This is an example showing example shows a sample report table, trial design, and results data of Study #123 dataset for study 123 for the determination of the in vitro genotoxicity potential of 10 tobacco products in using the in vitro Micronucleus Assay
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- red font - indicates potential for CT code lists
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| title | Study 123, Report (for reference only, will be deleted?) |
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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)
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micronucleus assay.
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| title | Sample Report Table for Study 123 |
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| Rows 1-2: | Show 2 records for TSPARMCD = "GLPTYP", using TSSEQ to indicate multiple records, since both GLP types apply for this example study. | | Row 3: | Shows that this study was conducted as a GLP study. | | Rows 4-5: | Show the study start date and study title. | | Rows 6-7: | Show the version of SEND Implementation Guide and version of Controlled Terminology used in this study. | | Row 8: | Shows the applicant's organization. | | Row 9: | Shows that the applicant's study reference ID is not applicable. | | Rows 10-13: | Show that TSGRPID has been used to link records (name, location, country) related to the test facility (TSGRPID = 1). The study director is associated with the test facility. | | Rows 14-16: | Show that TSGRPID (TSGRPID=2) has been used to link the information on the testing guideline followed on this study (TSTGDNAM, TSTGDORG, TSTGDVER). | | Shows the study type for this study. | | Shows that this study includes a Mammalian Cell Micronucleus Assay. | | Rows 19-20: | Show that the species is human and the cell line is TK6 lymphoblastoid in this study. |
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| Row | STUDYID | DOMAIN | TSSEQ | TSGRPID | TSPARMCD | TSPARM | TSVAL | TSVALNF |
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| 1 | 123 | TS | 1 |
| GLPTYP | Good Laboratory Practice Type | FDA |
| | 2 | 123 | TS | 2 |
| GLPTYP | Good Laboratory Practice Type | OECD |
| | 3 | 123 | TS | 1 |
| GLPFL | GLP Flag | Y |
| | 4 | 123 | TS | 1 |
| STSTDTC | Study Start Date | 2022-05-25 |
| | 5 | 123 | TS | 1 |
| STITLE | Study Title | Determination of the in vitro genotoxicity potential using the in vitro Neutral Red Uptake assay |
| | 6 | 123 | TS | 1 |
| SNDIGVER | SEND Implementation Guide Version | TOBACCO IMPLEMENTATION GUIDE VERSION 1.0 |
| | 7 | 123 | TS | 1 |
| SNDCTVER | SEND Controlled Terminology Version | SEND Terminology 2021-09-30 |
| | 8 | 123 | TS | 1 |
| APPLCNT | | Example Applicant, Inc. |
| | 9 | 123 | TS | 1 |
| APREFID | Study Reference ID |
| NOT APPLICABLE | | 10 | 123 | TS | 1 | 1 | TSTFNAM | Test Facility Name | Example Test Lab Name |
| | 11 | 123 | TS | 1 | 1 | TSTFLOC | Test Facility Location | 10 Somewhere Street, Montgomery, AL 10000 |
| | 12 | 123 | TS | 1 | 1 | TFCNTRY | Test Facility Country | USA |
| | 13 | 123 | TS | 1 | 1 | STDIR | Study Director | Dr. R. Smith |
| | 14 | 123 | TS | 1 | 2 | TSTGDNAM | Testing Guideline Name | GUIDELINE FOR THE TESTING OF CHEMICALS No. 487 |
| | 15 | 123 | TS | 1 | 2 | TSTGDORG | Testing Guideline Organization | OECD |
| | 16 | 123 | TS | 1 | 2 | TSTGDVER | Testing Guideline Version | 29-July-2016 |
| | 17 | 123 | TS | 1 |
| SSTYP | Study Type | GENOTOXICITY IN VITRO |
| | 18 | 123 | TS | 1 |
| GNTXAID | Genetic Toxicology Assay Identifier | MNvit |
| | 19 | 123 | TS | 1 |
| SPECIES | Species | HUMAN |
| | 20 | 123 | TS | 1 |
| CELLLN | Cell Line | |
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This example Trial Sets dataset shows information about the test conditions for set A1 and A2 in this example study. Sets A1 and A2 can be seen in the first and second rows respectively of the sample report Table 1 (above). For brevity, the TX dataset and the findings (GT) dataset do not show information for any other sets. Fully formed datasets for this example study would include information about the test conditions and findings for all sets.
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| Rows 1-23: | Show trial set parameters and values that comprise the test conditions for trial set A1. Set A1 is the data for the negative control (concentration 0) with short-term exposure and metabolic activation S9. The applicant has chosen to given a long name (SET) equal to "ST+S9_C0". Set A1 is associated with the first row in the sample report table for study 123. | | Rows 24-46: | Show trial set parameters and values that comprise the test conditions for trial set A2. Set A2 is the data for the short-term exposure with metabolic activation S9 at a concentration of 1250 ug/ml. The applicant has chosen to give the set a long name (SET) equal to "ST+S9_C1250". Set A2 is associated with the second row in the sample report table for study 123. |
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| Dataset2 |
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| Row | STUDYID | DOMAIN | SETCD | SET | TXSEQ | TXPARMCD | TXPARM | TXVAL |
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| 1 | 123 | TX | A1 | ST+S9_C0 | 1 | MTACTIND | Metabolic Activating Agent Name | +S9 | | 2 | 123 | TX | A1 | ST+S9_C0 | 2 | METACTFL | Presence of Metabolic Activation Flag | Y | | 3 | 123 | TX | A1 | ST+S9_C0 | 3 | IVTDMIN | In vitro Treatment Duration Minimum | 3 | | 4 | 123 | TX | A1 | ST+S9_C0 | 4 | IVTDTRG | In vitro Treatment Duration Target | 3.5 | | 5 | 123 | TX | A1 | ST+S9_C0 | 5 | IVTDMAX | In vitro Treatment Duration Maximum | 4 | | 6 | 123 | TX | A1 | ST+S9_C0 | 6 | IVTDU | In vitro Treatment Duration Unit | HOURS | | 7 | 123 | TX | A1 | ST+S9_C0 | 7 | RCVDMIN | Recovery Duration Minimum | 23.5 | | 8 | 123 | TX | A1 | ST+S9_C0 | 8 | RCVDTRG | Recovery Duration Target | 24 | | 9 | 123 | TX | A1 | ST+S9_C0 | 9 | RCVDMAX | Recovery Duration Maximum | 24.5 | | 10 | 123 | TX | A1 | ST+S9_C0 | 10 | RCVDU | Recovery Duration Unit | HOURS | | 11 | 123 | TX | A1 | ST+S9_C0 | 11 | INCBTMP | Incubation Temperature | 37 | | 12 | 123 | TX | A1 | ST+S9_C0 | 12 | INCBTMPU | Incubation Temperature Unit | C | | 13 | 123 | TX | A1 | ST+S9_C0 | 13 | ATMRHP | Atmospheric Relative Humidity Percent | 50 | | 14 | 123 | TX | A1 | ST+S9_C0 | 14 | ATMCO2P | Atmospheric CO2 Percent | 5 | | 15 | 123 | TX | A1 | ST+S9_C0 | 15 | SPTOBID | Applicant-defined tobacco identifier | CIG01a | | 16 | 123 | TX | A1 | ST+S9_C0 | 16 | EXPTYP | | Submerged | | 17 | 123 | TX | A1 | ST+S9_C0 | 17 | SAMTYP | Sample Type | Total Particulate Matter in DMSO | | 18 | 123 | TX | A1 | ST+S9_CO | 18 | ITVNAM | Intervention Article Name | Tobacco ProdA | | 19 | 123 | TX | A1 | ST+S9_C0 | 19 | ITVTYPE | Intervention Article Type | Negative Control | | 20 | 123 | TX | A1 | ST+S9_C0 | 20 | ITVCONC | Intervention Article Concentration | 0 | | 21 | 123 | TX | A1 | ST+S9_C0 | 21 | ITVCONCU | Intervention Article Concentration Unit | ug/ml | | 22 | 123 | TX | A1 | ST+S9_C0 | 22 | SPDEVID | Applicant-defined device identifier | PUFFMASTER3K | | 23 | 123 | TX | A1 | ST+S9_C0 | 23 | SMKRGM | Smoking Regimen | MEDIUM INTENSITY REGIMEN | | 24 | 123 | TX | A2 | ST+S9_C1250 | 24 | MTACTIND | Metabolic Activating Agent Name | +S9 | | 25 | 123 | TX | A2 | ST+S9_C1250 | 25 | METACTFL | Presence of Metabolic Activation Flag | Y | | 26 | 123 | TX | A2 | ST+S9_C1250 | 26 | IVTDMIN | In vitro Treatment Duration Minimum | 3 | | 27 | 123 | TX | A2 | ST+S9_C1250 | 27 | IVTDTRG | In vitro Treatment Duration Target | 3.5 | | 28 | 123 | TX | A2 | ST+S9_C1250 | 28 | IVTDMAX | In vitro Treatment Duration Maximum | 4 | | 29 | 123 | TX | A2 | ST+S9_C1250 | 29 | IVTDU | In vitro Treatment Duration Unit | HOURS | | 30 | 123 | TX | A2 | ST+S9_C1250 | 30 | RCVDMIN | Recovery Duration Minimum | 23.5 | | 31 | 123 | TX | A2 | ST+S9_C1250 | 31 | RCVDTRG | Recovery Duration Target | 24 | | 32 | 123 | TX | A2 | ST+S9_C1250 | 32 | RCVDMAX | Recovery Duration Maximum | 24.5 | | 33 | 123 | TX | A2 | ST+S9_C1250 | 33 | RCVDU | Recovery Duration Unit | HOURS | | 34 | 123 | TX | A2 | ST+S9_C1250 | 34 | INCBTMP | Incubation Temperature | 37 | | 35 | 123 | TX | A2 | ST+S9_C1250 | 35 | INCBTMPU | Incubation Temperature Unit | C | | 36 | 123 | TX | A2 | ST+S9_C1250 | 36 | ATMRHP | Atmospheric Relative Humidity Percent | 50 | | 37 | 123 | TX | A2 | ST+S9_C1250 | 37 | ATMCO2P | Atmospheric CO2 Percent | 5 | | 38 | 123 | TX | A2 | ST+S9_C1250 | 38 | SPTOBID | Applicant-defined tobacco identifier | CIG01a | | 39 | 123 | TX | A2 | ST+S9_C1250 | 39 | EXPTYP | | Submerged | | 40 | 123 | TX | A2 | ST+S9_C1250 | 40 | SAMTYP | Sample Type | Total Particulate Matter in DMSO | | 41 | 123 | TX | A2 | ST+S9_C1250 | 41 | ITVNAM | Intervention Article Name | Tobacco ProdA | | 42 | 123 | TX | A2 | ST+S9_C1250 | 42 | ITVTYPE | Intervention Article Type | Product | | 43 | 123 | TX | A2 | ST+S9_C1250 | 43 | ITVCONC | Intervention Article Concentration | 1250 | | 44 | 123 | TX | A2 | ST+S9_C1250 | 44 | ITVCONCU | Intervention Article Concentration Unit | ug/ml | | 45 | 123 | TX | A2 | ST+S9_C1250 | 45 | SPDEVID | Applicant-defined Device Identifier | PUFFMASTER2023 | | 46 | 123 | TX | A2 | ST+S9_C1250 | 46 | SMKRGM | Smoking Regimen | HIGH INTENSITY REGIMEN |
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| Row 1: | Shows the value of REFID=C0. This REFID refers to the trial set with a SETCD of "A1", as defined in the TX dataset. LEVEL=1 and LVLDESC="EXPERIMENTAL UNIT/TRIAL SET" indicates this identifier is referring to both the experimental unit and the unit to which the treatment is applied, and to the entire trial set. | | Rows 2-5: | Show the values of 4 observational units (C0_Count1 through C0_Count4) that are within the parent experimental unit, REFID=C0. In this example assay, these observational units are also all within the same trial set, as defined in the TX dataset. | | Row 6: | Shows the value of REFID=C1250. This REFID refers to the trial set with a SETCD of "A2", as defined in the TX dataset. LEVEL=1 and LVLDESC="EXPERIMENTAL UNIT/TRIAL SET" indicates this identifier is referring to both the experimental unit and the unit to which the treatment is applied, and to the entire trial set. | | Rows 7-10: | Show the values of 4 observational units (C1250_Count1 through C1250_Count4) that are within the parent experimental unit, REFID=C1250. In this example assay, these observational units are also all within the same trial set, as defined in the TX dataset. |
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| Row | STUDYID | SETCD | REFID | PARENT | LEVEL | LVLDESC |
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1 | 123 | | C0 |
| 1 | EXPERIMENTAL UNIT/TRIAL SET | 2 | 123 | A1 | C0-Count1 | C0 | 2 | OBSERVATIONAL UNIT | 3 | 123 | A1 | C0-Count2 | C0 | 2 | OBSERVATIONAL UNIT | 4 | 123 | A1 | C0-Count3 | C0 | 2 | OBSERVATIONAL UNIT | 5 | 123 | A1 | C0-Count4 | C0 | 2 | OBSERVATIONAL UNIT | 6 | 123 | A2 | C1250 |
| 1 | EXPERIMENTAL UNIT/TRIAL SET | | 7 | 123 | A2 | C1250-Count1 | C1250 | 2 | OBSERVATIONAL UNIT | | 8 | 123 | A2 | C1250-Count2 | C1250 | 2 | OBSERVATIONAL UNIT | | 9 | 123 | A2 | C1250-Count3 | C1250 | 2 | OBSERVATIONAL UNIT | | 10 | 123 | A2 | C1250-Count4 | C1250 | 2 | OBSERVATIONAL UNIT |
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Rows 1-3, 8: | Show percentage result values that apply to GTREFID=C0. REFID=C0, as shown in the RELREF dataset, relates this data to the trial set in the first row of table 1 in the sample report table for study 123. | | Rows 4-7: | Show the 4 micronucleated cell counts for the observational units with GTREFID from C0-Count1 through C0-Count4, for which their relationship to test conditions (in tx.xpt) and experimental units (in relref.xpt) are shown in the RELREF dataset. | Rows 9-11, 16: | Show percentage result values that apply to GTREFID=C1250. REFID=C1250, as shown in the RELREF dataset, relates this data to the trial set in the second row of table 1 in the sample report table for study 123. | | Rows 12-15: | Show the 4 micronucleated cell counts for the observational units with GTREFID from C1250-Count1 through C1250-Count4, for which their relationship to test conditions (in tx.xpt) and experimental units (in relref.xpt) are shown in the RELREF dataset. |
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| Row | STUDYID | DOMAIN | GTSEQ | GTREFID | GTTESTCD | GTTEST | GTCELLEV | GTORRES | GTORRESU | GTCOLSRT |
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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]
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Fold increase of MN
over background
Adjusted p- value
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Significant increase Y/N
ST+ S9
25.05.2022
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1250
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0.9
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0.9973
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N
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2500
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0.9
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0.9517
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N
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3750
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0.6
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0.2654
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N
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5000
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0.9
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0.9895
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N
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CPA [5µg/ml]
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3.1
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0.0003
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Y
ST-S9
25.05.2022
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1250
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1.6
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0.6408
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N
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2500
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1.3
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0.8995
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N
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3750
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2.9
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0.0106
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N
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5000
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1.0
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> 0.9999
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N
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Bleo [0.2µg/ml]
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3.8
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0.0002
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Y
LT-S9
25.05.2022
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1250
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0.7
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0.5958
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N
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2500
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1.3
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0.6378
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N
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3750
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0.5
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0.1146
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N
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5000
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1.1
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0.9929
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N
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Bleo [0.5µg/ml]
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2.9
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0.0047
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Y
Bleo: Bleomycin; CPA: Cyclophosphamid A; statistically significant increases are highlighted in bold.
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| title | Study 123, Raw data (for reference only, will be deleted?) |
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| title | ts.xpt (trial summary, study level parameters) |
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- 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)
- Do we need to document anything about extraction process steps from the smoking machine to a test material for an assay (MNvit) (ie, rinsing a filter??)
- Concentration = 0 is negative control, Bleo and CPA are positive controls - confirm
Row | STUDYID | ASSAYID | DOMAIN | TSSEQ | TSGRPID | TSPARMCD | TSPARM | TSVAL | TSVALNF |
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1 | 123 | MNvit | TS | 1 | GLPTYP | Good Laboratory Practice Type | FDA | 2 | 123 | MNvit | TS | 2 | GLPTYP | Good Laboratory Practice Type | OECD | 3 | 123 | MNvit | TS | 1 | STSTDTC | Study Start Date | 2022-05-25 | 4 | 123 | MNvit | TS | 1 | STITLE | Study Title | Determination of the in vitro genotoxicity potential of 10 tobacco products in the in vitro Micronucleus Assay | 5 | 123 | MNvit | TS | 1 | SNDIGVER | SEND Implementation Guide Version | TOBACCO IMPLEMENTATION GUIDE VERSION 1.0 | 6 | 123 | MNvit | TS | 1 | SNDCTVER | SEND Controlled Terminology Version | SEND Terminology 2021-09-30 | 7 | 123 | MNvit | TS | 1 | SSPONSOR | Sponsor Organization | Example Sponsor Inc. | 8 | 123 | MNvit | TS | 1 | SPREFID | Sponsor's Study Reference ID | NOT APPLICABLE | 9 | 123 | MNvit | TS | 1 | 1 | TSTFNAM | Test Facility Name | Example Tox Lab Name | 10 | 123 | MNvit | TS | 1 | 1 | TSTFLOC | Test Facility Location | 10 Somewhere Street, Montgomery, AL 10000 | 11 | 123 | MNvit | TS | 1 | 1 | TFCNTRY | Test Facility Country | USA | 12 | 123 | MNvit | TS | 1 | 1 | STDIR | Study Director | Dr. R. Smith | 13 | 123 | MNvit | TS | 1 | GLPFL | GLP Flag | Y | 14 | 123 | MNvit | TS | 1 | ASTD | Assay Standard | OECD Test No. 487 | 15 | 123 | MNvit | TS | 1 | ASTDV | Assay Standard Version | 2016-07-29 | 16 | 123 | MNvit | TS | 1 | SSTYP | Study Type | GENOTOXICITY IN VITRO | 17 | 123 | MNvit | TS | 1 | SSSTYP | Study Sub Type | In Vitro Micronucleus | 18 | 123 | MNvit | TS | 1 | SPECIES | Species | Homo Sapiens | 19 | 123 | MNvit | TS | 1 | TESTSYS | Test System | TK6 Lymphoblastoid Suspension Cells (also need Rat cells as an option) In OECD 487: Cultured primary human peripheral blood lymphocytes (5)(19)(42)(43) and a number of rodent cell lines such as CHO, V79, CHL/IU, and L5178Y cells may be used (18)(19)(20)(21)(22)(25)(26)(27)(28)(30). | | Expand |
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| title | to.xpt (tobacco identifiers, design paramters) |
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(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. |
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| 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. |
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to.xpt
Row | STUDYID | DOMAIN | SPTOBID | TOSEQ | TOTESTCD | TOTEST | TOCAT | TOORRES | TOORRESU | TOSTRESC | TOSTRESN | TOSTRESU |
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1 | TOB07 | TO | CIG01a | | TBPRDCAT | Tobacco Product Category | PRODUCT IDENTIFIER | Cigarette | Cigarette | 2 | TOB07 | TO | CIG01a | 2 | TBPRSCAT | Tobacco Product Subcategory | PRODUCT IDENTIFIER | Filtered, Combusted | Filtered, Combusted | 3 | TOB07 | TO | CIG01a | 3 | MANUF | Manufacturer | PRODUCT IDENTIFIER | Joes Cigs USA | Joes Cigs USA | 4 | TOB07 | TO | CIG01a | 4 | TRADENAM | Trade Name | PRODUCT IDENTIFIER | Treetop Menthol King Size | Treetop Menthol King Size | 5 | TOB07 | TO | CIG01a | 5 | PACKTYP | Package Type | PRODUCT DESCRIPTOR | HARD PACK | HARD PACK | | 6 | TOB07 | TO | CIG01a | 6 | PRDQUAN | Product Quantity | PRODUCT DESCRIPTOR | 20 | CIGARETTE | 20 | 20 | CIGARETTE |
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| 7 | TOB07 | TO | CIG01a | 7 | LENGTH | Length | PRODUCT DESCRIPTOR | 86.0 | mm | 86.0 | 86.0 | mm |
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| 8 | TOB07 | TO | CIG01a | 8 | CIRCUMF | Circumference | PRODUCT DESCRIPTOR | 26.0 | mm | 26.0 | 26.0 | mm |
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| 9 | TOB07 | TO | CIG01a | 9 | VENTLTN | Ventilation | PRODUCT DESCRIPTOR | 10.0 | % | 10.0 | 10.0 | % |
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10 | TOB07 | TO | CIG01a | 10 | CHARFLAV | Characterizing Flavor | PRODUCT DESCRIPTOR | MENTHOL | MENTHOL | | Expand |
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- 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: 
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A2: 
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| Row | STUDYID | ASSAYID | DOMAIN | SETCD | | TXSEQ | TXPARMCD | TXPARM | TXVAL |
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| 1 | 123 | MNvit | TX | A1 (table 1, row 1, ST exposure with S9) | ST+S9C0 | 1 | METACT | Metabolic Activation (this is the type of activation used) | +S9 |
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| 2 | 123 | MNvit | TX | A1 | ST+S9C0 | 2 | METACTFL | Y/N presence of metabolic activation (this indicates that metabolic activation was used) | Y |
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| 3 | 123 | MNvit | TX | A1 | ST+S9C0 | 3 | TRTDMIN | Treatment Duration Minimum | 3 |
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| 4 | 123 | MNvit | TX | A1 | ST+S9C0 | 4 | TRTDTRG | Treatment Duration Target | 3.5 |
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| 5 | 123 | MNvit | TX | A1 | ST+S9C0 | 5 | TRTDMAX | Treatment Duration Maximum | 4 |
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| 6 | 123 | MNvit | TX | A1 | ST+S9C0 | 6 | TRTDU | Treatment Duration Unit | HOURS |
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| 7 | 123 | MNvit | TX | A1 | ST+S9C0 | 7 | RCVDMIN | Recovery Duration Minimum | 23.5 |
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| 8 | 123 | MNvit | TX | A1 | ST+S9C0 | 8 | RCVDTRG | Recovery Duration Target | 24 |
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| 9 | 123 | MNvit | TX | A1 | ST+S9C0 | 9 | RCVDMAX | Recovery Duration Maximum | 24.5 |
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| 10 | 123 | MNvit | TX | A1 | ST+S9C0 | 10 | RCVDU | Recovery Duration Unit | HOURS |
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| 11 | 123 | MNvit | TX | A1 | ST+S9C0 | 11 | INCBTMP | Incubation Temperature | 37 |
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| 12 | 123 | MNvit | TX | A1 | ST+S9C0 | 12 | INCBTMPU | Incubation Temperature Unit | C |
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13 | 123 | MNvit | TX | A1 | ST+S9C0 | 13 | MEDIA | Composition of Media | Sartorius HEK293 |
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| 14 | 123 | MNvit | TX | A1 | ST+S9C0 | 14 | HUMID | Atmospheric Relative Humidity Percent | 50 |
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| 15 | 123 | MNvit | TX | A1 | ST+S9C0 | 15 | ATMCO2 | Atmospheric CO2 Percent | 5 |
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16 | 123 | MNvit | TX | A1 | ST+S9C0 | SPTOBID | Sponsor defined tobacco identifier | CIG01a | 17 | 123 | MNvit | TX | A1 | ST+S9C0 | EXPTYP | Exposure Type (See TIG NC workstream minutes 30-Jan here: Nonclinical) | Submerged | 123 | MNvit | TX | A1 | ST+S9C0 | 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 | | 18 | 123 | MNvit | TX | A1 | ST+S9C0 | 6 | INTRVN | Name of the Intervention Article can be: Tobacco ProdA, Bleomycin (positive control) or Cyclophosphamid A (positive control) | Tobacco ProdA |
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| 19 | 123 | MNvit | TX | A1 | ST+S9C0 | 7 | ITVTYPE | type of intervention article choices of values: product; negative control; positive control | Negative Control |
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| 20 | 123 | MNvit | TX | A1 | ST+S9C0 | 8 | ITVCONC | Concentration of intervention article | 0 |
| 21 | 123 | MNvit | TX | A1 | ST+S9C0 | 9 | ITVCONCU | Concentration Unit | ug/ml |
| 22 | 123 | MNvit | TX | A1 | ST+S9C0 | 10 | SPDEVID | Sponsor defined device identifier | PUFFMASTER3K |
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| 23 | 123 | MNvit | TX | A1 | ST+S9C0 | 11 | DUREFID | Smoke Regimen | Medium Intensity Regimen |
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24 | 123 | MNvit | TX | A1 | ST+S9C0 | 11 | SMKEXSYS | Smoke Exposure System | Cambridge filter pad, eluted in DMSO |
| 25 | 123 | MNvit | TX | A2 (table 1, row 2, ST exposure with S9 at concentration 1250) | ST+S9-1250 | 1 | METACT | Metabolic Activation (should there be two parms? Presence, type)? | +S9 |
| 26 | 123 | MNvit | TX | A2 | ST+S9-1250 | 2 | METACTFL | Y/N presence of metabolic activation (this indicates that metabolic activation was used) | Y |
| 27 | 123 | MNvit | TX | A2 | ST+S9-1250 | 3 | TRTDRTRG | Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable) | 3 |
28 | 123 | MNvit | TX | A2 | ST+S9-1250 | 4 | TRTDRTOL | Treatment Duration Tolerance | | 29 | 123 | MNvit | TX | A2 | ST+S9-1250 | 5 | TRTDURU | Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL) | H |
| 30 | 123 | MNvit | TX | A2 | ST+S9-1250 | 6 | INTRVN | name of the intervention article | Tobacco ProdA |
| 31 | 123 | MNvit | TX | A2 | ST+S9-1250 | 7 | ITVTYPE | type of intervention article | Product |
| 32 | 123 | MNvit | TX | A2 | ST+S9-1250 | 8 | ITVCONC | Concentration of i a | 1250 |
| 33 | 123 | MNvit | TX | A2 | ST+S9-1250 | 9 | ITVCONCU | Concentration Unit | ug/ml |
| 34 | 123 | MNvit | TX | A2 | ST+S9-1250 | 10 | SPDEVID | Sponsor defined device identifier | PUFFMASTER2023 |
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| 35 | 123 | MNvit | TX | A2 | ST+S9-1250 | 11 | DUREFID | Smoke Regimen | High Intensity Regimen |
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... | | Expand |
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| title | du.xpt smoke regimen definition (a findings domain for device in-use properties) |
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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
| STUDYID | DOMAIN | SPDEVID | DUSEQ | DUREFID | DUGRPID | DUTESTCD | DUTEST | DUORRES | DUORRESU | DUSTRESC | DUSTRESN | DUSTRESU |
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1 | 123 | DU | PUFFMASTER3K | 1 | Medium Intensity Regimen | PUFFPROF | Puff Profile | SQUARE | SQUARE | 2 | 123 | DU | PUFFMASTER3K | 2 | Medium Intensity Regimen | PUFFDUR | Puff Duration | 1.25 | sec | 1.25 | 1.25 | sec | 3 | 123 | DU | PUFFMASTER3K | 3 | Medium Intensity Regimen | PUFFINT | Puff Interval | 3 | PUFF/min | 3 | 3 | PUFF/min | 4 | 123 | DU | PUFFMASTER3K | 4 | Medium Intensity Regimen | PUFFBLCK | Puff Block | 25 | % | 25 | 25 | % | 5 | 123 | DU | PUFFMASTER3K | 5 | Medium Intensity Regimen | NUMPUFF | Total Number of Puffs | 200 | PUFF | 200 | 200 | PUFF | 6 | 123 | DU | PUFFMASTER3K | 6 | Medium Intensity Regimen | PUFFVOL | Puff Volume | 10 | mL | 10 | 10 | mL | 7 | 123 | DU | PUFFMASTER3K | 7 | Medium Intensity Regimen | PUFFRNG | Puff Range | 100-200 | 100-200 | | 8 | 123 | DU | PUFFMASTER3K | 8 | Medium Intensity Regimen | 1 | PUFFPAUS | Puff Pause | 60 | s | 60 | 60 | s |
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| 9 | 123 | DU | PUFFMASTER3K | 9 | Medium Intensity Regimen | 1 | PUFFPINT | Puff Pause Interval | 10 | PUFF | 10 | 10 | PUFF |
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10 | 123 | DU | PUFFMASTER2023 | 1 | Canadian Intense Regime | PUFFPROF | Puff Profile | SQUARE | SQUARE | 11 | 123 | DU | PUFFMASTER2023 | 2 | Canadian Intense Regime | PUFFDUR | Puff Duration | 2.00 | sec | 2.00 | 2.00 | sec | 12 | 123 | DU | PUFFMASTER2023 | 3 | Canadian Intense Regime | PUFFINT | Puff Interval | 4 | PUFF/min | 4 | 4 | PUFF/min | 13 | 123 | DU | PUFFMASTER2023 | 4 | Canadian Intense Regime | PUFFBLCK | Puff Block | 0 | % | 0 | 0 | % | 14 | 123 | DU | PUFFMASTER2023 | 5 | Canadian Intense Regime | NUMPUFF | Total Number of Puffs | 200 | PUFF | 200 | 200 | PUFF | 15 | 123 | DU | PUFFMASTER2023 | 6 | Canadian Intense Regime | PUFFVOL | Puff Volume | 10 | mL | 10 | 10 | mL | 16 | 123 | DU | PUFFMASTER2023 | 7 | Canadian Intense Regime | PUFFRNG | Puff Range | 100-200 | 100-200 | | 17 | 123 | DU | PUFFMASTER2023 | 8 | Canadian Intense Regime | 1 | PUFFPAUS | Puff Pause | 60 | s | 60 | 60 | s |
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| 18 | 123 | DU | PUFFMASTER2023 | 9 | Canadian Intense Regime | 1 | PUFFPINT | Puff Pause Interval | 10 | PUFF | 10 | 10 | PUFF |
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| Expand |
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| title | di.xpt (a study reference domain for unique device identification) |
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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 |
| Expand |
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| title | ei.xpt Entity Identifiers (dm-like) |
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- 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
| Row | STUDYID | ASSAYID | DOMAIN | ENID (Entity ID) | SETCD (from TX) | RUNID | REPLCTID (Replicate Number) | PLATEID (Plate ID) | COLID (Column number) | ROWID (Row number) |
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123 | MNvit | EI | 1-8-3 | A1 | 1 | 1-8-3 (plate - col- row) | 123 | MNvit | EI | 2-8-3 | A1 | 2 | | Expand |
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| title | gt.xpt (similar to LB) |
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A1: Image Removed A2: Image Removed - Different runs would be expected to have different ENID and GTDTC values. In ei.xpt, these are distinguished by different RUNID values.
| Row | STUDYID | ASSAYID | DOMAIN | ENID | GTSEQ | GTTESTCD | GTTEST | GTCELLEV
(cells evaluated) | GTORRES | GTORRESU | GTSTRESC | GTSTRESN | GTSTRESU | GTDTC |
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| 1 | 123 |
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MNvit | -8-31| C0 | | Relative Increase in Cell Count | 154 | 0 | % |
| 0 | 0 | % | 2022-05-25 | | 2 | 123 |
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MNvit1-8-3 | 2 | RCC | Relative Cell Count | 154 | 0 | % |
| 0 | 0 | % | 2022-05-25 | | 3 | 123 |
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MNvit1-8-3| C0 | RPD | Relative Population Doubling | 154 | 0 | % |
| 0 | 0 | % | 2022-05-25 | | 4 | 123 |
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MNvitGT18-34 | MNCELLS| Count1 | MNCE | Micronucleated Cells | 2205 | 15 |
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Cells | CellsMNvitGT18-35 | MNCELLS | Micronucleated Cells | 2474 | 13 |
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CellsCellsMNvit18-36 | MNCELLS | Micronucleated Cells | 2758 | 17 |
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CellsCellsMNvitGT18-37 | MNCELLS | Micronucleated Cells | 2669 | 12 |
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CellsCellsMNvit | 1--38AVGREL | Average Relative MN Frequency| MNCECE | Micronucleated Cells/Total Cells |
| 0.57 | % |
| 0.57 | 0.57 | % | 2022-05-25 | | 9 | 123 |
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MNvit | GT | 1 | C1250 | RICC | Relative Increase in Cell Count | 134 | 15.7 | % |
| 15.7 | 15.7 | % | 2022-05-25 | | 10 | 123 |
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MNvit | GT | 2 | C1250 | RCC | Relative Cell Count | 134 | 13.0 | % |
| 13.0 | 13.0 | % | 2022-05-25 | | 11 | 123 |
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MNvit | GT | 3 | C1250 | RPD | Relative Population Doubling | 134 | 7.9 | % |
| 7.9 | 7.9 | % | 2022-05-25 | | 12 | 123 |
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MNvitMNCELLS| C1250-Count1 | MNCE | Micronucleated Cells | 3266 | 20 |
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CellsCells | MNvitMNCELLS| MNCE | Micronucleated Cells | 2190 | 17 |
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CellsCellsMNvitMNCELLS| MNCE | Micronucleated Cells | 2758 | 13 |
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CellsCellsMNvit | MNCELLS| C1250-Count4 | MNCE | Micronucleated Cells | 2714 | 21 |
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CellsCellsMNvitAVGREL | | C1250 | MNCECE | Micronucleated Cells/Total Cells |
|
Average Relative MN Frequency...
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