Module: biospecimens

Module Contents

  1. 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

1 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 Cancer Care Ontario
12 USC Consortium
13 University of Melbourne
14 Cancer Research Center of Hawaii
15 Mayo Clinic
16 Fred Hutchinson, Seattle
17 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.

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


5 DATE_MADE string (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:
1980 Minimum year

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

6 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


7 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

Error Description
If IS_DEPLETED = 1, IS_DISPATCHABLE must be 2


8 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


9 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


10 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
IDENTITY_TEST_DATE must be greater or equal to DATE_MADE

11 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


12 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


13 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
4 Buffy Coat
5 White Blood Cells isolated using a Ficoll
6 Lymphoblastoid Cells
7 Buccal Smeart (BCFR Only)
8 Whole Blood
9 Granulocytes
11 Blood Spots (guithrie)
12 Mouth Wash
13 Lymphocyte pellet
14 Slide
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)
If BLOCK_PROD_CID is not null, NUC_ACID_SOURCE must be in (3,14,16)


14 BLOOD_PROD_CID string (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


15 BLOCK_PROD_CID string (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


16 FRESH_PROD_CID string (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


17 LCL_CID string (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


18 ORAL_SPEC_CID string (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


19 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


20 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


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