Bacterial Reverse Mutation Test (Ames) Example 1

This is an example showing trial design and results data of Study #8325064 for the determination of the in vitro bacterial reverse mutation test ~~potential of 10 tobacco products in the in vitro Micronucleus Assay~~

The bacterial reverse mutation test uses amino acid-requiring strains of Salmonella typhimurium (S. typhimurium) and Escherichia coli (E. coli) to detect point mutations, which involve substitution, addition or deletion of one or a few DNA base pairs. The principle of this bacterial reverse mutation test is that it detects chemicals that induce mutations which revert mutations present in the tester strains and restore the functional capability of the bacteria to synthesize an essential amino acid. The revertant bacteria are detected by their ability to grow in the absence of the amino acid required by the parent tester strain.

Plate number

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

Assumption: The intent of this dataset is to provide a summary of trial (study) information. This is not subject-level data.
What is the best ASSAYID, Species, Test System, GLP?

Row	STUDYID	ASSAYID	DOMAIN	TSSEQ	TSGRPID	TSPARMCD	TSPARM	TSVAL	TSVALNF
1	8325064	Ames	TS	1		GLPTYP	Good Laboratory Practice Type	FDA
2	8325064	Ames	TS	2		GLPTYP	Good Laboratory Practice Type	OECD
3	8325064	Ames	TS	1		STSTDTC	Study Start Date	2015-07-29
4			TS	1		STITLE	Study Title	~~Determination of the in vitro genotoxicity potential of 10 tobacco products in the in vitro Micronucleus Assay~~
5			TS	1		SNDIGVER	SEND Implementation Guide Version	TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6			TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-09-30
7			TS	1		SSPONSOR	Sponsor Organization	Example Sponsor Inc.
8			TS	1		SPREFID	Sponsor's Study Reference ID		NOT APPLICABLE
9			TS	1	1	TSTFNAM	Test Facility Name	Example Tox Lab Name
10			TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000
11			TS	1	1	TFCNTRY	Test Facility Country	USA
12			TS	1	1	STDIR	Study Director	Dr. R. Smith
13			TS	1		GLPFL	GLP Flag	N
14			TS	1		ASTD	Assay Standard	OECD Test No. 471
15	123		TS	1		ASTDV	Assay Standard Version	2020-06-29
16	123		TS	1		SSTYP	Study Type	GENOTOXICITY IN VITRO
17	123		TS	1		SSSTYP	Study Sub Type	Bacterial Reverse Mutation Test
18	123		TS	1		SPECIES	Species	Homo Sapiens
19	123		TS	1		??	Test System?	TK6 Lymphoblastoid Suspension Cells

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

STUDYID	ASSAYID	DOMAIN	SETCD	TXPARMCD	TXPARM	TXVAL
8325064	Ames	TX	SetA (TA98-DMSO)	METACT	Metabolic Activation (should there be two parms? Presence, type)?	None
8325064	Ames	TX	SetA	TRTDRTRG	Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)
		TX		TRTDRTOL	Treatment Duration Tolerance
		TX		TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
		TX		INTRVN	name of the intervention article (Tobacco ProdA, Bleomycin or Cyclophosphamid A)	DMSO
		TX		ITVTYPE	type of intervention article choices of values: product; negative control; positive control	Vehicle Control
		TX		ITVCONC	Concentration of intervention article	0
		TX		ITVCONCU	Concentration Unit	ug/ml
		TX		STRAIN	Strain/Substrain	TA98
		TX		REGIME	Smoking Regime
		TX		RUN	Assay run number	1
		TX		PORT	Port ID
		TX		SMPLID	Sample ID
		TX		SMKFRC	Smoke Fraction
		TX		REPNUM	Replicate Number
				MEAN
				STDDEV
				FOLDINC

		TX	P2	METACT	Metabolic Activation (should there be two parms? Presence, type)?	+S9
		TX	P2	TRTDRTRG	Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)	3
		TX	P2	TRTDRTOL	Treatment Duration Tolerance
		TX	P2	TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)	H
		TX	P2	INTRVN	name of the intervention article	DMSO TA1
		TX	P2	ITVTYPE	type of intervention article	Product
		TX	P2	ITVCONC	Concentration of i a	1250
		TX	P2	ITVCONCU	Concentration Unit	ug/ml
		TX	P2	STRAIN	Strain/Substrain	WP2 uvrA pKM10 1
		TX	P2	REGIME	Smoking Regime
		TX	P2	RUN	Assay run number	1
		TX	P2	PORT	Port ID
		TX	P2	SMPLID	Sample ID
		TX	P2	SMKFRC	Smoke Fraction
		TX	P2	REPNUM	Replicate Number

Do we need GTMETHOD?

Row	DOMAIN	TXSETCD	PLTWLID	GTSEQ	GTTESTCD	GTTEST	GTORRES	GTORRESU	GTSTRESC	GTSTRESN	GTSTRESU	GTDTC
1	GT	SETA (TA98-DMSO)	1	1	RPP	Revertant Numbers Per Plate	26		26	26		2015-08-03
2	GT	SETA (TA98-DMSO)	2	2	RPP	Revertant Numbers Per Plate	35		35	35		2015-08-03
3	GT	SETA (TA98-DMSO)	3	3	RPP	Revertant Numbers Per Plate	39		39	39		2015-08-03
4	GT	SETA (TA98-DMSO)	4	4	RPP	Revertant Numbers Per Plate	35		35	35		2015-08-03
5	GT	SETA (TA98-DMSO)	5	5	RPP	Revertant Numbers Per Plate	30		30	30		2015-08-03
6	GT	SETA (TA98-DMSO)	ALL	6	RPPMEAN	Mean of Revertant Numbers Per Plate	33.0
7	GT	SETA (TA98-DMSO)	ALL	7	RPPSTDDV	Standard Deviation of Revertant Numbers Per Plate
8	GT	SETA (TA98-DMSO)	ALL	8	RPPFLDINC	Fold Increase of Revertant Numbers Per Plate
9	GT	A2		9	RICC	Relative Increase in Cell Count	15.7	%	15.7	15.7	%	2022-05-25
10	GT	A2		10	RCC	Relative Cell Count	13.0	%	13.0	13.0	%	2022-05-25
11	GT	A2		11	RPD	Relative Population Doubling	7.9	%	7.9	7.9	%	2022-05-25
12	GT	A2		4	MNCELLS	Micronucleated Cells	20	Cells	20	20	Cells	2022-05-25
13	GT	A2		5	MNCELLS	Micronucleated Cells	17	Cells	17	17	Cells	2022-05-25
14	GT	A2		6	MNCELLS	Micronucleated Cells	13	Cells	13	13	Cells	2022-05-25
15	GT	A2		7	MNCELLS	Micronucleated Cells	21	Cells	21	21	Cells	2022-05-25
16	GT	A2		8	AVGREL	Average Relative MN Frequency	0.66	%	0.66	0.66	%	2022-05-25
...

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Bacterial Reverse Mutation Test (Ames) Example 1

SET (what sponsor calls it)