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 - questions yet to be resolved

micronucleus assay.

Expand

title	Sample Report Table for Study 123

Image Added

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.

Expand

title	ts.xpt (trial summary, study level parameters)

Assumption: Study can have more than one assay type
Assumption: ASSAYID value of ALL means it applies to all assays in the study
Replaced the ASSAYID values of MNT with MNvit (term used in OECD #487) - is this better? This is not a controlled term so we can use anything but what we use in our IG examples are often used in industry implementations so we should use realistic and best practice values as much as possible.
BLEO & CPA - are positive controls, should this be included/where is this captured? — in results for the record / row?
Where is TK6 cell type? is this test system (see below)

Row

STUDYID

ASSAYID

Dataset2

Row	STUDYID

DOMAIN	TSSEQ	TSGRPID	TSPARMCD	TSPARM	TSVAL	TSVALNF
1	123

ALL

TS

1

GLPTYP

Good Laboratory Practice Type

FDA

11123


2	123	TS	2	GLPTYP	Good Laboratory Practice Type	OECD
3	123	TS	1	GLPFL	GLP Flag	Y
4	123

ALL

TS

1

STSTDTC

Study Start Date

2007

2022-

12

05-

30

25

13


5	123

ALL

TS

1

STITLE

Study Title

Example

Determination of

a Crossover study in the Rat with 3 dose levels and 3 dosing periods

the in vitro genotoxicity potential using the in vitro Neutral Red Uptake assay
6

14

123

ALL

TS

1

SNDIGVER

SEND Implementation Guide Version

Tobacco

TOBACCO IMPLEMENTATION GUIDE VERSION 1.0

15


7	123

ALL

TS

1

SNDCTVER

SEND Controlled Terminology Version

SEND Terminology 2021-

03

09-

26

30

17


8	123

ALL

TS

1

SSPONSOR

APPLCNT

Sponsor Organization

Applicant

Example

Sponsor

Applicant, Inc.

18


9	123

ALL

TS

1

SPREFID

APREFID

Sponsor's

Study Reference ID

NOT APPLICABLE

19

10

123

ALL

TS

1

TSTFNAM

Test Facility Name

Example

Tox

Test Lab Name

20


11	123

ALL

TS

1

TSTFLOC

Test Facility Location

10 Somewhere Street, Montgomery, AL 10000

21


12	123

ALL

TS

1

TFCNTRY

Test Facility Country

USA

24


13	123

ALL

TS

1

STDIR

Study Director

Dr. R. Smith

28


14	123

ALL

TS

1

2

GLPFLGLP FlagY29123

TSTGDNAM	Testing Guideline Name	GUIDELINE FOR THE TESTING OF CHEMICALS No. 487
15	123

MNvit

TS

1

ASTDAssay Standard

2

TSTGDORG

Testing Guideline Organization

OECD

Test No. 487

30


16	123

MNvit

TS

1

ASTDV

2

TSTGDVER

Testing Guideline

Assay Standard

Version

2016

29-

07

July-

29

2016

31


17	123

MNvit

TS

1

SSTYP

Study Type

GENOTOXICITY IN VITRO

32


18	123

MNvit

TS

1

SSSTYPStudy Sub TypeIn Vitro Micronucleus

	GNTXAID	Genetic Toxicology Assay Identifier	MNvit
19	123

33123MNvit

TS

1

SPECIES

Species

Homo Sapiens

HUMAN

34


20	123

MNvit

TS

1

??Test System?TK6 Lymphoblastoid Suspension Cells35123NRUTS1ASTDAssay StandardNIH Publication No. 07-451936123NRUTS1ASTDVAssay Standard Version2006-1137123NRUTS1SSTYPStudy Type38123NRUTS1SSSTYPStudy Sub TypeIn Vitro Neutral Red Uptake39123NRUTS1SPECIESSpeciesHomo Sapiens

40

123NRUTS1??Test System??Normal Human Keratinocyte Expand

title	tx.xpt (trial sets)

Treatment Duration will be controlled? During CT definition/reviews will need to decide appropriate Treatment duration values; For now, we just include good example values based on our experience

RowSTUDYIDASSAYIDDOMAINSETCDSETTXSEQTXPARMCDTXPARMTXVAL1123MNvitTXA1METACTMetabolic Activation (should there be two parms? Presence, type)?+S92123MNvitTXA1TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)3

CELLLN

Cell 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.

Dataset wrap

Name	tx

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

Row	STUDYID	DOMAIN	SETCD	SET	TXSEQ	TXPARMCD	TXPARM	TXVAL
1	123	TX	A1	ST+S9_C0	1	MTACTIND	Metabolic Activating Agent Name	+S9
2	123	TX	A1	ST+S9_C0	2	METACTFL	Presence of Metabolic Activation Flag	Y
3	123	TX	A1	ST+S9_C0	3	IVTDMIN	In vitro Treatment Duration Minimum	3
4	123	TX	A1	ST+S9_C0	4	IVTDTRG	In vitro Treatment Duration Target	3.5
5	123	TX	A1	ST+S9_C0	5	IVTDMAX	In vitro Treatment Duration Maximum	4
6	123	TX	A1	ST+S9_C0	6	IVTDU	In vitro Treatment Duration Unit	HOURS
7	123	TX	A1	ST+S9_C0	7	RCVDMIN	Recovery Duration Minimum	23.5
8	123	TX	A1	ST+S9_C0	8	RCVDTRG	Recovery Duration Target	24
9	123	TX	A1	ST+S9_C0	9	RCVDMAX	Recovery Duration Maximum	24.5
10	123	TX	A1	ST+S9_C0	10	RCVDU	Recovery Duration Unit	HOURS
11	123	TX	A1	ST+S9_C0	11	INCBTMP	Incubation Temperature	37
12	123	TX	A1	ST+S9_C0	12	INCBTMPU	Incubation Temperature Unit	C
13	123	TX	A1	ST+S9_C0	13	ATMRHP	Atmospheric Relative Humidity Percent	50
14	123	TX	A1	ST+S9_C0	14	ATMCO2P	Atmospheric CO2 Percent	5
15	123	TX	A1	ST+S9_C0	15	SPTOBID	Applicant-defined tobacco identifier	CIG01a
16	123	TX	A1	ST+S9_C0	16	EXPTYP	Exposure Type	Submerged
17	123	TX	A1	ST+S9_C0	17	SAMTYP	Sample Type	Total Particulate Matter in DMSO
18	123	TX	A1	ST+S9_CO	18	ITVNAM	Intervention Article Name	Tobacco ProdA
19	123	TX	A1	ST+S9_C0	19	ITVTYPE	Intervention Article Type	Negative Control
20	123	TX	A1	ST+S9_C0	20	ITVCONC	Intervention Article Concentration	0
21	123	TX	A1	ST+S9_C0	21	ITVCONCU	Intervention Article Concentration Unit	ug/ml
22	123	TX	A1	ST+S9_C0	22	SPDEVID	Applicant-defined device identifier	PUFFMASTER3K
23	123	TX	A1	ST+S9_C0	23	SMKRGM	Smoking Regimen	MEDIUM INTENSITY REGIMEN
24	123	TX	A2	ST+S9_C1250	24	MTACTIND	Metabolic Activating Agent Name	+S9
25	123	TX	A2	ST+S9_C1250	25	METACTFL	Presence of Metabolic Activation Flag	Y
26	123	TX	A2	ST+S9_C1250	26	IVTDMIN	In vitro Treatment Duration Minimum	3
27	123	TX	A2	ST+S9_C1250	27	IVTDTRG	In vitro Treatment Duration Target	3.5
28	123	TX	A2	ST+S9_C1250	28	IVTDMAX	In vitro Treatment Duration Maximum	4
29	123	TX	A2	ST+S9_C1250	29	IVTDU	In vitro Treatment Duration Unit	HOURS
30	123	TX	A2	ST+S9_C1250	30	RCVDMIN	Recovery Duration Minimum	23.5
31	123	TX	A2	ST+S9_C1250	31	RCVDTRG	Recovery Duration Target	24
32	123	TX	A2	ST+S9_C1250	32	RCVDMAX	Recovery Duration Maximum	24.5
33	123	TX	A2	ST+S9_C1250	33	RCVDU	Recovery Duration Unit	HOURS
34	123	TX	A2	ST+S9_C1250	34	INCBTMP	Incubation Temperature	37
35	123	TX	A2	ST+S9_C1250	35	INCBTMPU	Incubation Temperature Unit	C
36	123	TX	A2	ST+S9_C1250	36	ATMRHP	Atmospheric Relative Humidity Percent	50
37	123	TX	A2	ST+S9_C1250	37	ATMCO2P	Atmospheric CO2 Percent	5
38	123	TX	A2	ST+S9_C1250	38	SPTOBID	Applicant-defined tobacco identifier	CIG01a
39	123	TX	A2	ST+S9_C1250	39	EXPTYP	Exposure Type	Submerged
40	123	TX	A2	ST+S9_C1250	40	SAMTYP	Sample Type	Total Particulate Matter in DMSO
41	123	TX	A2	ST+S9_C1250	41	ITVNAM	Intervention Article Name	Tobacco ProdA
42	123	TX	A2	ST+S9_C1250	42	ITVTYPE	Intervention Article Type	Product
43	123	TX	A2	ST+S9_C1250	43	ITVCONC	Intervention Article Concentration	1250
44	123	TX	A2	ST+S9_C1250	44	ITVCONCU	Intervention Article Concentration Unit	ug/ml
45	123	TX	A2	ST+S9_C1250	45	SPDEVID	Applicant-defined Device Identifier	PUFFMASTER2023
46	123	TX	A2	ST+S9_C1250	46	SMKRGM	Smoking Regimen	HIGH INTENSITY REGIMEN

Dataset wrap

Name	relref

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

tableid	relref

Row	STUDYID	SETCD	REFID	PARENT	LEVEL	LVLDESC
1	123	A1	C0		1	EXPERIMENTAL UNIT/TRIAL SET
2	123	A1	C0-Count1	C0	2	OBSERVATIONAL UNIT
3	123	A1	C0-Count2	C0	2	OBSERVATIONAL UNIT
4	123	A1	C0-Count3	C0	2	OBSERVATIONAL UNIT
5	123	A1	C0-Count4	C0	2	OBSERVATIONAL UNIT
6	123	A2	C1250		1	EXPERIMENTAL UNIT/TRIAL SET
7	123	A2	C1250-Count1	C1250	2	OBSERVATIONAL UNIT
8	123	A2	C1250-Count2	C1250	2	OBSERVATIONAL UNIT
9	123	A2	C1250-Count3	C1250	2	OBSERVATIONAL UNIT
10	123	A2	C1250-Count4	C1250	2	OBSERVATIONAL UNIT

RICC

Dataset wrap

Name	gt

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.

Dataset2

Row	STUDYID	DOMAIN	GTSEQ	GTREFID	GTTESTCD	GTTEST	GTCELLEV	GTORRES	GTORRESU	GTCOLSRT	GTSTRESC	GTSTRESN	GTSTRESU	GTDTC
1	123	GT	1	C0	RICC	Relative Increase in Cell Count

TRTDRTOL

Treatment Duration Tolerance

TRTDURU

Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)

H

3

123

MNvit

TX

A1

PRDCONC

Concentration of product

0

4

123

MNvit

TX

A1

PRDCONCU

Concentration Unit

ug/ml

5

123

MNvit

TX

A1

Product

Product Name

6

123

MNvit

TX

A1

Smoking Regime

7

123

MNvit

TX

A1

Smoke Fraction

123

MNvit

TX

A2

METACT

Metabolic Activation

+S9

123

MNvit

TX

A2

TRTDUR

Treatment Duration

Short Term

123

MNvit

TX

A2

PRDCONC

Concentration of product

1250

123

MNvit

TX

A2

PRDCONCU

Concentration Unit

ug/ml

123

MNvit

TX

A2

Product

Product Name

123

MNvit

TX

A2

Smoking Regime

123

MNvit

TX

A2

Smoke Fraction

123

MNvit

TX

B1

METACT

Metabolic Activation

-S9

123

MNvit

TX

B1

TRTDRTRG

Treatment Duration target

4

TRTDRTOL

Treatment Duration Tolerance

.25

??

123

MNvit

TX

B1

TRTDURU

Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)

H

123

MNvit

TX

B1

PRDCONC

Concentration of product

0

123

MNvit

TX

B1

PRDCONCU

Concentration Unit

ug/ml

123

MNvit

TX

B1

Product

Product Name

123

MNvit

TX

B1

Smoking Regime

123

MNvit

TX

B1

Smoke Fraction

123

MNvit

TX

C1

METACT

Metabolic Activation

-S9

123

MNvit

TX

C1

TRTDUR

Treatment Duration

24

??

123

MNvit

TX

C1

TRTDURU

Treatment Duration Unit

H

123

MNvit

TX

C1

PRDCONC

Concentration of product

0

123

MNvit

TX

C1

PRDCONCU

Concentration Unit

ug/ml

123

MNvit

TX

C1

Product

Product Name

123

MNvit

TX

C1

Smoking Regime

123

MNvit

TX

C1

Smoke Fraction

Expand

title	gt.xpt (similar to LB)

Row

STUDYID

ASSAYID

DOMAIN

TXCD

GTSEQ

GTTESTCD

GTTEST

GTCELLEV
(cells evaluated)

GTORRES

GTORRESU

GTSTRESC

GTSTRESN

GTSTRESU

GTDTC

GTNOMDY

GTELTM

GTTPTREF

1

123

MNvit

GT

A2

1

RICC

134

15.7

%

15.7

%

2022-05-25

2

123

MNvit

GT

A2

2

RCC

134

13.0

%

13.0

%

2022-05-25

3

123

MNvit

GT

A2

3

RPD

134

7.9

%

7.9

%

2022-05-25

4

123

MNvit

GT

A2

4

MNCELLS

Micronucleated Cells

3266

20

Cells

20

Cells

2022-05-25

5

123

MNvit

GT

A2

5

MNCELLS

Micronucleated Cells

2190

17

Cells

17

Cells

2022-05-25

6

123

MNvit

GT

A2

6

MNCELLS

Micronucleated Cells

2758

13

Cells

13

Cells

2022-05-25

7

123

MNvit

GT

A2

7

MNCELLS

Micronucleated Cells

2714

21

Cells

21

Cells

2022-05-25

8

123

MNvit

GT

A2

8

AVGREL

Average Relative MN Frequency

0.66

%

0.66

%

2022-05-25

9

123

MNvit

GT

A1

1

154

0

%

0

%

2022-05-25

10

2

123

MNvit

GT

A1

2

C0

RCC

Relative Cell Count

154

0

%

0

%

2022-05-25

11

3

123

MNvit

GT

A1

3

C0

RPD

Relative Population Doubling

154

0

%

0

%

2022-05-25

12

4

123

MNvit

GT

A1

4

C0-Count1

MNCELLS

MNCE	Micronucleated Cells

3266

2205

15

Cells

15

Cells

2022-05-25

13

5

123

MNvit

GT

A1

5

C0-Count2

MNCELLS

MNCE	Micronucleated Cells

2190

2474

13

Cells

13

Cells

2022-05-25

14

6

123

MNvit

GT

A1

6

C0-Count3

MNCELLS

MNCE

Micronucleated Cells

2758

17

Cells

17

Cells

2022-05-25

15

7

123

MNvit

GT

A1

7

C0-Count4

MNCELLS

MNCE	Micronucleated Cells

2714

2669

12

Cells

12

Cells

2022-05-25

16

8

123

MNvit

GT

A1

8

C0

AVGREL

MNCECE

Micronucleated Cells/Total Cells

Average Relative MN Frequency

0.57

%

0.57

%

2022-05-25

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

Expand

title	Notes for Developing Nonclinical in vitro study concept maps

Product, Smoking Regime (e.g. Traditional combustible, ENDS), Smoke Fraction, etc.

https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=969610#null

One study (Original sample of TK6 cells)

Multiple products
Multiple Assays (Multiple types of assays)

Assay (MN)
3 assay/test conditions;
Treatment duration (2: ST, LT);
Presence of metabolic activation (2: presence, type)

Concentrations of product (6 of these: 0, x, y, z,..., +CNTL);
CytoTox % (3 different percentages from testing 1 portion of the original sample)
4 MN counts conducted (on 4 different portions of original sample?)

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

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

ARMCD


9	123	GT	1	C1250	RICC	Relative Increase in Cell Count	134	15.7	%	15.7	15.7	%	2022-05-25
10	123	GT	2	C1250	RCC	Relative Cell Count	134	13.0	%	13.0	13.0	%	2022-05-25
11	123	GT	3	C1250	RPD	Relative Population Doubling	134	7.9	%	7.9	7.9	%	2022-05-25
12	123	GT	4	C1250-Count1	MNCE	Micronucleated Cells	3266	20		20	20		2022-05-25
13	123	GT	5	C1250-Count2	MNCE	Micronucleated Cells	2190	17		17	17		2022-05-25
14	123	GT	6	C1250-Count3	MNCE	Micronucleated Cells	2758	13		13	13		2022-05-25
15	123	GT	7	C1250-Count4	MNCE	Micronucleated Cells	2714	21		21	21		2022-05-25
16	123	GT	8	C1250	MNCECE	Micronucleated Cells/Total Cells		0.66	%	0.66	0.66	%	2022-05-25

Expand

title	te.xpt (trial elements)

Row

STUDYID

ASSAYID

DOMAIN

ETCD

ELEMENT

Expand

title	ta.xpt (trial arms)

Row

STUDYID

ASSAYID

DOMAIN

ARMCD

ARM

TAETORD

ETCD

ELEMENT

Expand

title	ei.xpt (dm-like)

Not needed.

Row

STUDYID

DOMAIN

ENID (Entity ID)

RICC

RCC

RPD

Sum of cell ev.

Cells with MN

SMKFID (Smoke Fraction)

REPLCTID

(Replicate Number)

PLATEID (Plate ID)

COLID

(Column number)

ROWID (Row number)

SETCD (Set Code, TX)

RFSTDTC

RFENDTC

RFXSTDTC

RFXENDTC

RFCSTDTC

RFCENDTC

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