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titlets.xpt (trial summary, study level parameters)
  • Assumption: The intent of this dataset is to provide a summary of trial (study) information. This is not subject-level data. 
  • Assumption: A Trial (study) can have more than one assay type
  • Assumption: ASSAYID value of ALL indicates that it applies to all assays in the study
  • Assumption: SPDEVID and DUREFID should only be in TX (with the same value for all sets if there is only one device used)
  • Assumption:  SPDEVID (sponsor defined device identifier) should be added at the trial set level (tx.xpt) - we can discuss if this should be .  While it is possible to show a value in TS when there is only one device for a study, we will make it a rule that it goes in TX for consistency and cross-study analysis.
    • This allows for studies where there are multiple products and different product(s) per trial set, one record for each product that is being tested in each particular trial set (tx.xpt)

Row

STUDYID

ASSAYID

DOMAIN

TSSEQ

TSGRPID

TSPARMCD

TSPARM

TSVAL

TSVALNF

1123MNvitTS1
GLPTYPGood Laboratory Practice TypeFDA
2123MNvitTS2
GLPTYPGood Laboratory Practice TypeOECD
3123MNvitTS1
STSTDTCStudy Start Date2022-05-25
4123MNvitTS1
STITLEStudy Title

Determination of the in vitro genotoxicity potential of 10 tobacco products in the in vitro Micronucleus Assay


5123MNvitTS1
SNDIGVERSEND Implementation Guide VersionTOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6123MNvitTS1
SNDCTVERSEND Controlled Terminology VersionSEND Terminology 2021-09-30
7123MNvitTS1
SSPONSORSponsor OrganizationExample Sponsor Inc.
8123MNvitTS1
SPREFIDSponsor's Study Reference ID
NOT APPLICABLE
9123MNvitTS11TSTFNAMTest Facility NameExample Tox Lab Name
10123MNvitTS11TSTFLOCTest Facility Location10 Somewhere Street, Montgomery, AL 10000
11123MNvitTS11TFCNTRYTest Facility CountryUSA
12123MNvitTS11STDIRStudy DirectorDr. R. Smith
13123MNvitTS1
GLPFLGLP FlagY
14123MNvitTS1
ASTDAssay StandardOECD Test No. 487 
15123MNvitTS1
ASTDVAssay Standard Version2016-07-29
16123MNvitTS1
SSTYPStudy TypeGENOTOXICITY IN VITRO
17123MNvitTS1
SSSTYPStudy Sub TypeIn Vitro Micronucleus
18123MNvitTS1
SPECIESSpeciesHomo Sapiens
19123MNvitTS1
TESTSYSTest System

TK6 Lymphoblastoid Suspension Cells


Expand
titleto.xpt (tobacco identifiers, design paramters)

(This is a copy from the SDTM Example. Cigarette Design Parameters, will need scription team)

Rows 1-4:Show the records for the product identifiers for the tobacco product identified in SPTOBID. These records are categorized as product identifiers by TOCAT = PRODUCT IDENTIFIERS.
Rows 5-10:Show the records for the product descriptors for the tobacco product identified in SPTOBID. These records are categorized as product identifiers by TOCAT = PRODUCT DESCRIPTOR.


to.xpt

Row

STUDYID

DOMAIN

SPTOBID

TOSEQ

TOTESTCD

TOTEST

TOCAT

TOORRES

TOORRESU

TOSTRESC

TOSTRESN

TOSTRESU

1TOB07TOCIG01a

1

TBPRDCATTobacco Product CategoryPRODUCT IDENTIFIERCigarette
Cigarette

2TOB07TOCIG01a2TBPRSCATTobacco Product SubcategoryPRODUCT IDENTIFIERFiltered, Combusted
Filtered, Combusted

3TOB07TOCIG01a3MANUFManufacturerPRODUCT IDENTIFIERJoes Cigs USA
Joes Cigs USA

4TOB07TOCIG01a4TRADENAMTrade NamePRODUCT IDENTIFIERTreetop Menthol King Size
Treetop Menthol King Size

5TOB07TOCIG01a5PACKTYPPackage TypePRODUCT DESCRIPTORHARD PACK
HARD PACK

6TOB07TOCIG01a6PRDQUANProduct QuantityPRODUCT DESCRIPTOR20CIGARETTE2020CIGARETTE
7TOB07TOCIG01a7LENGTHLengthPRODUCT DESCRIPTOR86.0mm86.086.0mm
8TOB07TOCIG01a8CIRCUMFCircumferencePRODUCT DESCRIPTOR26.0mm26.026.0mm
9TOB07TOCIG01a9VENTLTNVentilationPRODUCT DESCRIPTOR10.0%10.010.0%
10TOB07TOCIG01a10CHARFLAVCharacterizing FlavorPRODUCT DESCRIPTORMENTHOL
MENTHOL

1
Expand
titletx.xpt (trial sets)
  • 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
  • Do we need both SPDEVID AND DUREFID?
  • What are good values (realistic) for "SET"?
  • Check Essential Data list 

A1: Image Removed

A2:                                   Image Removed

  • Assumption:  SPDEVID (sponsor defined device identifier), and Test System  should be added at the trial set level (tx.xpt).  While it is possible to show a value in TS when there is only one device for a study, we will make it a rule that it goes in TX for consistency and cross-study analysis.
    • This allows for studies where there are multiple products and different product(s) per trial set, one record for each product that is being tested in each particular trial set (tx.xpt)
  • Assumption: SPDEVID and DUREFID should only be in TX (with the same value for all sets if there is only one device used)
  • Assumption:  SPDEVID (sponsor defined device identifier) should be added at the trial set level (tx.xpt).  While it is possible to show a value in TS when there is only one device for a study, we will make it a rule that it goes in TX for consistency and cross-study analysis.
    • This allows for studies where there are multiple products and different product(s) per trial set, one record for each product that is being tested in each particular trial set (tx.xpt)
  • Do we need both SPDEVID AND DUREFID?
  • What are good values (realistic) for "SET"?
  • Check Essential Data list 

A1: Image Added


A2:                                   Image Added

RowSTUDYIDASSAYIDDOMAINSETCDSETTXSEQTXPARMCDTXPARMTXVAL
1123MNvitTX

A1

(table 1, row 1, ST exposure with S9)

ST+S9C01TESTSYSTest systemTK6 Lymphoblastoid Suspension Cells
2123MNvitTX

A1

ST+S9C02METACTMetabolic Activation  (this is the type of activation used)+S9
3123MNvitTXA1ST+S9C03METACTFLY/N presence of metabolic activation (this indicates that metabolic activation was used)Y
4123MNvitTX

A1

ST+S9C04TRTDMINTreatment Duration Minimum3
5123MNvitTXA1ST+S9C05TRTDTRGTreatment Duration Target3.5
6123MNvitTXA1ST+S9C06TRTDMAXTreatment Duration Maximum4
7123MNvitTX

A1

ST+S9C07TRTDUTreatment Duration UnitHOURS
8123MNvitTXA1ST+S9C08RCVDMINRecovery Duration Minimum23.5
9123MNvitTXA1ST+S9C09RCVDTRGRecovery Duration Target24
10123MNvitTX

A1

ST+S9C010RCVDMAXRecovery Duration Maximum24.5
11123MNvitTXA1ST+S9C011RCVDURecovery Duration UnitHOURS
12123MNvitTXA1ST+S9C012INCBTMPIncubation Temperature37
13123MNvitTX

A1

ST+S9C013INCBTMPUIncubation Temperature UnitC
14
RowSTUDYIDASSAYIDDOMAINSETCDSETTXSEQTXPARMCDTXPARMTXVAL
123MNvitTXA1
(table 1, row 1,
ST
exposure with S9)ST
+S9C0
1
14
METACTMetabolic Activation  (this is the type of activation used)+S9
HUMIDAtmospheric Relative Humidity  Percent50
15
2
123MNvitTX

A1

ST+S9C0
2
15
METACTFLY/N presence of metabolic activation (this indicates that metabolic activation was used)Y
ATMCO2Atmospheric CO2 Percent5
16
3
123MNvitTXA1ST+S9C0
3
16
TRTDMINTreatment Duration Minimum3
SPTOBID

Sponsor defined tobacco identifier

CIG01a
17
4
123MNvitTXA1ST+S9C0
4
17
TRTDTRGTreatment Duration Target3.5
EXPTYP

Exposure Type (See TIG NC workstream minutes 30-Jan here: Nonclinical)

Submerged
18
5
123MNvitTXA1ST+S9C0
5TRTDMAXTreatment Duration Maximum4
18SAMTYP 

Sample Type

(e.g. TPM, GVP, whole aerosol, whole smoke conditioned media, aqueous extracts, etc., see notes here: Nonclinical)

Total Particulate Matter in DMSO
19
6
123MNvitTXA1ST+S9C0
6TRTDUTreatment Duration UnitHOURS
19INTRVN

Name of the Intervention Article

can be:  Tobacco ProdA, Bleomycin (positive control) or Cyclophosphamid A (positive control)

Tobacco ProdA
20
7
123MNvitTXA1ST+S9C0
7RCVDMINRecovery Duration Minimum23.5
20ITVTYPE

type of intervention article

choices of values:  product; negative control; positive control

Negative Control
21
8123MNvitTXA1ST+S9C08RCVDTRGRecovery Duration Target249
123MNvitTXA1ST+S9C0
9
21
RCVDMAXRecovery Duration Maximum24.5
ITVCONCConcentration of intervention article0
22
10
123MNvitTXA1ST+S9C0
10
22
RCVDU
ITVCONCU
Recovery Duration
Concentration Unit
HOURS
ug/ml
11
23123MNvitTXA1ST+S9C0
11
23
INCBTMPIncubation Temperature37
SPDEVIDSponsor defined device identifierPUFFMASTER3K
24
12
123MNvitTXA1ST+
S9C0
S9C024
12
DUREFID
INCBTMPUIncubation Temperature Unit
Smoke RegimenMedium Intensity Regimen
25
C
123MNvitTX
A1

A2

(table 1, row 2, ST exposure with S9 at concentration 1250)

ST+
S9C0
S9-1250
13
1
MEDIAComposition of MediaSartorius HEK29313
TESTSYSTest system
26123MNvitTX
A1

A2

ST+
S9C0
S9-1250
14
2
HUMIDAtmospheric Relative Humidity  Percent50
METACTMetabolic Activation  (this is the type of activation used)
27
14
123MNvitTX
A1
A2ST+
S9C0
S9-1250
15
3
ATMCO2Atmospheric CO2 Percent5
METACTFLY/N presence of metabolic activation (this indicates that metabolic activation was used)
28
15
123MNvitTX
A1
A2ST+
S9C0
S9-1250
16
4
SPTOBID

Sponsor defined tobacco identifier

CIG01a16
TRTDMINTreatment Duration Minimum
29123MNvitTX
A1
A2ST
+S9C017EXPTYP

Exposure Type (See TIG NC workstream minutes 30-Jan here: Nonclinical)

Submerged
+S9-12505TRTDTRGTreatment Duration Target
30
17
123MNvitTX
A1
A2ST+
S9C0
S9-1250
18
6
SAMTYP 

Sample Type

(e.g. TPM, GVP, whole aerosol, whole smoke conditioned media, aqueous extracts, etc., see notes here: Nonclinical)

Total Particulate Matter in DMSO
TRTDMAXTreatment Duration Maximum
31
18
123MNvitTX
A1
A2ST+
S9C0
S9-1250
6
7
INTRVN

Name of the Intervention Article

can be:  Tobacco ProdA, Bleomycin (positive control) or Cyclophosphamid A (positive control)

Tobacco ProdA
TRTDUTreatment Duration Unit
32
19
123MNvitTX
A1
A2ST+
S9C0
S9-1250
7
8
ITVTYPE

type of intervention article

choices of values:  product; negative control; positive control

Negative Control
RCVDMINRecovery Duration Minimum
33
20
123MNvitTX
A1
A2ST+
S9C0
S9-1250
821
9
ITVCONCConcentration of intervention article0
RCVDTRGRecovery Duration Target
34
123MNvitTX
A1
A2ST+
S9C0
S9-1250
922
10
ITVCONCUConcentration Unitug/ml
RCVDMAXRecovery Duration Maximum
35
123MNvitTX
A1
A2ST+
S9C0
S9-1250
10
11
SPDEVIDSponsor defined device identifierPUFFMASTER3K
RCVDURecovery Duration Unit
36
23
123MNvitTX
A1
A2ST+
S9C0
S9-1250
11
12
DUREFID
INCBTMP
Smoke Regimen
Incubation Temperature
37
Medium Intensity Regimen
123MNvitTX
A1
A2ST+
S9C0
S9-1250
11
13
SMKEXSYSSmoke Exposure SystemCambridge filter pad, eluted in DMSO
INCBTMPUIncubation Temperature Unit
38
25
123MNvitTXA2
(table 1, row 2,
ST
exposure with S9 at concentration 1250)ST
+S9-1250
1
14
METACTMetabolic Activation  (should there be two parms? Presence, type)?+S9
HUMIDAtmospheric Relative Humidity  Percent
39
26
123MNvitTXA2ST+S9-1250
2
15
METACTFLY/N presence of metabolic activation (this indicates that metabolic activation was used)Y27
ATMCO2Atmospheric CO2 Percent
40123MNvitTXA2ST+S9-1250
3
16
TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range?  start/end, target and tolerance?, one text field not-analyzable)3
SPTOBID

Sponsor defined tobacco identifier


41
28
123MNvitTXA2ST+S9-1250
4
17
TRTDRTOLTreatment Duration Tolerance
EXPTYP

Exposure Type (See TIG NC workstream minutes 30-Jan here: Nonclinical)


42
29
123MNvitTXA2ST+S9-125018
5
SAMTYP 
TRTDURU

Sample Type

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

(e.g. TPM, GVP, whole aerosol, whole smoke conditioned media, aqueous extracts, etc., see notes here: Nonclinical)


43
30
123MNvitTXA2ST+S9-1250
6
19INTRVN
name

Name of the

intervention articleTobacco ProdA

Intervention Article

can be:  Tobacco ProdA, Bleomycin (positive control) or Cyclophosphamid A (positive control)


44
31
123MNvitTXA2ST+S9-1250
7
20ITVTYPE

type of intervention article

Product

choices of values:  product; negative control; positive control


45
32
123MNvitTXA2ST+S9-1250
8
21ITVCONCConcentration of
i a 
intervention article
1250

46
33
123MNvitTXA2ST+S9-1250
9
22ITVCONCUConcentration Unit
ug/ml

47
34
123MNvitTXA2ST+S9-1250
10
23SPDEVIDSponsor defined device identifier
PUFFMASTER2023

48
35
123MNvitTXA2ST+S9-1250
11
24DUREFIDSmoke
RegimenHigh Intensity
Regimen
...








Expand
titledu.xpt smoke regimen definition (a findings domain for device in-use properties)

 We use DU for smoking regimen. Note that a separate DI dataset will be needed to show identifying parameters of the "PUFFMASTER3K" smoking machine

  • Details of the smoking regimen are represented as device in-use properties, linked to the stability data in PT above by matching values of PTREFID/DUREFID = "Medium Intensity Regimen" (We will update with a realistic value for the regimen, with input).
  • Smoking regimen is represented in --REFID (we made up a value of "Medium Intensity Regimen"; we can update with something realistic)
  • The smoking regimen is carried out by the smoking machine/device shown in SPDEVID, Sponsor defined device identifier, "PUFFMASTER3K"

du.xpt

Row

STUDYID

DOMAIN

SPDEVID

DUSEQ

DUREFID

DUGRPID

DUTESTCD

DUTEST

DUORRES

DUORRESU

DUSTRESC

DUSTRESN

DUSTRESU

1123DUPUFFMASTER3K1Medium Intensity Regimen
PUFFPROFPuff ProfileSQUARE
SQUARE

2123DUPUFFMASTER3K2Medium Intensity Regimen

PUFFDUR

Puff Duration

1.25

sec

1.25

1.25

sec

3123DUPUFFMASTER3K3Medium Intensity Regimen

PUFFINT

Puff Interval

3

PUFF/min

3

3

PUFF/min

4123DUPUFFMASTER3K4Medium Intensity Regimen

PUFFBLCK

Puff Block

25

%

25

25

%

5123DUPUFFMASTER3K5Medium Intensity Regimen
NUMPUFFTotal Number of Puffs

200

PUFF

200

200

PUFF

6123DUPUFFMASTER3K6Medium Intensity Regimen
PUFFVOLPuff Volume

10

mL

10

10

mL

7123DUPUFFMASTER3K7Medium Intensity Regimen
PUFFRNGPuff Range

100-200


100-200



8123DUPUFFMASTER3K8Medium Intensity Regimen1PUFFPAUSPuff Pause

60

s

60

60

s

9123DUPUFFMASTER3K9Medium Intensity Regimen1PUFFPINTPuff Pause Interval

10

PUFF

10

10

PUFF

10123DUPUFFMASTER20231

Canadian Intense Regime


PUFFPROFPuff ProfileSQUARE
SQUARE

11123DUPUFFMASTER20232Canadian Intense Regime

PUFFDUR

Puff Duration

2.00

sec

2.00

2.00

sec

12123DUPUFFMASTER20233Canadian Intense Regime

PUFFINT

Puff Interval

4

PUFF/min

4

4

PUFF/min

13123DUPUFFMASTER20234

Canadian Intense Regime


PUFFBLCK

Puff Block

0

%

0

0

%

14123DUPUFFMASTER20235Canadian Intense Regime
NUMPUFFTotal Number of Puffs

200

PUFF

200

200

PUFF

15123DUPUFFMASTER20236Canadian Intense Regime
PUFFVOLPuff Volume

10

mL

10

10

mL

16123DUPUFFMASTER20237

Canadian Intense Regime


PUFFRNGPuff Range

100-200


100-200



17123DUPUFFMASTER20238Canadian Intense Regime1PUFFPAUSPuff Pause

60

s

60

60

s

18123DUPUFFMASTER20239Canadian Intense Regime1PUFFPINTPuff Pause Interval

10

PUFF

10

10

PUFF

...