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gt.xpt, Genetic Toxicology In-Vivo - Findings. One record per test per observation time per entity, Tabulation.

Variable Name

Variable Label

Type

Controlled Terms, Codelist, or Format

Role

CDISC Notes

Core

STUDYID

Study Identifier

Char

 

Identifier

Unique identifier for a study.

Req

DOMAIN

Domain Abbreviation

Char

GT            

Identifier

Two-character abbreviation for the domain.

Req

SETCD

Set Code

Char

 

Identifier

Short name of a specific Trial Set to which the results are attributed. Maximum size is 8 characters

Exp

ENID

Entity Identifier

Char

 

Identifier

Entity identifier used within the study. If EXENID is entered, EI records must exist for each entity and the SETCD must be null. Either SETCD or ENID must be populated.

Exp

GTSEQ

Sequence Number

Num

 

Identifier

The sequence number must be unique for each record within an ENID.

Req

GTGRPID

Group ID

Char

 

Identifier

Optional group identifier, used to link together a block of related records within a subject in a domain.

Perm

GTREFID

Specimen Identifier

Char

 

Identifier

Slide or gel label (for example 1101-1 or 1101-2 for the first and second slides for animal 1101), or sample label for flow cytometry results. May be blank for example when the record represents an animal level result.

Perm

GTTESTCD

Lab Test or Examination Short Name

Char

(GTTESTCD)

Topic

Short name of the measurement, test, or examination described in GTTEST. It can be used as a column name when converting a dataset from a vertical to a horizontal format. The value in GVTESTCD cannot be longer than 8 characters, nor can it start with a number (e.g., “1TEST” is not valid). GVTESTCD cannot contain characters other than letters, numbers, or underscores. Examples: RVERT, CYTOTOX.

Req

GTTEST

Lab Test or Examination Name

Char

(GTTEST)

Synonym Qualifier

Long name for GTTESTCD. The value in GTTEST cannot be longer than 40 characters. Examples: Revertants, Cytotoxicity.

Req

GTTSTDTL

Measurement, Test or Examination Detail 

Char

(terminology needed)

Variable Qualifier of --TESTCD and --TEST

Further description of --TESTCD and --TEST. Example:


Perm

GTORRES

Result or Findings as Collected

Char

 

Result Qualifier

Result of the measurement or finding as originally received or collected.

Exp

GTORRESU

Unit of the Original Result

Char

(UNIT)

Variable Qualifier

The unit for the original result. The unit of the original result should be mapped to a synonymous unit on the Controlled Terminology list.

Exp

GTSTRESC

Standardized Result in Character Format

Char

New code list needed

 

Result Qualifier

Contains the result value for all findings, copied or derived from GTORRES in a standard format or standard units. GTSTRESC should store all results or findings in character format; if results are numeric, they should also be stored in numeric format in GTSTRESN. For example, if a test has results NONE, NEG, and NEGATIVE in GTORRES and these results effectively have the same meaning, they could be represented in standard format in GTSTRESC as NEGATIVE. For other examples, see general assumptions.

Exp

GTSTRESN

Standardized Result in Numeric Format

Num

 

Result Qualifier

Used for numeric results or findings in standard format; contains the numeric form of GTSTRESC. GTSTRESN should store all numeric test results or findings.

Exp

GTSTRESU

Unit of the Standardized Result

Char

(UNIT)

Variable Qualifier

Standardized unit used for GTSTRESC, GTSTRESN, GTSTRLO, and GTSTRHI.

Exp

GTSTNRLO

Reference Range Lower Limit-Std Unit

Num

 

Variable Qualifier

Lower end of normal range or reference range for standardized results (e.g., GTSTRESC, GTSTRESN) represented in standardized units (GTSTRESU).

Exp

GTSTNRHI

Reference Range Upper Limit-Std Unit

Num

 

Variable Qualifier

Upper end of normal range or reference range for standardized results (e.g., GTSTRESC, GTSTRESN) represented in standardized units (GTSTRESU).

Exp

GTSTAT

Completion Status

Char

(ND)

Record Qualifier

Used to indicate when a test is not done or result is missing. Should be null if a result exists in GTORRES.

Perm

GTREASND

Reason Not Done

Char

 

Record Qualifier

Describes why GTSTAT is NOT DONE, such as BROKEN EQUIPMENT or SPECIMEN LOST.

Perm

GTSPCCND

Specimen Condition

Char

?

Record Qualifier

Free or standardized text describing the condition of the specimen. Example: PRECIPITATION PRESENT, CONTAMINATION PRESENT, etc.  If multiple conditions are present on a sample, concatenate the values with a semicolon and no spaces as a separator

Perm

GTSPCUFL

Specimen Usability for the Test

Char

(NY)

Record Qualifier

Describes the usability of the specimen for the test. Should be N if the specimen is not usable; otherwise it should be null.

Perm

GTMETHOD

Method of Test or Examination

Char


Record Qualifier

Method of the test or examination. Examples: MANUALLY COUNTED, INSTRUMENT COUNTED

Exp

GTEXCLFL

Exclusion Flag

Char

(NY)

Record Qualifier

Y if the result should be excluded from all calculations, otherwise null.

Perm

GTREASEX

Reason for Exclusion

Char

 

Record Qualifier

The reason the result should be excluded from all calculations. Used only when GTEXCLFL is Y.

Perm

6.3.?.1  ASSUMPTIONS FOR Genetic Toxicology In-Vitro TEST RESULTS (GT) DOMAIN MODEL

  1. GT Definition: This domain captures in vitro genetic toxicology data collected by the lab executing the study or received from a provider.  This domain is designed for exchanging sample (entity) level in-vitro  Neutral Red Update, Ames, MNT, MLA assay data. Other in vitro genetic toxicology tests have not yet been modeled in this version of this domain.

  2. Results Definition:
    1. GTSTRESC and the corresponding numeric GTSTRESN should generally be used to represent standardized format of original results.
    2. GTSTNRLO and GTSTNRHI for reference range in standard units are "Expected" because this is critically important to understand the results of many of the test results. Follow guidelines from OECD when appropriate.
    3. GTSTAT and GTREASND are Permissible and used to indicate when a test was not completed. In these cases GTSTAT should contain “NOT DONE”; GTORRES, GTSTRESC, and GTSTRESN should be null; and GTREASND should contain the reason for not completing the test.
  3. Timing Variables:
    1. The The planned incubation time is represented in the EI variables RFENDLO and RFENDHI.
  4. Other Assumptions:
    1. The discussion in Section 4.5.1.3 concerning TESTS NOT DONE does not apply to this domain.
    2. GTEXCLFL and GTREASEX are Permissible and used to indicate when a test is to be excluded from further analysis. In these cases GTREASEX should contain the reason for exclusion.




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