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ts.xpt (trial summary, study level parameters)
Assumption: Study can have more than one assay type Assumption: ASSAYID value of ALL means it applies to all assays in the study Replaced 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) Row
STUDYID
ASSAYID DOMAIN
TSSEQ
TSGRPID
TSPARMCD
TSPARM
TSVAL
TSVALNF
1 123 ALL
TS 1 GLPTYP Good Laboratory Practice Type FDA 2 123 ALL
TS 2 GLPTYP Good Laboratory Practice Type OECD 3 123 ALL TS 1 STSTDTC Study Start Date 2022-05-25 4 123 ALL TS 1 STITLE Study Title 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 IMPLEMENTATION GUIDE VERSION 1.0 6 123 ALL
TS 1 SNDCTVER SEND Controlled Terminology Version SEND Terminology 2021-09-30 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 Uptake123 NRU TS 1 SPECIES Species Salmonella enterica 123 NRU TS 1 STRAIN Strain/Substrain Salmonella enterica enterica123 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
tx.xpt (trial sets)
During CT definition/reviews will decide appropriate TXPARM and TXVAL; For now, we just include good example values based on our experience TXPARMCD/TXPARM = TSPARMCD/TSPARM Row STUDYID ASSAYID DOMAIN SETCD TXSEQ TXPARMCD TXPARM TXVAL 1 123 NRU TX 1-1-A(plate-col-row in the 96-well plate) CSC-10(through SLS-200) PLATENUM. (e.g., 1 or 2) 1 1 2 123 NRU TX 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 INTRVN name of the intervention article 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 PRODUCT 5 123 NRU TX 1-1-A CSC-10 ITVCONC intervention concentration 10 6 123 NRU TX 1-1-A CSC-10 ITVCONCU intervention unit ug/ml 7 123 NRU TX 1-1-B CSC-10 PLATENUM Plate number 1 8 123 NRU TX 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 INTRVN name of the intervention article sodium laurel sulfate 123 NRU TX 1-10-H SLS-10 ITVTYPE type of intervention article POSITIVE CONTROL 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 2-A 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
gt.xpt (similar to LB)
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 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
