Nuc-acid

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
11Sinai Health Systems (formerly Cancer Care Ontario)
12Cedars-Sinai & Cleveland Clinic (formerly USC Consortium)
13University of Melbourne
14University of Hawaii Cancer Center
15Mayo Clinic
16Fred Hutch, Seattle
17UCSF: University of California at San Franscisco (formerly CPIC, originally Northern 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



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


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



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


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


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

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

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

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

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

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


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