purple font = requires further discussion (or has not yet been discussed) by workstream
gt.xpt, Genetic Toxicology in vitro
TOBA-14
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STATUS
- 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 NEW (must go to SDTM) | Entity Identifier | Char |
| Identifier | Entity identifier are unique identifiers used within the study to define the entity or assay platform being exposed (e.g. well, plate) to the test article and the relationship to the trial set or test conditions. Both SETCD and ENID must be populated. | Exp |
GTSEQ | Sequence Number | Num |
| Identifier | The sequence number must be unique for each record within an ENID Sequence number given to ensure uniqueness of records within a domain. May be any valid number. |
|
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 (Do we need this in addition to ENID? Is this for an internal identifier? contractor organization uses?) | 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 (Do we need this? Can we cite useful examples?) | 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
GT Definition: This domain captures in vitro data collected by the lab executing the study or received from a provider. This domain is designed for exchanging sample (entity) level data for the following in vitro tests: Neutral Red Cytotoxity Assay, Bacterial Reverse Mutation Assay, Mammalian Cell Gene Mutation Assay, and Micronucleus Assay. Other in vitro tests have not yet been modeled in this version of this domain.
- Entity Identifier:
- ENID is unique within the assay (and a study can have many assays)
- Replicates vs. Run
- need planned (ei.xpt) separate from the actual (gt.xpt)
- If tests run at the same time, they are replicates and are assigned the same RUNID
- If tests are run at separate times, they are runs and the RUNIDs are distinct
- Different runs would be expected to have different ENID and GTDTC values. In ei.xpt, these are distinguished by different RUNID values.
- Entities that are replicates of each other would be expected to
- have different ENID values
- be in the same trial set (SETCD values)
- have the same RUNID values
- Results Definition:
- GTSTRESC and the corresponding numeric GTSTRESN should generally be used to represent standardized format of original results.
- 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.
- 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.
- Other Assumptions:
- The discussion in Section 4.5.1.3 concerning TESTS NOT DONE does not apply to this domain.
- 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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