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title	ts.xpt (trial summary, study level parameters)

Assumption: Study A Trial (study) can have more than one assay type
Assumption: ASSAYID value of ALL means indicates that it applies to all assays in the studyReplaced the ASSAYID values of MNT with MNvit (term used in OECD #487) - is this better? This is not a controlled term so we can use anything but what we use in our IG examples are often used in industry implementations so we should use realistic and best practice values as much as possible.
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	ASSAYID	DOMAIN	TSSEQ	TSGRPID	TSPARMCD	TSPARM	TSVAL	TSVALNF
1	123	ALL	TS	1		GLPTYP	Good Laboratory Practice Type	FDA

3

2	123	ALL	TS	2		GLPTYP	Good Laboratory Practice Type	OECD

	123	ALL	TS	1		STSTDTC	Study Start Date

2007

2022-

05-


4	123	ALL	TS	1		STITLE	Study Title

Example of a Crossover study in the Rat with 3 dose levels and 3 dosing periods

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
5	123	ALL	TS	1		SNDIGVER	SEND Implementation Guide Version

Tobacco

TOBACCO IMPLEMENTATION GUIDE VERSION 1.0


6	123	ALL	TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-

09-


7	123	ALL	TS	1		SSPONSOR	Sponsor Organization	Example Sponsor Inc.


8	123	ALL	TS	1		SPREFID	Sponsor's Study Reference ID		NOT APPLICABLE

9	123	ALL	TS	1	1	TSTFNAM	Test Facility Name	Example Tox Lab Name


10	123	ALL	TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000


11	123	ALL	TS	1	1	TFCNTRY	Test Facility Country	USA


...	123	ALL	TS	1	1	STDIR	Study Director	Dr. R. Smith


	123	ALL	TS	1		GLPFL	GLP Flag	Y


	123	MNvit	TS	1		ASTD	Assay Standard	OECD Test No. 487


	123	MNvit	TS	1		ASTDV	Assay Standard Version	2016-07-29


	123	MNvit	TS	1		SSTYP	Study Type	GENOTOXICITY IN VITRO


	123	MNvit	TS	1		SSSTYP	Study Sub Type	In Vitro Micronucleus


	123	MNvit	TS	1		SPECIES	Species	Homo Sapiens


	123	MNvit	TS	1		??	Test System?	TK6 Lymphoblastoid Suspension Cells


	123	NRU	TS	1		ASTD	Assay Standard	NIH Publication No. 07-4519


	123	NRU	TS	1		ASTDV	Assay Standard Version	2006-11


	123	NRU	TS	1		SSTYP	Study Type

GENOTOXICITY IN VITRO
	123	NRU	TS	1		SSSTYP	Study Sub Type	In Vitro Neutral Red Uptake


	123	NRU	TS	1		SPECIES	Species

Homo Sapiens40

Salmonella enterica
123	NRU	TS	1	STRAIN	Strain/Substrain	Salmonella enterica enterica
123	NRU	TS	1	??	Test System??	Normal Human Keratinocyte
123	NRU	TS	1	REGIME	Smoking Regime	Traditional combustible
123	NRU	TS	1	RUNPRT	run-port number?? (always same for whole assay?)	1-1
123	NRU	TS	1	SMPLID	Sample ID	030001
123	NRU	TS	1	SMKFRC	Smoke Fraction	A
123	NRU	TS	1	REPNUM	Replicate Number	1

Expand

title	tx.xpt (trial sets)

Treatment Duration will be controlled?

During CT definition/reviews will

need to

decide appropriate TXPARM and TXVAL; Treatment duration

values

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.

Row	STUDYID	ASSAYID	DOMAIN	SETCD	SET (what sponsor calls it)	TXSEQ	TXPARMCD	TXPARM	TXVAL
1	123

MNvit

NRU

METACT

Metabolic Activation (should there be two parms? Presence, type)?

1-1-A

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

CSC-10

(through SLS-200)

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

+S9


2	123

MNvit

NRU

A1TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)3

1-1-A	CSC-10		WELLNUM (e.g., 1-A through 10-H)	Number representing the location of the well in the 96-well plate	1-A
3	123	NRU	TX	1-1-A	CSC-10

TRTDRTOLTreatment Duration ToleranceTRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)H

INTRVN

name of the intervention article

Bleomycin or Cyclophosphamid AITVTYPE

	Cigarette Smoke Condensate
4	123	NRU	TX	1-1-A	CSC-10		ITVTYPE (CT e.g, Product, positive control, negative control)	type of intervention article

choices of values: product; negative control; positive control3

PRODUCT
5	123

MNvit

NRU

1-1-A

CSC-10

ITVCONC

Concentration of i a 04

intervention concentration	10
6	123

MNvit

NRU

1-1-A

CSC-10

ITVCONCU

Concentration Unit

intervention unit

ug/ml

123

MNvit

NRU

A1ProductProduct Name

	1-1-B	CSC-10		PLATENUM	Plate number	1
8

123

MNvit

NRU

A1Smoking Regime7123MNvitTXA1Smoke Fraction123MNvitTXA2METACTMetabolic Activation+S9123MNvitTXA2TRTDURTreatment DurationShort Term123MNvitTXA2PRDCONCConcentration of product1250123MNvitTXA2PRDCONCUConcentration Unitug/ml123MNvitTXA2ProductProduct Name123MNvitTXA2Smoking Regime123MNvitTXA2Smoke FractionA6METACT

1-1-B	CSC-10		WELLNUM	Number representing the location of the well in the 96-well plate	2-A
9	123	NRU	TX	1-1-B	CSC-10	INTRVN	name of the intervention article	Cigarette Smoke Condensate
10	123	NRU	TX	1-1-B	CSC-10	ITVTYPE	type of intervention article	PRODUCT
11	123	NRU	TX	1-1-B	CSC-10	ITVCONC	intervention concentration	10
12	123	NRU	TX	1-1-B	CSC-10	ITVCONCU	intervention unit	ug/ml
...				...
	123	NRU	TX	1-10-H	SLS-10	PLATENUM	Plate number	1
	123	NRU	TX	1-10-H	SLS-10	WELLNUM	Number representing the location of the well in the 96-well plate	10-H
	123	NRU	TX	1-10-H	SLS-10

TRTDUR

INTRVN

name of the intervention article

Cyclophosphamid A

	sodium laurel sulfate
	123	NRU	TX	1-10-H	SLS-10		ITVTYPE	type of intervention article

Positive control

POSITIVE CONTROL

ITVCONCConcentration of i a 5A6ITVCONCUConcentration Unitug/mlA6TCNTL123MNvitTX

METACTMetabolic Activation-S9123MNvitTX

TRTDRTRGTreatment Duration target4TRTDRTOLTreatment Duration Tolerance.25??123MNvitTXB1TRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)H

	123	NRU	TX	1-10-H	SLS-10	ITVCONC	intervention concentration	200
	123	NRU	TX	1-10-H	SLS-10	ITVCONCU	intervention unit	ug/ml
...				...
	123	NRU	TX	2-10-H	SLS-10	PLATENUM	Plate number	2
	123	NRU	TX	2-10-H	SLS-10	WELLNUM	Number representing the location of the well in the 96-well plate	10-H
	123	NRU	TX	2-10-H	SLS-10	INTRVN	name of the intervention article	sodium laurel sulfate
	123	NRU	TX	2-10-H	SLS-10	ITVTYPE	type of intervention article	POSITIVE CONTROL
	123	NRU	TX	2-10-H	SLS-10	ITVCONC	intervention concentration	200
	123	NRU	TX	2-10-H	SLS-10	ITVCONCU	intervention unit	ug/ml

123MNvitTX

PRDCONCConcentration of product0123MNvitTX

PRDCONCUConcentration Unitug/ml123MNvitTXB1ProductProduct Name123MNvitTXB1Smoking Regime123MNvitTXB1Smoke Fraction


	123	MNvit	TX

METACT

Metabolic

Activation

Activation (should there be two parms? Presence, type)?

S9
	123	MNvit	TX

TRTDUR

TRTDRTRG

Treatment Duration

24??

target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)	3
	123	MNvit	TX


	123	MNvit	TX				TRTDRTOL

TRTDURU

Treatment Duration

UnitH

Tolerance
	123	MNvit	TX

PRDCONCConcentration of product0

			TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)	H
	123	MNvit	TX

PRDCONCUConcentration Unitug/ml

			INTRVN	name of the intervention article	Bleomycin or Cyclophosphamid A
	123	MNvit	TX

Product

ITVTYPE

type of intervention article

choices of values: product; negative control; positive control

Product Name


	123	MNvit	TX

ITVCONC

Concentration of i a

Smoking Regime


	123	MNvit	TX

ITVCONCU

Concentration Unit

ug/ml

Smoke Fraction

AVGREL

Expand

title	gt.xpt (similar to LB)

Image AddedImage Added

Row	STUDYID	ASSAYID	DOMAIN	TXCD	GTSEQ	GTTESTCD	GTTEST	GTCELLEV (cells evaluated)	GTORRES	GTORRESU	GTSTRESC	GTSTRESN	GTSTRESU	GTDTC	GTNOMDY	GTELTM	GTTPTREF


1	123	NRU	GT	1-1-A	1

	RELABS	Relative Absorbance Reading		100	ug/ml	100	100	ug/ml
2	123	NRU	GT	1-1-B	1	RELABS	Relative Absorbance Reading		107	ug/ml	100	100	ug/ml
3	123	NRU	GT	1-1-C	1	RELABS	Relative Absorbance Reading		98.6	ug/ml	100	100	ug/ml
54	123	NRU	GT	1-1-D	1	RELABS	Relative Absorbance Reading		94.9	ug/ml	100	100	ug/ml
6	123	NRU	GT	1-1-E	1	RELABS	Relative Absorbance Reading		111
7	123	NRU	GT	1-1-F	1	RELABS	Relative Absorbance Reading		96.9
8	123	NRU	GT	1-1-G	1	RELABS	Relative Absorbance Reading		105
9	123	NRU	GT	1-1-H	1	RELABS	Relative Absorbance Reading		95.2
10	123	NRU	GT	1-2-A	1	RELABS	Relative Absorbance Reading		83.0
11	123	NRU	GT	1-2-B	1	RELABS	Relative Absorbance Reading		77.7
...				...
80	123	NRU	GT	1-10-H	1	RELABS	Relative Absorbance Reading		0.791
...				...
160	123	NRU	GT	2-10-H	1	RELABS	Relative Absorbance Reading		0.780

RICC

...


1	123	MNvit	GT	A2	1	RICC	Relative Increase in Cell Count	134	15.7	%	15.7	15.7	%	2022-05-25
2	123	MNvit	GT	A2	2	RCC	Relative Cell Count	134	13.0	%	13.0	13.0	%	2022-05-25
3	123	MNvit	GT	A2	3	RPD	Relative Population Doubling	134	7.9	%	7.9	7.9	%	2022-05-25
4	123	MNvit	GT	A2	4	MNCELLS	Micronucleated Cells	3266	20	Cells	20	20	Cells	2022-05-25
5	123	MNvit	GT	A2	5	MNCELLS	Micronucleated Cells	2190	17	Cells	17	17	Cells	2022-05-25
6	123	MNvit	GT	A2	6	MNCELLS	Micronucleated Cells	2758	13	Cells	13	13	Cells	2022-05-25
7	123	MNvit	GT	A2	7	MNCELLS	Micronucleated Cells	2714	21	Cells	21	21	Cells	2022-05-25
8	123	MNvit	GT	A2	8	AVGREL	Average Relative MN Frequency		0.66	%	0.66	0.66	%	2022-05-25
9	123	MNvit	GT	A1	1	RICC	Relative Increase in Cell Count	154	0	%	0	0	%	2022-05-25
10	123	MNvit	GT	A1	2	RCC	Relative Cell Count	154	0	%	0	0	%	2022-05-25
11	123	MNvit	GT	A1	3	RPD	Relative Population Doubling	154	0	%	0	0	%	2022-05-25
12	123	MNvit	GT	A1	4	MNCELLS	Micronucleated Cells	3266	15	Cells	15	15	Cells	2022-05-25
13	123	MNvit	GT	A1	5	MNCELLS	Micronucleated Cells	2190	13	Cells	13	13	Cells	2022-05-25
14	123	MNvit	GT	A1	6	MNCELLS	Micronucleated Cells	2758	17	Cells	17	17	Cells	2022-05-25
15	123	MNvit	GT	A1	7	MNCELLS	Micronucleated Cells	2714	12	Cells	12	12	Cells	2022-05-25
16	123	MNvit	GT	A1	8	AVGREL	Average Relative MN Frequency		0.57	%	0.57	0.57	%	2022-05-25

Page tree

Versions Compared

Old Version 33

New Version 34

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

...

Expand
title te.xpt (trial elements)
(Do we need this? a single element (treatment)?)
Row STUDYID ASSAYID DOMAIN ETCD ELEMENT
...

Page tree

Page History

Versions Compared

Old Version 33

New Version 34

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

... Expandtitlete.xpt (trial elements)(Do we need this? a single element (treatment)?)RowSTUDYIDASSAYIDDOMAINETCDELEMENT...

...

Expand
title te.xpt (trial elements)
(Do we need this? a single element (treatment)?)
Row STUDYID ASSAYID DOMAIN ETCD ELEMENT
...