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This is an example showing example shows a sample report table, trial design, and results data of Study #123 dataset for study 123 for the determination of the in vitro genotoxicity potential of 10 tobacco products in using the in vitro Micronucleus Assay

Info
  • red font - indicates potential for CT code lists
  • green font - links to other domains
  • purple font - to be discussed
Expand
titleStudy 123, Report Table

Image Removed

micronucleus assay.

Expand
titleSample Report Table for Study 123

Image Added

ASSAYID
Dataset wrap
Rowcaps
Rows 1-2:Show 2 records for TSPARMCD = "GLPTYP", using TSSEQ to indicate multiple records, since both GLP types apply for this example study. 
Row 3:Shows that this study was conducted as a GLP study.
Rows 4-5:Show the study start date and study title.
Rows 6-7:Show the version of SEND Implementation Guide and version of Controlled Terminology used in this study.
Row 8:Shows the applicant's organization.
Row 9:Shows that the applicant's study reference ID is not applicable.
Rows 10-13:Show that TSGRPID has been used to link records (name, location, country) related to the test facility (TSGRPID = 1). The study director is associated with the test facility.
Rows 14-16:

Show that TSGRPID (TSGRPID=2) has been used to link the information on the testing guideline followed on this study (TSTGDNAM, TSTGDORG, TSTGDVER).

Row 17:

Shows the study type for this study.

Row 18:

Shows that this study includes a Mammalian Cell Micronucleus Assay.
Rows 19-20:Show that the species is human and the cell line is TK6 lymphoblastoid in this study.
Dataset2
Row

STUDYID

Expand
titlets.xpt (trial summary, study level parameters)
  • Assumption: The intent of this dataset is to provide a summary of trial (study) information. This is not subject-level data. 
  • Assumption: A Trial (study) can have more than one assay type
  • Assumption: ASSAYID value of ALL indicates that it applies to all assays in the study

Row

STUDYID

DOMAIN

TSSEQ

TSGRPID

TSPARMCD

TSPARM

TSVAL

TSVALNF

1123
MNvit
TS1
GLPTYPGood Laboratory Practice TypeFDA
2123
MNvit
TS2
GLPTYPGood Laboratory Practice TypeOECD
3123
TS1
GLPFLGLP FlagY
4123
MNvit
TS1
STSTDTCStudy Start Date2022-05-25
4

5123
MNvit
TS1
STITLEStudy Title

Determination of the in vitro genotoxicity potential

of 10 tobacco products in both the in vitro Micronucleus Assay and the in vitro

using the in vitro Neutral Red Uptake assay

5

6123
MNvit
TS1
SNDIGVERSEND Implementation Guide VersionTOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6

7123
MNvit
TS1
SNDCTVERSEND Controlled Terminology VersionSEND Terminology 2021-09-30
7

8123
MNvit
TS1
SSPONSOR

APPLCNT
Sponsor Organization

Applicant

Example
Sponsor
Applicant, Inc.
8

9123
MNvit
TS1
SPREFID

APREFID
Sponsor's
Study Reference ID
NOT APPLICABLE
9
10123
MNvit
TS11TSTFNAMTest Facility NameExample
Tox
Test Lab Name
10

11123
MNvit
TS11TSTFLOCTest Facility Location10 Somewhere Street, Montgomery, AL 10000
11

12123
MNvit
TS11TFCNTRYTest Facility CountryUSA
12

13123
MNvit
TS11STDIRStudy DirectorDr. R. Smith
13

14123
MNvit
TS12
GLPFLGLP FlagY
TSTGDNAMTesting Guideline NameGUIDELINE FOR THE TESTING OF CHEMICALS No. 487
15
14
123
MNvit
TS1
ASTDAssay Standard
2TSTGDORGTesting Guideline OrganizationOECD
Test No. 487 
15

16123
MNvit
TS1
ASTDV
2TSTGDVERTesting Guideline
Assay Standard
Version
2016
29-
07
July-
29
2016
16

17123
MNvit
TS1
SSTYPStudy TypeGENOTOXICITY IN VITRO
17

18123
MNvit
TS1
SSSTYPStudy Sub TypeIn Vitro Micronucleus

GNTXAIDGenetic Toxicology Assay IdentifierMNvit
19123
18123MNvit
TS1
SPECIESSpecies
Homo Sapiens
HUMAN
19

20123
MNvit
TS1
??Test System?TK6 Lymphoblastoid Suspension Cells Expand
titletx.xpt (trial sets)

CELLLNCell Line

TK6 LYMPHOBLASTOID


This example Trial Sets dataset shows information about the test conditions for set A1 and A2 in this example study. Sets A1 and A2 can be seen in the first and second rows respectively of the sample report Table 1 (above). For brevity, the TX dataset and the findings (GT) dataset do not show information for any other sets. Fully formed datasets for this example study would include information about the test conditions and findings for all sets. 

SET (what sponsor calls it)
Dataset wrap
Nametx
Rowcaps
Rows 1-23:

Show trial set parameters and values that comprise the test conditions for trial set A1. Set A1 is the data for the negative control (concentration 0) with short-term exposure and metabolic activation S9.  The applicant has chosen to given a long name (SET) equal to "ST+S9_C0".

Set A1 is associated with the first row in the sample report table for study 123.

Rows 24-46:

Show trial set parameters and values that comprise the test conditions for trial set A2. Set A2 is the data for the short-term exposure with metabolic activation S9 at a concentration of 1250 ug/ml. The applicant has chosen to give the set a long name (SET) equal to "ST+S9_C1250".

Set A2 is associated with the second row in the sample report table for study 123.

Dataset2
RowSTUDYIDDOMAINSETCDSET
  • During CT definition/reviews will decide appropriate TXPARM and TXVAL; Treatment duration may be controlled;  For now, we just include good example values based on our experience
  • Assumption: The Trial Sets (TX) domain provides the list of distinct sets of subjects having different experimental factors, treatment factors, inherent characteristics, or distinct sponsor designations as specified in the trial design.
  • Where is TK6 cell type?  is this test system (see below)
    • needs to be allowed to vary down to the well level / result level

A1: Image Removed

A2:                                   Image Removed

RowSTUDYIDASSAYIDDOMAINSETCD
TXSEQTXPARMCDTXPARMTXVAL
1123
MNvit
TXA1

(table 1, row 1, ST exposure with S9)

METACTMetabolic Activation  (should there be two parms? Presence, type)?+S9
ST+S9_C01MTACTINDMetabolic Activating Agent Name+S9
2123TXA1ST+S9_C02METACTFLPresence of Metabolic Activation FlagY
3123
123MNvit
TXA1
TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range?  start/end, target and tolerance?, one text field not-analyzable)3123MNvitTXA1TRTDRTOLTreatment Duration Tolerance123MNvitTXA1TRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)H123MNvitTXA1INTRVN

name of the intervention article

(Tobacco ProdA, Bleomycin or Cyclophosphamid A)

Tobacco ProdA123MNvitTXA1ITVTYPE

type of intervention article

choices of values:  product; negative control; positive control

Product123MNvitTXA1ITVCONCConcentration of intervention article0123MNvitTXA1ITVCONCUConcentration Unitug/ml123MNvitTX

A2

(table 1, row 2)

METACTMetabolic Activation  (should there be two parms? Presence, type)?+S9123MNvitTXA2TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range?  start/end, target and tolerance?, one text field not-analyzable)3123MNvitTXA2TRTDRTOLTreatment Duration Tolerance123MNvitTXA2TRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)H123MNvitTXA2INTRVNname of the intervention articleTobacco ProdA123MNvitTXA2ITVTYPEtype of intervention articleProduct123MNvitTXA2ITVCONCConcentration of i a 1250123MNvitTXA2ITVCONCUConcentration Unitug/ml...
ST+S9_C03

IVTDMIN

In vitro Treatment Duration Minimum3
4123TXA1ST+S9_C04IVTDTRGIn vitro Treatment Duration Target3.5
5123TXA1ST+S9_C05IVTDMAXIn vitro Treatment Duration Maximum4
6123TXA1ST+S9_C06IVTDUIn vitro Treatment Duration UnitHOURS
7123TXA1ST+S9_C07RCVDMINRecovery Duration Minimum23.5
8123TXA1ST+S9_C08RCVDTRGRecovery Duration Target24
9123TXA1ST+S9_C09RCVDMAXRecovery Duration Maximum24.5
10123TXA1ST+S9_C010RCVDURecovery Duration UnitHOURS
11123TXA1ST+S9_C011INCBTMPIncubation Temperature37
12123TXA1ST+S9_C012INCBTMPUIncubation Temperature UnitC
13123TXA1ST+S9_C013ATMRHPAtmospheric Relative Humidity Percent50
14123TXA1ST+S9_C014ATMCO2PAtmospheric CO2 Percent5
15123TXA1ST+S9_C015

SPTOBID

Applicant-defined tobacco identifier

CIG01a
16123TXA1ST+S9_C016EXPTYP

Exposure Type

Submerged
17123TXA1ST+S9_C017SAMTYP

Sample Type

Total Particulate Matter in DMSO
18123TXA1ST+S9_CO18ITVNAM

Intervention Article Name

Tobacco ProdA
19123TXA1ST+S9_C019ITVTYPE

Intervention Article Type

Negative Control
20123TXA1ST+S9_C020ITVCONCIntervention Article Concentration0
21123TXA1ST+S9_C021ITVCONCUIntervention Article Concentration Unitug/ml
22123TXA1ST+S9_C022

SPDEVID

Applicant-defined device identifierPUFFMASTER3K
23123TXA1ST+S9_C023

SMKRGM

Smoking RegimenMEDIUM INTENSITY REGIMEN
24123TXA2ST+S9_C125024MTACTINDMetabolic Activating Agent Name+S9
25123TXA2ST+S9_C125025METACTFLPresence of Metabolic Activation FlagY
26123TXA2ST+S9_C125026

IVTDMIN

In vitro Treatment Duration Minimum3
27123TXA2ST+S9_C125027IVTDTRGIn vitro Treatment Duration Target3.5
28123TXA2ST+S9_C125028IVTDMAXIn vitro Treatment Duration Maximum4
29123TXA2ST+S9_C125029IVTDUIn vitro Treatment Duration UnitHOURS
30123TXA2ST+S9_C125030RCVDMINRecovery Duration Minimum23.5
31123TXA2ST+S9_C125031RCVDTRGRecovery Duration Target24
32123TXA2ST+S9_C125032RCVDMAXRecovery Duration Maximum24.5
33123TXA2ST+S9_C125033RCVDURecovery Duration UnitHOURS
34123TXA2ST+S9_C125034INCBTMPIncubation Temperature37
35123TXA2ST+S9_C125035INCBTMPUIncubation Temperature UnitC
36123TXA2ST+S9_C125036ATMRHPAtmospheric Relative Humidity Percent50
37123TXA2ST+S9_C125037ATMCO2PAtmospheric CO2 Percent5
38123TXA2ST+S9_C125038

SPTOBID

Applicant-defined tobacco identifier

CIG01a
39123TXA2ST+S9_C125039EXPTYP

Exposure Type

Submerged
40123TXA2ST+S9_C125040SAMTYP

Sample Type

Total Particulate Matter in DMSO
41123TXA2ST+S9_C125041ITVNAM

Intervention Article Name

Tobacco ProdA
42123TXA2ST+S9_C125042ITVTYPE

Intervention Article Type

Product
43123TXA2ST+S9_C125043ITVCONCIntervention Article Concentration1250
44123TXA2ST+S9_C125044ITVCONCUIntervention Article Concentration Unitug/ml
45123TXA2ST+S9_C125045SPDEVIDApplicant-defined Device IdentifierPUFFMASTER2023
46123TXA2ST+S9_C125046

SMKRGM

Smoking RegimenHIGH INTENSITY REGIMEN
Dataset wrap
Namerelref
Rowcaps
Row 1:Shows the value of REFID=C0. This REFID refers to the trial set with a SETCD of "A1", as defined in the TX dataset. LEVEL=1 and LVLDESC="EXPERIMENTAL UNIT/TRIAL SET" indicates this identifier is referring to both the experimental unit and the unit to which the treatment is applied, and to the entire trial set.
Rows 2-5:Show the values of 4 observational units (C0_Count1 through C0_Count4) that are within the parent experimental unit, REFID=C0. In this example assay, these observational units are also all within the same trial set, as defined in the TX dataset.
Row 6:Shows the value of REFID=C1250. This REFID refers to the trial set with a SETCD of "A2", as defined in the TX dataset. LEVEL=1 and LVLDESC="EXPERIMENTAL UNIT/TRIAL SET" indicates this identifier is referring to both the experimental unit and the unit to which the treatment is applied, and to the entire trial set.
Rows 7-10:

Show the values of 4 observational units (C1250_Count1 through C1250_Count4) that are within the parent experimental unit, REFID=C1250. In this example assay, these observational units are also all within the same trial set, as defined in the TX dataset.

Dataset2
tableidrelref

Row

STUDYID

SETCD

REFID

PARENT

LEVEL

LVLDESC

1

123

A1

C0
1

EXPERIMENTAL UNIT/TRIAL SET

2

123

A1

C0-Count1C02OBSERVATIONAL UNIT

3

123

A1

C0-Count2C02OBSERVATIONAL UNIT

4

123

A1

C0-Count3C02OBSERVATIONAL UNIT

5

123

A1

C0-Count4C02OBSERVATIONAL UNIT

6

123A2C1250
1EXPERIMENTAL UNIT/TRIAL SET
7123A2C1250-Count1C12502OBSERVATIONAL UNIT
8123A2C1250-Count2C12502OBSERVATIONAL UNIT
9123A2C1250-Count3C12502OBSERVATIONAL UNIT
10123A2C1250-Count4C12502OBSERVATIONAL UNIT
Dataset wrap
Namegt
Rowcaps

Rows 1-3, 8:

Show percentage result values that apply to GTREFID=C0. REFID=C0, as shown in the RELREF dataset, relates this data to the trial set in the first row of table 1 in the sample report table for study 123.
Rows 4-7:Show the 4 micronucleated cell counts for the observational units with GTREFID from C0-Count1 through C0-Count4, for which their relationship to test conditions (in tx.xpt) and experimental units (in relref.xpt) are shown in the RELREF dataset.

Rows 9-11, 16:

Show percentage result values that apply to GTREFID=C1250. REFID=C1250, as shown in the RELREF dataset, relates this data to the trial set in the second row of table 1 in the sample report table for study 123.
Rows 12-15:Show the 4 micronucleated cell counts for the observational units with GTREFID from C1250-Count1 through C1250-Count4, for which their relationship to test conditions (in tx.xpt) and experimental units (in relref.xpt) are shown in the RELREF dataset.
Expand
titlegt.xpt (similar to LB)

A1: Image Removed

A2:                                   Image Removed

RowSTUDYIDASSAYIDDOMAINTXSETCDGTSEQGTTESTCDGTTESTGTCELLEV
(cells evaluated)
GTORRESGTORRESU
Dataset2
RowSTUDYIDDOMAINGTSEQ

GTREFID

GTTESTCDGTTESTGTCELLEVGTORRESGTORRESU

GTCOLSRT

GTSTRESCGTSTRESNGTSTRESUGTDTC
1123
MNvit
GT
A1
1
1
C0

RICC

Relative Increase in Cell Count1540%
00%2022-05-25
2123
MNvit
GT
A1
2
2
C0RCCRelative Cell Count1540%
00%2022-05-25
3123
MNvit
GT
A1
3
3
C0RPDRelative Population Doubling1540%
00%2022-05-25
4123
MNvit
GT
A1
4
4
C0-Count1
MNCELLS
MNCEMicronucleated Cells220515
Cells



1515
Cells

2022-05-25
5123
MNvit
GT
A1
5
5
C0-Count2
MNCELLS
MNCEMicronucleated Cells247413
Cells


1313
Cells

2022-05-25
6123
MNvit
GT
A1
6
6
C0-Count3
MNCELLS
MNCEMicronucleated Cells275817
Cells


1717
Cells

2022-05-25
7123
MNvit
GT
A1
7
7
C0-Count4
MNCELLS
MNCEMicronucleated Cells266912
Cells


1212
Cells

2022-05-25
8123
MNvit
GT
A1
8
8
C0
AVGRELAverage Relative MN Frequency
MNCECEMicronucleated Cells/Total Cells
0.57%
0.570.57%2022-05-25
9123
MNvit
GT
A2
1
1
C1250RICCRelative Increase in Cell Count13415.7%
15.715.7%2022-05-25
10123
MNvit
GT
A2
2
2
C1250RCCRelative Cell Count13413.0%
13.013.0%2022-05-25
11123
MNvit
GT
A2
3
3
C1250RPDRelative Population Doubling1347.9%
7.97.9%2022-05-25
12123
MNvit
GT
A2
4
4
C1250-Count1
MNCELLS
MNCEMicronucleated Cells326620
Cells


2020
Cells

2022-05-25
13123
MNvit
GT
A2
5
5
C1250-Count2
MNCELLS
MNCEMicronucleated Cells219017
Cells


1717
Cells

2022-05-25
14123
MNvit
GT
A2
6
6
C1250-Count3
MNCELLS
MNCEMicronucleated Cells275813
Cells


1313
Cells

2022-05-25
15123
MNvit
GT
A2
7
7
C1250-Count4
MNCELLS
MNCEMicronucleated Cells271421
Cells


2121
Cells

2022-05-25
16123
MNvit
GT
A2
8
8
C1250
AVGREL
MNCECE

Micronucleated Cells/Total Cells

Average Relative MN Frequency


0.66%
0.660.66%2022-05-25
...

Below this line are domains we currently do not see a use for

(Do we need this? a single element (treatment)?)

(Do we need this? one arm for each trial set?)

ARMCD
Expand
titlete.xpt (trial elements)
RowSTUDYIDASSAYIDDOMAINETCDELEMENT
Expand
titleta.xpt (trial arms)
RowSTUDYIDASSAYIDDOMAINARMCDARMTAETORDETCDELEMENT
Expand
titleei.xpt (dm-like)

Not needed.

RowSTUDYIDDOMAINENID (Entity ID)RICCRCCRPDSum of cell ev.Cells with MNSMKFID (Smoke Fraction)

REPLCTID

(Replicate Number)

PLATEID (Plate ID)

COLID

(Column number)

ROWID (Row  number)SETCD (Set Code, TX)RFSTDTCRFENDTCRFXSTDTCRFXENDTCRFCSTDTCRFCENDTC