Bacterial Reverse Mutation Test (Ames) Example

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.

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	123	Ames	TS	1		GLPTYP	Good Laboratory Practice Type	FDA
2	123	Ames	TS	2		GLPTYP	Good Laboratory Practice Type	OECD
3	123	Ames	TS	1		STSTDTC	Study Start Date	2015-07-29
4	123		TS	1		STITLE	Study Title	~~Determination of the in vitro genotoxicity potential of 10 tobacco products in the in vitro Micronucleus 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		SSPONSOR	Sponsor Organization	Example Sponsor Inc.
8	123		TS	1		SPREFID	Sponsor's Study Reference ID		NOT APPLICABLE
9	123		TS	1	1	TSTFNAM	Test Facility Name	Example Tox 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	N
14	123		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

A1:

A2:

Row	STUDYID	ASSAYID	DOMAIN	SETCD	TXPARMCD	TXPARM	TXVAL
	123	MNvit	TX	A1 (table 1, row 1, ST exposure with S9)	METACT	Metabolic Activation (should there be two parms? Presence, type)?	+S9
	123	MNvit	TX	A1	TRTDRTRG	Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)	3
	123	MNvit	TX	A1	TRTDRTOL	Treatment Duration Tolerance
	123	MNvit	TX	A1	TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)	H
	123	MNvit	TX	A1	INTRVN	name of the intervention article (Tobacco ProdA, Bleomycin or Cyclophosphamid A)	Tobacco ProdA
	123	MNvit	TX	A1	ITVTYPE	type of intervention article choices of values: product; negative control; positive control	Product
	123	MNvit	TX	A1	ITVCONC	Concentration of intervention article	0
	123	MNvit	TX	A1	ITVCONCU	Concentration Unit	ug/ml
	123	MNvit	TX	A2 (table 1, row 2)	METACT	Metabolic Activation (should there be two parms? Presence, type)?	+S9
	123	MNvit	TX	A2	TRTDRTRG	Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)	3
	123	MNvit	TX	A2	TRTDRTOL	Treatment Duration Tolerance
	123	MNvit	TX	A2	TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)	H
	123	MNvit	TX	A2	INTRVN	name of the intervention article	Tobacco ProdA
	123	MNvit	TX	A2	ITVTYPE	type of intervention article	Product
	123	MNvit	TX	A2	ITVCONC	Concentration of i a	1250
	123	MNvit	TX	A2	ITVCONCU	Concentration Unit	ug/ml
...

A1:

A2:

Row	STUDYID	ASSAYID	DOMAIN	TXSETCD	GTSEQ	GTTESTCD	GTTEST	GTCELLEV (cells evaluated)	GTORRES	GTORRESU	GTSTRESC	GTSTRESN	GTSTRESU	GTDTC
1	123	MNvit	GT	A1	1	RICC	Relative Increase in Cell Count	1540000	0	%	0	0	%	2022-05-25
2	123	MNvit	GT	A1	2	RCC	Relative Cell Count	154	0	%	0	0	%	2022-05-25
3	123	MNvit	GT	A1	3	RPD	Relative Population Doubling	154	0	%	0	0	%	2022-05-25
4	123	MNvit	GT	A1	4	MNCELLS	Micronucleated Cells	2205	15	Cells	15	15	Cells	2022-05-25
5	123	MNvit	GT	A1	5	MNCELLS	Micronucleated Cells	2474	13	Cells	13	13	Cells	2022-05-25
6	123	MNvit	GT	A1	6	MNCELLS	Micronucleated Cells	2758	17	Cells	17	17	Cells	2022-05-25
7	123	MNvit	GT	A1	7	MNCELLS	Micronucleated Cells	2669	12	Cells	12	12	Cells	2022-05-25
8	123	MNvit	GT	A1	8	AVGREL	Average Relative MN Frequency		0.57	%	0.57	0.57	%	2022-05-25
9	123	MNvit	GT	A2	1	RICC	Relative Increase in Cell Count	134	15.7	%	15.7	15.7	%	2022-05-25
10	123	MNvit	GT	A2	2	RCC	Relative Cell Count	134	13.0	%	13.0	13.0	%	2022-05-25
11	123	MNvit	GT	A2	3	RPD	Relative Population Doubling	134	7.9	%	7.9	7.9	%	2022-05-25
12	123	MNvit	GT	A2	4	MNCELLS	Micronucleated Cells	3266	20	Cells	20	20	Cells	2022-05-25
13	123	MNvit	GT	A2	5	MNCELLS	Micronucleated Cells	2190	17	Cells	17	17	Cells	2022-05-25
14	123	MNvit	GT	A2	6	MNCELLS	Micronucleated Cells	2758	13	Cells	13	13	Cells	2022-05-25
15	123	MNvit	GT	A2	7	MNCELLS	Micronucleated Cells	2714	21	Cells	21	21	Cells	2022-05-25
16	123	MNvit	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

SET (what sponsor calls it)