SEND Example.In vitro Micronucleus Assay

This example shows a sample report table, trial design, and results dataset for study 123 for the determination of the in vitro genotoxicity potential of tobacco products using the in vitro micronucleus assay. TOBA-642 - Getting issue details... STATUS

TOBA-456 - Getting issue details... STATUS

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 8:	Shows that the applicant's study reference ID is not applicable.
Rows 9-12:	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). TOBA-56 - Jira project doesn't exist or you don't have permission to view it.

ts.xpt

xx.xpt

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		STSTDTC	Study Start Date	2022-05-25
4	123	TS	1		STITLE	Study Title	Determination of the in vitro genotoxicity potential using the in vitro Neutral Red Uptake assay
5	123	TS	1		SNDIGVER	SEND Implementation Guide Version	TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6	123	TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-09-30
7	123	TS	1		APPLCNT	Applicant Organization TOBA-356 - Jira project doesn't exist or you don't have permission to view it.	Example Applicant, Inc.
8	123	TS	1		APREFID	Study Reference ID		NOT APPLICABLE
9	123	TS	1	1	TSTFNAM	Test Facility Name	Example Test Lab Name
10	123	TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000
11	123	TS	1	1	TFCNTRY	Test Facility Country	USA
12	123	TS	1	1	STDIR	Study Director	Dr. R. Smith
13	123	TS	1		GLPFL	GLP Flag	Y
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

Dataset Debug Messages

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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. TOBA-457 - Getting issue details... STATUS

Rows 1-17:	Show the experimental parameters that are common for table 1 of study 123.
Rows 18, 25:	Show that sets A1 and A2 each have a parent set code of A. As a child of set A, each of these sets inherit the test conditions of set A.
Rows 18-24:	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 25-31:	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.

tx.xpt

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

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Dataset Wrapper Debug Message

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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) TOBA-687 - Jira project doesn't exist or you don't have permission to view it. 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.

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relref.xpt

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

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Dataset Wrapper Debug Message

Please add a row column to your dataset.

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.

gt.xpt

Row	STUDYID	DOMAIN	GTREFID	GTSEQ	GTTESTCD	GTTEST	GTCELLEV	GTORRES	GTORRESU	GTSTRESC	GTSTRESN	GTSTRESU	GTDTC
1	123	GT	C0	1	RICC TOBA-643 - Jira project doesn't exist or you don't have permission to view it.	Relative Increase in Cell Count	154	0	%	0	0	%	2022-05-25
2	123	GT	C0	2	RCC	Relative Cell Count	154	0	%	0	0	%	2022-05-25
3	123	GT	C0	3	RPD	Relative Population Doubling	154	0	%	0	0	%	2022-05-25
4	123	GT	C0-Count1	4	MNCE	Micronucleated Cells	2205	15	Cells	15	15	Cells	2022-05-25
5	123	GT	C0-Count2	5	MNCE	Micronucleated Cells	2474	13	Cells	13	13	Cells	2022-05-25
6	123	GT	C0-Count3	6	MNCE	Micronucleated Cells	2758	17	Cells	17	17	Cells	2022-05-25
7	123	GT	C0-Count4	7	MNCE	Micronucleated Cells	2669	12	Cells	12	12	Cells	2022-05-25
8	123	GT	C0	8	MNCECE	Micronucleated Cells/Total Cells		0.57	%	0.57	0.57	%	2022-05-25
9	123	GT	C1250	1	RICC	Relative Increase in Cell Count	134	15.7	%	15.7	15.7	%	2022-05-25
10	123	GT	C1250	2	RCC	Relative Cell Count	134	13.0	%	13.0	13.0	%	2022-05-25
11	123	GT	C1250	3	RPD	Relative Population Doubling	134	7.9	%	7.9	7.9	%	2022-05-25
12	123	GT	C1250-Count1	4	MNCE	Micronucleated Cells	3266	20	Cells	20	20	Cells	2022-05-25
13	123	GT	C1250-Count2	5	MNCE	Micronucleated Cells	2190	17	Cells	17	17	Cells	2022-05-25
14	123	GT	C1250-Count3	6	MNCE	Micronucleated Cells	2758	13	Cells	13	13	Cells	2022-05-25
15	123	GT	C1250-Count4	7	MNCE	Micronucleated Cells	2714	21	Cells	21	21	Cells	2022-05-25
16	123	GT	C1250	8	MNCECE	Micronucleated Cells/Total Cells		0.66	%	0.66	0.66	%	2022-05-25

Dataset Debug Message

When the JIRA issue(s) present in the dataset have been resolved, and their resolution has been confirmed by governance, please remove them.

Dataset Wrapper Debug Message

Please add a row column to your dataset.

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SEND Example.In vitro Micronucleus Assay