Module: biospecimens

Module Contents

nuc-acid
- 1.CENTER_NO (*PK)
- 2.PERSON_ID
- 3.NUC_ACID_CID (*PK)
- 4.NUC_ACID_TYPE
- 5.DATE_MADE
- 6.IS_DEPLETED
- 7.IS_DISPATCHABLE
- 8.LOCATION
- 9.IDENTITY_TEST
- 10.IDENTITY_TEST_DATE
- 11.NUC_ACID_AMT_REM
- 12.NUC_ACID_AMT_REM_DISP
- 13.NUC_ACID_SOURCE
- 14.BLOOD_PROD_CID
- 15.BLOCK_PROD_CID
- 16.FRESH_PROD_CID
- 17.LCL_CID
- 18.ORAL_SPEC_CID
- 19.QC_A260_280
- 20.QC_MATCH
- 21.QUANTITATION_METHOD

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	University of Southern California Consortium (USCC)
13	University of Melbourne
14	University of Hawaii Cancer Center
15	Mayo Clinic
16	Fred Hutch, Seattle
17	University of California at San Francisco (UCSF) (formerly CPIC, originally Northern California (NCCC))

2	PERSON_ID	string (12)	Required:true
	Number that uniquely identifies an individual.

3	NUC_ACID_CID (*PK)	string (12)	Required:true
	Identifier used internally by centers for a nucleic acid sample from a single extraction. Center Identification Number. *CENTER_NO + NUC_ACID_CID are the primary key for the table.

NUC_ACID_TYPE

number (1,0)

Required:true

Type of nucleic acid.

Allowable Values
1	DNA
2	RNA
9	Unknown

DATE_MADE

string (8)

Required:true

Date specimen was made. 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:
1980	Minimum year

IS_DEPLETED

number (1,0)

Required:true

Indicates whether the material has been depleted through testing, processing, and dispatching.

Allowable Values
1	Yes
2	No

IS_DISPATCHABLE

number (1,0)

Required:true

Indicates whether the center is willing or able to dispatch the material to external investigators.

Allowable Values
1	Yes
2	No

LOCATION

number (1,0)

Required:true

Storage site for a specimen.

Allowable Values
1	Center
2	CORIELL
3	SAIC
4	Multiple Sites
9	Unknown/lost

IDENTITY_TEST

number (1,0)

Required:false

Indicates the outcome of identity testing. The identity of a DNA aliquot is compared to the identity of the stock DNA from which it originated.

Allowable Values
1	Pass/Yes match
2	Fail/No match
3	Not done

IDENTITY_TEST_DATE

string (8)

Required:false

Indicated the date for QC identity testing.

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:
1980	Minimum year

Error Description
must be a valid date of format with minimum year of 1980
Error Description
IDENTITY_TEST_DATE must be greater or equal to DATE_MADE
This check will pass under the following conditions: IDENTITY_TEST_DATE is valid date{Minimum year:1980}

NUC_ACID_AMT_REM

number (6,2)

Required:false

Amount of nucleic acid remaining at time of reporting in micrograms (includes material held in reserve).

Allowable Values
0 to 99999.99 or -9	Range
-9	Unknown quantity

NUC_ACID_AMT_REM_DISP

number (7,2)

Required:false

Amount of nucleic acid remaining at time of reporting in micrograms that is available for dispatch (excludes material held in reserve).

Allowable Values
0 to 99999.99 or -9	Range
-9	Unknown quantity

Error Description
must be less than or equal to NUC_ACID_AMT_REM
range check will pass under the following conditions: {NUC_ACID_AMT_REM_DISP>=0 and NUC_ACID_AMT_REM_DISP<=0 } This special value check will pass under the following conditions: NUC_ACID_AMT_REM_DISP in {-9}

NUC_ACID_SOURCE

number (2,0)

Required:false

Specimen type for source of nucleic acid.

Allowable Values
1	Whole Blood Aliquot cryo-preserved with DMSO (BCFR Only)
2	Frozen Tissue
3	Paraffin Block Section (Tubes or Slides)
4	Buffy Coat
5	White Blood Cells isolated using a Ficoll
6	Lymphoblastoid Cells
7	Buccal Smear (BCFR Only)
8	Whole Blood
9	Granulocytes
11	Blood Spots (guthrie)
12	Mouth Wash
13	Lymphocyte pellet
15	Saliva
16	Whole Genome amplified DNA
99	Unknown

Error Description
If BLOOD_PROD_CID is not null, NUC_ACID_SOURCE must be in (1,4,5,8,9,11,16)
Error Description
If BLOCK_PROD_CID is not null, NUC_ACID_SOURCE must be in (3,14,16)
This special value check will pass under the following conditions: NUC_ACID_SOURCE in {1,2,3,4,5,6,7,8,9,11,12,13,15,16,99 }

BLOOD_PROD_CID

string (12)

Required:false

Unique local identifier used at a center to uniquely identify a blood tissue specimen.

BLOCK_PROD_CID

string (15)

Required:false

Unique local identifier used at a center to uniquely identify a block.

FRESH_PROD_CID

string (15)

Required:false

Identifier used internally by centers for a product of a fresh tissue specimen.

LCL_CID

string (10)

Required:false

Identifier used internally by centers for a lymphocytic cell line transformation or expansion.

ORAL_SPEC_CID

string (40)

Required:false

Identifier used internally by centers for an oral sample.

QC_A260_280

number (6,2)

Required:false

A ratio of the optical density of a nucleic acid at 260 nm and 280 nm. This ratio provides an indication about the DNA or RNA quality purity.

Allowable Values
0.0 to 3.0 or -9	Range
-9	Unknown

Error Description
If NUC_ACID_SOURCE in (1,2,3,4,5,6,7,8,9,12,13,14,15,16), QC_A260_280 must not be null
range check will pass under the following conditions: {QC_A260_280>=0.0 and QC_A260_280<=0.0 } This special value check will pass under the following conditions: QC_A260_280 in {-9}

QC_MATCH

number (1,0)

Required:false

Confirmation that Nucleic Acid from LCL/GC/WBC/paraffin DNA match. For example, the DNA stock form once source is compared with the DNA stock from an alternate source from the same person.

Allowable Values
1	Yes match
2	No match
9	Not done

QUANTITATION_METHOD

number (1,0)

Required:false

Method by which nucleic acid samples have their amount remaining value quantified.

Allowable Values
1	Fluorescence (e.g., Picogreen, Qubit)
2	Spectrophotometry (e.g., Nanodrop)
4	Other (e.g., Trinean DropSense96, Bioanalyser, TapeStation)