Module: biospecimens

Module Contents

  1. nuc-acid

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


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

3NUC_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.

4NUC_ACID_TYPEnumber (1,0)Required:true
Type of nucleic acid.
Allowable Values
1DNA
2RNA
9Unknown

5DATE_MADEstring (8)Required:true
Date specimen was made.
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:
1980Minimum year

Error Description
must be a valid date of format with minimum year of 1980


6IS_DEPLETEDnumber (1,0)Required:true
Indicates whether the material has been depleted through testing, processing, and dispatching.
Allowable Values
1Yes
2No


7IS_DISPATCHABLEnumber (1,0)Required:true
Indicates whether the center is willing or able to dispatch the material to external investigators.
Allowable Values
1Yes
2No

Error Description
If IS_DEPLETED = 1, IS_DISPATCHABLE must be 2

8LOCATIONnumber (1,0)Required:true
Storage site for a specimen.
Allowable Values
1Center
2CORIELL
3SAIC
4Multiple Sites
9Unknown/lost


9IDENTITY_TESTnumber (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
1Pass/Yes match
2Fail/No match
3Not done

10IDENTITY_TEST_DATEstring (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:
1980Minimum year

Error Description
must be a valid date of format with minimum year of 1980
IDENTITY_TEST_DATE must be greater or equal to DATE_MADE


11NUC_ACID_AMT_REMnumber (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 -9Range
-9Unknown quantity


12NUC_ACID_AMT_REM_DISPnumber (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 -9Range
-9Unknown quantity

Error Description
must be less than or equal to NUC_ACID_AMT_REM

13NUC_ACID_SOURCEnumber (2,0)Required:false
Specimen type for source of nucleic acid.
Allowable Values
1Whole Blood Aliquot cryo-preserved with DMSO
2Frozen Tissue
3Paraffin Block Section
4Buffy Coat
5White Blood Cells isolated using a Ficoll
6Lymphoblastoid Cells
7Buccal Smeart
8Whole Blood
9Granulocytes
11Blood Spots (guithrie)
12Mouth Wash
13Lymphocyte pellet
14Slide
15Saliva
16Whole Genome amplified DNA

Error Description
If BLOOD_PROD_CID is not null, NUC_ACID_SOURCE must be in (1,4,5,8,9,11,16)
If BLOCK_PROD_CID is not null, NUC_ACID_SOURCE must be in (3,14,16)

14BLOOD_PROD_CIDstring (12)Required:false
Unique local identifier used at a center to uniquely identify a blood tissue specimen.

Error Description
If NUC_ACID_SOURCE is in (1,4,5,8,9,11), BLOOD_PROD_CID must not be null
If NUC_ACID_SOURCE not in (1,4,5,8,9,11), BLOOD_PROD_CID must be null

15BLOCK_PROD_CIDstring (15)Required:false
Unique local identifier used at a center to uniquely identify a block.

Error Description
If NUC_ACID_SOURCE is in (3,14), BLOCK_PROD_CID must not be null
If NUC_ACID_SOURCE is not in (3,14), BLOCK_PROD_CID must be null

16FRESH_PROD_CIDstring (15)Required:false
Identifier used internally by centers for a product of a fresh tissue specimen.

Error Description
If NUC_ACID_SOURCE is 2, FRESH_PROD_CID must not be null
If NUC_ACID_SOURCE is not 2, FRESH_PROD_CID must be null

17LCL_CIDstring (10)Required:false
Identifier used internally by centers for a lymphocytic cell line transformation or expansion.

Error Description
If NUC_ACID_SOURCE is 6, LCL_CID must not be null
If NUC_ACID_SOURCE is not 6, LCL_CID must be null

18ORAL_SPEC_CIDstring (40)Required:false
Identifier used internally by centers for an oral sample.

Error Description
If NUC_ACID_SOURCE in (7,12,15), ORAL_SPEC_CID must not be null
If NUC_ACID_SOURCE not in (7,12,15), ORAL_SPEC_CID must be null

19QC_A260_280number (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 -9Range
-9Unknown

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

20QC_MATCHnumber (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
1Yes match
2No match
9Not done


21QUANTITATION_METHODnumber (1,0)Required:false
Method by which nucleic acid samples have their amount remaining value quantified.
Allowable Values
1PICO Green
2Spectrophotometry
3Nano-drop
4Other