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

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red font - indicates potential for CT code lists green font - links to other domains

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The following shows the tabulated data as shown in the report for this study:

Neutral Red Cytotoxicity Assay Results (Relative Absorbance Data)
Run-Port Number	Sample ID	Smoke Fraction	Replicate Number	Plate Number	Well Number	Relative Assay Plate Absorbance Readings
						Cigarette Smoke Condensate (µg/mL)								SLS (µg/mL)
						10	50	75	100	120	140	160	200	110	200
1-1	030001	A	1	1	1	100	83.0	56.7	29.5	13.0	8.57	4.44	1.76	13.7	0.547
1-1	030001	A	1	1	2	107	77.7	65.7	30.2	15.6	9.79	5.41	2.49	8.09	0.791
1-1	030001	A	1	1	3	98.6	77.4	57.7	35.8	8.09	7.36	3.22	0.791	6.38	0.061
1-1	030001	A	1	1	4	94.9	81.5	38.2	31.2	7.60	5.17	3.22	0.791	5.17	0.304
1-1	030001	A	1	1	5	111	78.1	64.5	32.9	8.82	5.90	2.74	1.28	10.3	0.547
1-1	030001	A	1	1	6	96.6	76.2	48.0	26.8	7.84	4.20	2.74	1.52	8.09	4.93
1-1	030001	A	1	1	7	105	77.9	58.2	28.3	8.09	4.68	1.76	0.547	8.57	1.76
1-1	030001	A	1	1	8	95.2	74.0	47.2	24.4	8.57	3.71	3.47	0.304	11.2	0.791
Average						101	78.2	54.5	29.9	9.70	6.17	3.37	1.19	8.94	1.22
Std. Dev.						6	2.9	9.4	3.6	2.95	2.19	1.12	0.72	2.72	1.58
Coeff. Var.						5.8	3.6	17.2	11.9	30.4	35.5	33.1	61.0	30.5	129.9
1-1	030001	A	1	2	1	93.4	74.0	56.0	35.1	11.8	8.70	5.10	1.98	5.34	1.02
1-1	030001	A	1	2	2	102	75.2	53.3	35.1	11.8	7.74	5.58	3.66	5.34	1.02
1-1	030001	A	1	2	3	107	79.0	55.0	26.5	10.1	6.06	3.66	1.74	7.02	0.780
1-1	030001	A	1	2	4	104	80.2	55.3	29.8	8.94	3.90	3.66	1.50	6.30	0.780
1-1	030001	A	1	2	5	101	75.7	54.1	26.7	4.86	4.38	1.26	1.02	6.30	1.02
1-1	030001	A	1	2	6	110	85.7	67.7	26.0	5.34	4.62	3.42	1.50	6.30	0.540
1-1	030001	A	1	2	7	104	77.8	64.9	27.7	8.22	3.18	2.46	1.02	6.30	0.780
1-1	030001	A	1	2	8	103	71.6	58.9	25.5	9.42	4.14	3.90	1.26	4.38	0.780
Average						103	77.4	58.1	29.0	8.82	5.34	3.63	1.71	5.91	0.840
Std. Dev.						5	4.4	5.3	4.0	2.63	1.97	1.37	0.86	0.83	0.170
Coeff. Var.						4.6	5.6	9.2	13.6	29.8	36.9	37.6	50.0	14.1	20.2

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title	ts.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
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)
- needs to be allowed to vary down to the well level / result level
For the items highlighted in orange - what is the lowest level where this could vary? e.g. at the level of a well in a 96-well plate, or a slide vs. assay level vs. product level
- Smoke Regime needs to be allowed to vary down to the well level / result level
- run - also at result level
- port - (smoking product on the machine, you assign a run number or port-number for multiple replicates depending on linear vs. rotary machines; machine bias), needs to be allowed to vary down to the well level / result level)
- replicate - (e.g., multiple samples from one vial), could be a replicate per exposure (e.g., 3 plates, multiple analyses for exposure)
- sample ID - typically a unique number assigned (at CRO) or supplied by sponsor - result level
- Smoke fraction - result level (e.g.tpm particulate vs. gas gvp)

...

Row

...

STUDYID

...

DOMAIN

...

TSSEQ

...

TSGRPID

...

TSPARMCD

...

TSPARM

...

TSVAL

...

TSVALNF

...

ALL

...

ALL

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Determination of the in vitro genotoxicity potential of 10 tobacco products in both the in vitro Micronucleus Assay and the in vitro Neutral Red Uptake

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ALL

...

ALL

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title	tx.xpt (trial sets)

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.

...

SET (what sponsor calls it)

...

(plate-col-row in the 96-well plate)

...

(through SLS-200)

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PLATENUM. (e.g., 1 or 2)

...

WELLNUM (e.g., 1-A through 10-H)

...

micronucleus assay.

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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.

Dataset2

Row	STUDYID	DOMAIN	TSSEQ	TSGRPID	TSPARMCD	TSPARM	TSVAL	TSVALNF
1	123	TS	1		GLPTYP	Good Laboratory Practice Type	FDA
2	123	TS	2		GLPTYP	Good Laboratory Practice Type	OECD
3	123	TS	1		GLPFL	GLP Flag	Y
4	123	TS	1		STSTDTC	Study Start Date	2022-05-25
5	123	TS	1		STITLE	Study Title	Determination of the in vitro genotoxicity potential using the in vitro Neutral Red Uptake assay
6	123	TS	1		SNDIGVER	SEND Implementation Guide Version	TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
7	123	TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-09-30
8	123	TS	1		APPLCNT	Applicant	Example Applicant, Inc.
9	123	TS	1		APREFID	Study Reference ID		NOT APPLICABLE
10	123	TS	1	1	TSTFNAM	Test Facility Name	Example Test Lab Name
11	123	TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000
12	123	TS	1	1	TFCNTRY	Test Facility Country	USA
13	123	TS	1	1	STDIR	Study Director	Dr. R. Smith
14	123	TS	1	2	TSTGDNAM	Testing Guideline Name	GUIDELINE FOR THE TESTING OF CHEMICALS No. 487
15	123	TS	1	2	TSTGDORG	Testing Guideline Organization	OECD
16	123	TS	1	2	TSTGDVER	Testing Guideline Version	29-July-2016
17	123	TS	1		SSTYP	Study Type	GENOTOXICITY IN VITRO
18	123	TS	1		GNTXAID	Genetic Toxicology Assay Identifier	MNvit
19	123	TS	1		SPECIES	Species	HUMAN
20	123	TS	1		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

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	GTSTRESC	GTSTRESN	GTSTRESU	GTDTC
1	123	GT	1	C0	RICC	Relative Increase in Cell Count	154	0	%	0	0	%	2022-05-25
2	123	GT	2	C0	RCC	Relative Cell Count	154	0	%	0	0	%	2022-05-25
3	123	GT	3	C0	RPD	Relative Population Doubling	154	0	%	0	0	%	2022-05-25
4	123	GT	4	C0-Count1	MNCE	Micronucleated Cells	2205	15		15	15		2022-05-25
5	123	GT	5	C0-Count2	MNCE	Micronucleated Cells	2474	13		13	13		2022-05-25
6	123	GT	6	C0-Count3	MNCE	Micronucleated Cells	2758	17		17	17		2022-05-25
7	123	GT	7	C0-Count4	MNCE	Micronucleated Cells	2669	12		12	12		2022-05-25
8	123	GT	8	C0	MNCECE	Micronucleated Cells/Total Cells		0.57	%	0.57	0.57	%	2022-05-25
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

...

(CT e.g, Product, positive control, negative control)

...

Assay run number (how is this different from REPNUM)

...

1

...

title	gt.xpt (similar to LB)

Image RemovedImage Removed

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83.0

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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

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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Versions Compared

Old Version 36

New Version Current

Key

SET (what sponsor calls it)

(plate-col-row in the 96-well plate)

(through SLS-200)

PLATENUM. (e.g., 1 or 2)

WELLNUM (e.g., 1-A through 10-H)

(CT e.g, Product, positive control, negative control)

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

Page tree

Page History

Versions Compared

Old Version 36

New Version Current

Key

SET (what sponsor calls it)

(plate-col-row in the 96-well plate)

(through SLS-200)

PLATENUM. (e.g., 1 or 2)

WELLNUM (e.g., 1-A through 10-H)

(CT e.g, Product, positive control, negative control)

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