SEND Example.In vitro Bacterial Reverse Mutation Assay

populate units of COLONIES
recreate the data table - clean up, add "S" to the first set A
move assumptions out of all of the examples
add row captions to highlight exceptions/assumptions

This is an example showing trial design and results from the in vitro bacterial reverse mutation test of Study #8325064.

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.

Assumption: When the experimental unit is derived from the species and strain, such as a cell line, then TESTSYS should be supplied.

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	8325064	Ames	TS	1		STITLE	Study Title	The Bacterial Reverse Mutation Test, Study 8325064-1
5	8325064	Ames	TS	1		SNDIGVER	SEND Implementation Guide Version	TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6	8325064	Ames	TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-09-30
7	8325064	Ames	TS	1		SSPONSOR	Sponsor Organization	Example Sponsor Inc.
8	8325064	Ames	TS	1		SPREFID	Sponsor's Study Reference ID		NOT APPLICABLE
9	8325064	Ames	TS	1	1	TSTFNAM	Test Facility Name	Example Tox Lab Name
10	8325064	Ames	TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000
11	8325064	Ames	TS	1	1	TFCNTRY	Test Facility Country	USA
12	8325064	Ames	TS	1	1	STDIR	Study Director	Dr. R. Smith
13	8325064	Ames	TS	1		GLPFL	GLP Flag	N
14	8325064	Ames	TS	1		ASTD	Assay Standard	OECD Test No. 471
15	8325064	Ames	TS	1		ASTDV	Assay Standard Version	2020-06-29
16	8325064	Ames	TS	1		SSTYP	Study Type	GENOTOXICITY IN VITRO
17	8325064	Ames	TS	1		SSSTYP	Study Sub Type	Bacterial Reverse Mutation Test
18	8325064	Ames	TS	1	2	SPECIES	Species	Salmonella
19	8325064	Ames	TS	1	2	STRAIN	Strain	TA98
20	8325064	Ames	TS	1	2	STRAIN	Strain	TA100
21	8325064	Ames	TS	1	2	STRAIN	Strain	TA1535
22	8325064	Ames	TS	1	2	STRAIN	Strain	TA1537
23	8325064	Ames	TS	1	3	SPECIES	Species	Escherichia coli
24	8325064	Ames	TS	1	3	STRAIN	Strain	WP2 uvrA pKM101

How do we handle "toxic, no revertant colonies"? (LAK will add 6 records with GTSTAT = NOT DONE, GTREASND = "TOO MUCH CYTOTOXICITY,"
Condition of background bacterial lawn? Slight thinning, Very thin? - refer to SEND team's marked-up table.
- new Test code of Cytotoxicity with GTORRES = S, V (controlled terms)
- Each plate we would have one result record for Revertent count and another for the lawn evaluation (NORMAL, SLIGHT THINNING, VERY THIN)
When "-" in Mean, Std Dev, Fold Inc - refer to SEND team's marked-up table (GTSTAT = NOT DONE; variety of REASND)

Below the SETS shown in the TX table are rows A, F, I, and R (probably don't need R)

Row	STUDYID	ASSAYID	DOMAIN	SETCD	SET (what sponsor calls it)	TXPARMCD	TXPARM	TXVAL
1	8325064	Ames	TX	SetA	A-TA98-C0	SPECIES	Species	Salmonella typhimurium
2	8325064	Ames	TX	SetA	A-TA98-C0	STRAIN	Strain/Substrain	TA98
3	8325064	Ames	TX	SetA (Row 1)	A-TA98-C0	METACT	Metabolic Activation
4						METACTFL	Y/N presence of metabolic activation	N
5	8325064	Ames	TX	SetA		TRTDMIN	Treatment Duration Minimum	71.5
6	8325064	Ames	TX	SetA		TRTDTRG	Treatment Duration Target	72
7	8325064	Ames	TX	SetA		TRTDMAX	Treatment Duration Maximum	72.5
8	8325064	Ames	TX	SetA		TRTDU	Treatment Duration Unit	HOURS
9	8325064	Ames	TX	SetA		INCBTMP	Incubation Temperature	37
10	8325064	Ames	TX	SetA		INCBTMPU	Incubation Temperature Unit	C
11	8325064	Ames	TX	SetA		HUMID	Atmospheric Relative Humidity Percent	50
12	8325064	Ames	TX	SetA		ATMCO2	Atmospheric CO2 Percent	5
13	8325064	Ames	TX	SetA		SPTOBID	Sponsor defined tobacco identifier	CIG01a
14	8325064	Ames	TX	SetA		EXPTYP	Exposure Type (See TIG NC workstream minutes 30-Jan here: Nonclinical)	Submerged
15	8325064	Ames	TX	SetA		SAMTYP	Sample Type	Total Particulate Matter in PBS
16	8325064	Ames	TX	SetA		INTRVN	name of the intervention article	TA1
17	8325064	Ames	TX	SetA		ITVTYPE	type of intervention article	Vehicle Control
18	8325064	Ames	TX	SetA		ITVCONC	Concentration of intervention article	0
19	8325064	Ames	TX	SetA		ITVCONCU	Concentration Unit	ug/plate
20	8325064	Ames	TX	SetA		TRTV	Treatment Vehicle	DMSO
21	8325064	Ames	TX	SetA		SPDEVID	Sponsor defined device identifier	PUFFMASTER3K
...						DUREFID	Smoke Regimen	Medium Intensity Regimen
	8325064	Ames	TX	SetF (row 6)		METACT	Metabolic Activation (should there be two parms? Presence, type)?	None
	8325064	Ames	TX	SetF		TRTDRTRG	Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)
	8325064	Ames	TX	SetF		TRTDRTOL	Treatment Duration Tolerance
	8325064	Ames	TX	SetF		TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
	8325064	Ames	TX	SetF		INTRVN	name of the intervention article (Tobacco ProdA, Bleomycin or Cyclophosphamid A)	TA1
	8325064	Ames	TX	SetF		ITVTYPE	type of intervention article choices of values: product; negative control; positive control	Product
	8325064	Ames	TX	SetF		ITVCONC	Concentration of intervention article	500
	8325064	Ames	TX	SetF		ITVCONCU	Concentration Unit	ug/plate
	8325064	Ames	TX	SetF		STRAIN	Strain/Substrain	TA98
	8325064	Ames	TX	SetF		REGIME	Smoking Regime	ISO Regime
...
	8325064	Ames	TX	SetG (row 7) do G not I!!!		METACT	Metabolic Activation (should there be two parms? Presence, type)?	None
	8325064	Ames	TX	SetI (row 9)		TRTDRTRG	Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)
	8325064	Ames	TX	SetI		TRTDRTOL	Treatment Duration Tolerance
	8325064	Ames	TX	SetI		TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
	8325064	Ames	TX	SetI		INTRVN	name of the intervention article (Tobacco ProdA, Bleomycin or Cyclophosphamid A)	2-Nitrofluorine
	8325064	Ames	TX	SetI		ITVTYPE	type of intervention article choices of values: product; negative control; positive control	Positive Control
	8325064	Ames	TX	SetI		ITVCONC	Concentration of intervention article	5
	8325064	Ames	TX	SetI		ITVCONCU	Concentration Unit	ug/plate
	8325064	Ames	TX	SetI		REGIME	Smoking Regime	ISO
...
	8325064	Ames	TX	SetR (Row 18)		METACT	Metabolic Activation (should there be two parms? Presence, type)?	None
	8325064	Ames	TX	SetR		TRTDRTRG	Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)
	8325064	Ames	TX	SetR		TRTDRTOL	Treatment Duration Tolerance
	8325064	Ames	TX	SetR		TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
	8325064	Ames	TX	SetR		INTRVN	name of the intervention article (Tobacco ProdA, Bleomycin or Cyclophosphamid A)	4-Nitroquinoline-1-oxide
	8325064	Ames	TX	SetR		ITVTYPE	type of intervention article choices of values: product; negative control; positive control	Positive Control
	8325064	Ames	TX	SetR		ITVCONC	Concentration of intervention article	2
	8325064	Ames	TX	SetR		ITVCONCU	Concentration Unit	ug/plate
	8325064	Ames	TX	SetR		STRAIN	Strain/Substrain	TA98
	8325064	Ames	TX	SetR		REGIME	Smoking Regime	ISO

Ou.xpt!!!

Row	STUDYID	ASSAYID	DOMAIN	TXSETCD	EUID	OUID	GTSEQ	GTTESTCD	GTTEST	GTORRES	GTORRESU	GTCOLSRT (coll. summ. result type)	GTSTRESC	GTSTRESN	GTSTRESU	GTDTC	GTMETHOD
1	8325064	Ames	GT	SETA	A	0_1	1	RPP	Revertant Numbers Per Plate	26	COLONIES		26	26	COLONIES	2015-08-03	INSTRUMENT COUNTED
2	8325064	Ames	GT	SETA	A	0_2	2	RPP	Revertant Numbers Per Plate	35	COLONIES		35	35		2015-08-03	INSTRUMENT COUNTED
3	8325064	Ames	GT	SETA	A	0_3	3	RPP	Revertant Numbers Per Plate	39	COLONIES		39	39		2015-08-03	INSTRUMENT COUNTED
4	8325064	Ames	GT	SETA	A	0_4	4	RPP	Revertant Numbers Per Plate	35	COLONIES		35	35		2015-08-03	INSTRUMENT COUNTED
5	8325064	Ames	GT	SETA	A	0_5	5	RPP	Revertant Numbers Per Plate	30	COLONIES		30	30		2015-08-03	INSTRUMENT COUNTED
	8325064	Ames	GT	SETA				RPP	Revertant Numbers Per Plate	33.0	COLONIES	MEAN	33.0	33.0
7	8325064	Ames	GT	SETA		ALL	7	RPP	Revertant Numbers Per Plate	5.0	COLONIES	STANDARD DEVIATION	5.0	5.0			INSTRUMENT COUNTED
	8325064	Ames	GT	SETF		5_1	1	RPP	Revertant Numbers Per Plate	8			8	8			MANUALLY COUNTED
	8325064	Ames	GT	SETF		5_1	1
	8325064	Ames	GT	SETF		5_2	2	RPP	Revertant Numbers Per Plate	10			10	10			MANUALLY COUNTED
	8325064	Ames	GT	SETF		5_3	3	RPP	Revertant Numbers Per Plate	12			12	12			MANUALLY COUNTED
	8325064	Ames	GT	SETF		ALL	6	RPPMEAN	Mean of Revertant Numbers Per Plate	10.0			10.0	10.0
	8325064	Ames	GT	SETF		ALL	7	RPPSTDDV	Standard Deviation of Revertant Numbers Per Plate	2.0			2.0	2.0
	8325064	Ames	GT	SETF		ALL	8	RPPFDINC	Fold Increase of Revertant Numbers Per Plate	0.3			0.3	0.3
								CYTOTOX	Cytotoxicity	Very thin background bacterial lawn			V
	8325064	Ames	GT	SETI		5_1	1	RPP	Revertant Numbers Per Plate	1104			1104	1104
	8325064	Ames	GT	SETI		5_2	2	RPP	Revertant Numbers Per Plate	1037			1037	1037
	8325064	Ames	GT	SETI		5_3	3	RPP	Revertant Numbers Per Plate	971			971	971
	8325064	Ames	GT	SETI		ALL	6	RPPMEAN	Mean of Revertant Numbers Per Plate	1037.3			1037.3	1037.3
	8325064	Ames	GT	SETI		ALL	7	RPPSTDDV	Standard Deviation of Revertant Numbers Per Plate	66.5			66.5	66.5
	8325064	Ames	GT	SETI		ALL	8	RPPFLDINC	Fold Increase of Revertant Numbers Per Plate	31.4			31.4	31.4

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SEND Example.In vitro Bacterial Reverse Mutation Assay

SET (what sponsor calls it)