOSITY must be 9
This special value check will pass under the following conditions: ZYGOSITY in {1,2,3,9 }

SEVERITY

number (1,0)

Required:false

Type of mutation

Allowable Values
1	Deleterious
2	Polymorphism, assumed neutral
3	Unclassified variant
4	Unclassified 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
Error Description
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then SEVERITY must be null
Error Description
If VARIANT_ORIGIN in (1,2) AND TEST_RESULT = 1, then SEVERITY must be null
This special value check will pass under the following conditions: SEVERITY in {1,2,3,4}

INSIGHT_SEVERITY

number (1,0)

Required:false

This will be the 5-point severity code which InSiGHT use.

Allowable Values
5	Pathogenic
4	Likely Pathogenic
3	Unclassified
2	Likely Neutral
1	Neutral
9	Unknown

Error Description
If TEST_RESULT is not 1 or 9, then INSIGHT_SEVERITY must be null
Error Description
If DETECTION_METHOD = 10 AND CENTER_NO in (11,16) then INSIGHT_SEVERITY must be null
Error Description
If TEST_RESULT=1 and SEVERITY=null, INSIGHT_SEVERITY then must be null
Error Description
If GENE in (6,7), then INSIGHT_SEVERITY must be null
This special value check will pass under the following conditions: INSIGHT_SEVERITY in {5,4,3,2,1,9}

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

30	LAB_OTHER_TEXT	string (50)	Required:false
	Name of other/private lab

DATE_TEST

string (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:
2002	Minimum year