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This is an example showing trial design and results data of Study #123 for the determination of the in vitro genotoxicity potential of 10 tobacco products in the in vitro Micronucleus Assay


For the purposes of team review of the example data, the report is  included in this section: 

Sample data #1: Determination of the in vitro genotoxicity potential of 10 tobacco products in the in vitro Micronucleus Assay

Study info: This study was performed to assess the in vitro genotoxicity of 10 different tobacco products containing 1% to 2% nicotine. The genotoxic potential was determined using the in vitro micronucleus test with TK6 lymphoblastoid suspension cells. The study was conducted in compliance with the following documents:

  • OECD TG 487 (2010): Guideline for the testing of chemicals: In vitro mammalian cell micronucleus test.
  • BL SOP 132: Determination of the in vitro genotoxicity of condensates from tobacco products and ingredients for tobacco products / electronic vapour products – in vitro micronucleus test (IVM) with TK6 cells.

The cells were exposed to increasing dose levels of tobacco product using short term treatment in the presence and absence of an external metabolic activation system (ST+/-S9 mix) as well as a long term treatment in the absence of an external metabolic activation system (LT-S9 mix).

Toxicity was calculated as relative increase in cell count (RICC), relative cell count (RCC) and relative population doubling (RPD). RPD is the cytotoxicity measure used for the assessment. RICC and RCC are also reported but not considered for the assessment.

Note: OECD GUIDELINE FOR THE TESTING OF CHEMICALS

Population Doubling = [log (Post-treatment cell number ÷ Initial cell number)] ÷ log 2


Conclusion: All tobacco product evaluated did not induce any signs of severe toxicity or genotoxicity in any of the treatments and do not fulfil the criteria to be classified as genotoxic.

Reported results: (only listed the result of one tobacco product as an example)

  1. Statistical analysis

Adjusted p-values calculated for the micronucleus frequencies for every dose level as compared to the corresponding solvent control after ST in the presence and absence of S9 mix as well as LT in the absence of S9 mix. One way ANOVA with posthoc Dunnett’s test for multiple comparisons for the dose response and a two tailed unpaired student’s t-test for the comparison of positive and negative control were used. The difference between the samples is considered statistically significant at p≤0.05.




Treatment


Test date


Concentration [µg/ml]

Fold increase of MN

over background


Adjusted p- value

Significant increase Y/N


ST+ S9


25.05.2022

1250

0.9

0.9973

N

2500

0.9

0.9517

N

3750

0.6

0.2654

N

5000

0.9

0.9895

N

CPA [5µg/ml]

3.1

0.0003

Y


ST-S9


25.05.2022

1250

1.6

0.6408

N

2500

1.3

0.8995

N

3750

2.9

0.0106

N

5000

1.0

> 0.9999

N

Bleo [0.2µg/ml]

3.8

0.0002

Y


LT-S9


25.05.2022

1250

0.7

0.5958

N

2500

1.3

0.6378

N

3750

0.5

0.1146

N

5000

1.1

0.9929

N

Bleo [0.5µg/ml]

2.9

0.0047

Y

Bleo: Bleomycin; CPA: Cyclophosphamid A; statistically significant increases are highlighted in bold.


  • 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 in TS when there is only one device for a study
    • 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


(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

  • 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:


A2:                                   

RowSTUDYIDASSAYIDDOMAINSETCD
SET (what sponsor calls it, more meaningful label for Tables)
TXSEQTXPARMCDTXPARMTXVAL
1123MNvitTX

A1

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

ST+S9C01METACTMetabolic Activation  (this is the type of activation used)+S9
2123MNvitTXA1ST+S9C02METACTFLY/N presence of metabolic activation (this indicates that metabolic activation was used)Y
3123MNvitTX

A1

ST+S9C03TRTDMINTreatment Duration Minimum3
4123MNvitTXA1ST+S9C04TRTDTRGTreatment Duration Target3.5
5123MNvitTXA1ST+S9C05TRTDMAXTreatment Duration Maximum4
6123MNvitTX

A1

ST+S9C06TRTDUTreatment Duration UnitHOURS
7123MNvitTXA1ST+S9C07RCVDMINRecovery Duration Minimum23.5
8123MNvitTXA1ST+S9C08RCVDTRGRecovery Duration Target24
9123MNvitTX

A1

ST+S9C09RCVDMAXRecovery Duration Maximum24.5
10123MNvitTXA1ST+S9C010RCVDURecovery Duration UnitHOURS
11123MNvitTXA1ST+S9C011INCBTMPIncubation Temperature37
12123MNvitTX

A1

ST+S9C012INCBTMPUIncubation Temperature UnitC
13123MNvitTXA1ST+S9C013MEDIAComposition of MediaSartorius HEK293
14123MNvitTXA1ST+S9C014HUMIDAtmospheric Relative Humidity  Percent50
15123MNvitTX

A1

ST+S9C015ATMCO2Atmospheric CO2 Percent5
16123MNvitTXA1ST+S9C016SPTOBID

Sponsor defined tobacco identifier

CIG01a
17123MNvitTXA1ST+S9C017EXPTYP

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

Submerged

123MNvitTXA1ST+S9C018SAMTYP 

Sample Type

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

Total Particulate Matter in DMSO
18123MNvitTXA1ST+S9C06INTRVN

Name of the Intervention Article

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

Tobacco ProdA
19123MNvitTXA1ST+S9C07ITVTYPE

type of intervention article

choices of values:  product; negative control; positive control

Negative Control
20123MNvitTXA1ST+S9C08ITVCONCConcentration of intervention article0
21123MNvitTXA1ST+S9C09ITVCONCUConcentration Unitug/ml
22123MNvitTXA1ST+S9C010SPDEVIDSponsor defined device identifierPUFFMASTER3K
23123MNvitTXA1ST+S9C011DUREFIDSmoke RegimenMedium Intensity Regimen
24123MNvitTXA1ST+S9C011SMKEXSYSSmoke Exposure SystemCambridge filter pad, eluted in DMSO
25123MNvitTX

A2

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

ST+S9-12501METACTMetabolic Activation  (should there be two parms? Presence, type)?+S9
26123MNvitTXA2ST+S9-12502METACTFLY/N presence of metabolic activation (this indicates that metabolic activation was used)Y
27123MNvitTXA2ST+S9-12503TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range?  start/end, target and tolerance?, one text field not-analyzable)3
28123MNvitTXA2ST+S9-12504TRTDRTOLTreatment Duration Tolerance
29123MNvitTXA2ST+S9-12505TRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)H
30123MNvitTXA2ST+S9-12506INTRVNname of the intervention articleTobacco ProdA
31123MNvitTXA2ST+S9-12507ITVTYPEtype of intervention articleProduct
32123MNvitTXA2ST+S9-12508ITVCONCConcentration of i a 1250
33123MNvitTXA2ST+S9-12509ITVCONCUConcentration Unitug/ml
34123MNvitTXA2ST+S9-125010SPDEVIDSponsor defined device identifierPUFFMASTER2023
35123MNvitTXA2ST+S9-125011DUREFIDSmoke RegimenHigh Intensity Regimen
...








 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

di.xpt (copied v1.0 of medical devices IG)

  • This example is a copy of Example 1 from di.xpt in SDTMIG-MD v1.0 but with values for SPDEVID and DIVAL revised slightly. 
  • Should I remove the FDA UDI (row 5) unless CTP has or plans to establish UDI values?

Example 1
This shows records for two three devices where the sponsor felt that the type, manufacturer, model number, and serial number were necessary for unique identification. In addition, there was a post-marketing UDI identifier available for the first device.

  • Rows 1-5 show the records for a device given a SPDEVID of PUFFMASTER3K
  • Rows 5-8 show the records for a device given a SPDEVID of PUFFMASTER2023
  • Rows 9-12 show


Row

STUDYID

DOMAIN

SPDEVID

DISEQ

DIPARMCD

DIPARM

DIVAL

1

123

DI

PUFFMASTER3K

1

DEVTYPE

Device Type

ENDS

2

123

DI

PUFFMASTER3K

2

MANUF

Manufacturer

Acme Machines

3

123

DI

PUFFMASTER3K

3

MODEL

Model Number

45-JFI

4

123

DI

PUFFMASTER3K

4

SERIAL

Serial Number

456789132-AXQ

5

123

DI

PUFFMASTER3K

5

FDAUDI

FDA Unique Device Identifier

456789123xyz

6

123

DI

PUFFMASTER2023

1

DEVTYPE

Device Type

SmokeMachine

7

123

DI

PUFFMASTER2023

2

MANUF

Manufacturer

Acme Machines

8

123

DI

PUFFMASTER2023

3

MODEL

Model Number

62-PLC

9

123

DI

PUFFMASTER2023

4

SERIAL

Serial Number

215964564-NFS

10

123

DI

UsualCTCigarette

1

DEVTYPE

Device Type

Combustible Tobacco Cigarette

11

123

DI

UsualCTCigarette

2

MANUF

Manufacturer

Philip Morris International

12

123

DI

UsualCTCigarette

3

MODEL

Model Number

Marlboro Red

13

123

DI

UsualCTCigarette

4

SERIAL

Serial Number

123456789

  • Entity IDs are unique within the assay (and a study can have many assays)
  • Replicates vs. Run 
    • need planned (ei.xpt) separate from the actual (gt.xpt)
    • If tests run at the same time, they are replicates and are assigned the same RUNID
    • If tests are run at separate times, they are runs and the RUNIDs are distinct
  • Different runs would be expected to have different ENID and GTDTC values. In ei.xpt, these are distinguished by different RUNID values.
  • Entities that are replicates of each other would be expected to
    • have different ENID values
    • be in the same trial set (SETCD values)
    • have the same RUNID values


RowSTUDYIDASSAYIDDOMAINENID (Entity ID)SETCD (from TX)

RUNID 

REPNUM (perm)


123MNvitEI1-8-3A1

1

1


123MNvitEI2-8-3A1

1

1


123MNvitEI2-9-3A1

2

1


123MNvitEI3-7-1A2

1

1


123MNvitEI2-7-1A2

1

2



A1:


A2:                                   


  • Different runs would be expected to have different ENID and GTDTC values. In ei.xpt, these are distinguished by different RUNID values.
RowSTUDYIDASSAYIDDOMAINENIDGTSEQGTTESTCDGTTESTGTCELLEV
(cells evaluated)
GTORRESGTORRESUGTSTRESCGTSTRESNGTSTRESUGTDTC
1123MNvitGT1-8-31RICCRelative Increase in Cell Count1540%00%2022-05-25
2123MNvitGT1-8-32RCCRelative Cell Count1540%00%2022-05-25
3123MNvitGT1-8-33RPDRelative Population Doubling1540%00%2022-05-25
4123MNvitGT1-8-34MNCELLSMicronucleated Cells220515Cells1515Cells2022-05-25
5123MNvitGT1-8-35MNCELLSMicronucleated Cells247413Cells1313Cells2022-05-25
6123MNvitGT1-8-36MNCELLSMicronucleated Cells275817Cells1717Cells2022-05-25
7123MNvitGT1-8-37MNCELLSMicronucleated Cells266912Cells1212Cells2022-05-25
8123MNvitGT1-8-38AVGRELAverage Relative MN Frequency
0.57%0.570.57%2022-05-25
9123MNvitGT2-8-31RICCRelative Increase in Cell Count13415.7%15.715.7%2022-05-25
10123MNvitGT2-8-32RCCRelative Cell Count13413.0%13.013.0%2022-05-25
11123MNvitGT2-8-33RPDRelative Population Doubling1347.9%7.97.9%2022-05-25
12123MNvitGT2-8-34MNCELLSMicronucleated Cells326620Cells2020Cells2022-05-25
13123MNvitGT2-8-35MNCELLSMicronucleated Cells219017Cells1717Cells2022-05-25
14123MNvitGT2-8-36MNCELLSMicronucleated Cells275813Cells1313Cells2022-05-25
15123MNvitGT2-8-37MNCELLSMicronucleated Cells271421Cells2121Cells2022-05-25
16123MNvitGT2-8-38AVGRELAverage Relative MN Frequency
0.66%0.660.66%2022-05-25
...













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