This is an example showing the report table, trial design, and results from the in vitro bacterial reverse mutation test of an example study, Study #8325064. This bacterial reverse mutation test uses four different amino acid-requiring strains of Salmonella typhimurium (S. typhimurium) and one strain of Escherichia coli (E. coli) to detect point mutations, which involve substitution, addition or deletion of one or a few DNA base pairs. TOBA-129
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Getting issue details...STATUS
In this example, the Trial Summary dataset,TOBA-368
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Getting issue details...STATUS ts.xpt, includes many informational fields that may provide context at the study level, for Study 8325064. Also, TSGRPID has been used to link records (name, location, country) related to the test facility (TSGRPID = 1) and records related to the Test Site (TSGRPID = 2). The Study Director is associated with the Test Facility and the Principal Investigator is associated with the Test Site. Finally, the Primary Treatment CAS Registry Number is not known and this is recorded as an empty TSVAL and UNKNOWN in the corresponding TSVALNF.
This table shows the assay results for Study 8325064, Test Article TA1, and three strains of Salmonella (TA98, TA100, and TA1535) at varying concentrations. For ease of reference, each row has been labeled in the right hand margin with the applicant-defined trial set label (e.g., SetA). For brevity, the remaining tables (e.g., additional strains, samples prepared without metabolic activation, etc.) are not included.
Rows 1-2:
Show two records for TSPARMCD = "GLPTYP", using TSSEQ to indicate multiple records,TOBA-366
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since both GLP Types apply for this example study.
Row 8:
Shows that the applicant's study reference ID is not applicable.
Rows 9-12:
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=4) has been used to link the information on the testing guideline followed on this study (TSTGDNAM, TSTGDORG, TSTGDVER). TOBA-56
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Rows 18-26:TOBA-367
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Show that this example study includes two different species of bacteria and a total of five strains.
Rows 18-23:
Show that TSGRPID (TSGRPID = 2) has been used to link the information for one species (Salmonella) with four different strains that are tested in this example study.
Rows 24-26:
Show that TSGRPID (TSGRPID = 3) has been used to link the information for one species (Escherichia coli) with the strain that is tested in this example study.
Row Captions Debug Message
Please move all content other than the row caption labels out of the first column of the table.
ts.xpt
xx.xpt
Row
STUDYID
GNTXAID
DOMAIN
TSSEQ
TSGRPID
TSPARMCD
TSPARM
TSVAL
TSVALNF
1
8325064
Ames
TS
1
GLPTYP
Good Laboratory Practice Type
FDA
2
8325064
Ames
TS
2
GLPTYP
Good Laboratory Practice Type
OECD
3
8325064
Ames
TS
1
STSTDTC
Study Start Date
2015-07-29
4
8325064
Ames
TS
1
STITLE
Study Title
The Bacterial Reverse Mutation Test, Study 8325064-1
5
8325064
Ames
TS
1
SNDIGVER
SEND Implementation Guide Version
TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6
8325064
Ames
TS
1
SNDCTVER
SEND Controlled Terminology Version
SEND Terminology 2021-09-30
7
8325064
Ames
TS
1
SAPPLCNT
Applicant Organization
Example Applicant Inc.
8
8325064
Ames
TS
1
SPREFID
Applicant's Study Reference ID
NOT APPLICABLE
9
8325064
Ames
TS
1
1
TSTFNAM
Test Facility Name
Example Tox Lab Name
10
8325064
Ames
TS
1
1
TSTFLOC
Test Facility Location
10 Somewhere Street, Montgomery, AL 10000
11
8325064
Ames
TS
1
1
TFCNTRY
Test Facility Country
USA
12
8325064
Ames
TS
1
1
STDIR
Study Director
Dr. R. Smith
13
8325064
Ames
TS
1
GLPFL
GLP Flag
N
14
8325064
Ames
TS
1
4
TSTGDNAM
Testing Guideline Name
Test NO. 471
15
8325064
Ames
TS
1
4
TSTGDORG
Testing Guideline Organization
OECD
16
8325064
Ames
TS
1
4
TSTGDVER
Testing Guideline Version
2020-06-29
17
8325064
Ames
TS
1
SSTYP
Study Type
GENOTOXICITY IN VITRO
18
8325064
Ames
TS
1
SSSTYP
Study Sub Type
BACTERIAL REVERSE MUTATION TEST
19
8325064
Ames
TS
1
2
SPECIES
Species
SALMONELLA TYPHIMURIUM TOBA-123
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20
8325064
Ames
TS
1
2
STRAIN
Strain/Substrain
TA98
21
8325064
Ames
TS
1
2
STRAIN
Strain/Substrain
TA100
22
8325064
Ames
TS
1
2
STRAIN
Strain/Substrain
TA1535
23
8325064
Ames
TS
1
2
STRAIN
Strain/Substrain
TA1537
24
8325064
Ames
TS
1
2
CELLLN
Cell Line
25
8325064
Ames
TS
1
3
SPECIES
Species
Escherichia coli
26
8325064
Ames
TS
1
3
STRAIN
Strain/Substrain
WP2 uvrA pKM101
27
8325064
Ames
TS
1
3
CELLLN
Cell Line
Dataset Debug Message
When the JIRA issue(s) present in the dataset have been resolved, and their resolution has been confirmed by governance, please remove them.
Dataset Wrapper Debug Message
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This example trial set dataset, tx.xpt, shows information about the test conditions for SetA and SetR in this example study. For brevity, this does not show information for SetF, SetG, or any other sets. A fully formed tx.xpt for this example study would include information about the test conditions for all sets.
Rows 1-14:
Show trial set, SetSTM, with trial set parameters and trial set values that comprise the test conditions for all data for the species Salmonella Typhimurium.
Rows 15, 24, 33, 42:
Show that SetA, SetF, SetG, and SetR each have a parent set code of SetSTM. As a child set of SetSTM, each of these sets inherit the test conditions of SetSTM.
Rows 16-23:
Show trial set parameters and trial set values that comprise the test conditions for the set SetA. SetA is the data for the vehicle control (i.e., Strain of TA98, vehicle control with concentration value of 0). SetA is associated with the first row, labeled "SetA", in the report table for example study 8325064.
Rows 25-32:
Show trial set parameters and trial set values that comprise the test conditions for the set SetF. SetF is the data for the strain of TA98 with a concentration value of 500 µg/plate. SetF is associated with the sixth row, labeled "SetF", in the report table for example study 8325064.
Rows 33-41:
Show trial set parameters and trial set values that comprise the test conditions for the set SetG. SetG is the data for the strain of TA98 with a concentration value of 1600 µg/plate. SetG is associated with the seventh row, labeled "SetG", in the report table for example study 8325064.
Rows 42-50:
Show trial set parameters and trial set values that comprise the test conditions for the set SetR. SetR is the data for the strain of TA100, positive control with a concentration value of 2 µg/plate. SetR is associated with the eighteenth row, labeled "SetR", in the report table for example study 8325064.
Row 10:
Shows a value for SPTOBID=CIG01a. SPTOBID is Applicant-Defined Tobacco Product ID that is used to uniquely identify the tobacco product. The value of SPTOBID, in this case CIG01a, matches the value for SPTOBID in all the TOPARMCD-TOVAL pairs in the Tobacco Product Identifiers and Descriptors (TO) dataset example in Section 3.1.2 Product Design Parameters and Conformance Testing Example 1. The TOPARMCD-TOVAL pairs identify this unique product, CIG01a.
Shows a value for SPDEVID. SPDEVID is the applicant-defined device identifier that is used to uniquely identify the device in the Unique Device Identification (DI) dataset. The value of SPDEVID, in this case PUFFMASTER3K, matches the value of SPDEVID in all the DIPARMCD-DIVAL pairs that identify this unique device in the DI dataset. This is shown in the di.xpt in SDTM Example.Product HPHC ENDS Testing.
Shows a value for DUREFID. DUREFID serves as a link to the Device-In Use Properties (DU) domain, where a matching value of DUREFID indicates parameters of the smoking regimen performed by the smoking machine, as in the du.xpt in SDTM Example.Product HPHC ENDS Testing.
REFID values are defined by the applicant to uniquely identify the observational unit within an experimental unit. In the simplified picture of an assay (below), the test tube that contains the possible mutagen is an example of an entity that would have a REFID indicating information at the level of trial set. The petri plate created from that test tube and used to count revertant numbers is an example of an entity that would be at an observational level.
This picture does not depict the more complicated procedures, trial sets, or observational units for our example study, 8325064. For study 8325064, the applicant chose to define the REFIDs at the trial set level with a single character (e.g., A, F, G, R) and chose to define REFIDs at the observational level based on the location of each tube in one of multiple exposure/incubation plates (e.g, 6_1 for plate 6, position 1).
Row 1:
Shows the value of REFID=STM, This REFID refers to the trial set with a SETCD of 'SetSTM', as defined in the trial set dataset, tx.xpt. LEVEL=1 and LVLDESC='TRIAL SET' indicates this identifier relates to the entire trial set.
Rows 1, 2, 8, 12, 16:
Show that the trial set, SetSTM, is the parent of set codes SetA, SetF, SetG, and SetR.
Row 2:
Shows the value of REFID=A, This REFID refers to the trial set with a SETCD of 'SetA', as defined in the trial set dataset, tx.xpt. LEVEL=2 and LVLDESC='TRIAL SET' indicates this identifier relates to the entire trial set.
Rows 3-7:
Show the values of five observational units 1_1 through 1_5 that are within the parent experimental unit, REFID=A
Row 8:
Shows the value of REFID=F, This REFID refers to the trial set with a SETCD of 'SetF', as defined in the trial set dataset, tx.xpt. LEVEL=2 and LVLDESC='TRIAL SET' indicates this identifier relates to the entire trial set.
Rows 9-11:
Show the values of three observational units 6_1 through 6_3 that are within the parent experimental unit, REFID=F
Row 12:
Shows the value of REFID=G, This REFID refers to the trial set with a SETCD of 'SetG', as defined in the trial set dataset, tx.xpt. LEVEL=2 and LVLDESC='TRIAL SET' indicates this identifier relates to the entire trial set.
Rows 13-15:
Show the values of three observational units 7_1 through 7_3 that are within the parent experimental unit, REFID=G
Row 16:
Shows the value of REFID=R. This REFID refers to the trial set with a SETCD of 'SetG', as defined in the trial set dataset, tx.xpt. LEVEL=2 and LVLDESC='TRIAL SET' indicates this identifier relates to the entire trial set.
Rows 17-19:
Show the values of three observational units 18_1 through 18_3 that are within the parent experimental unit, REFID=R
$titleHtml
relref.xpt
Row
STUDYID
GNTXAID
SETCD
REFID
PARENT
LEVEL
LVLDESC
1
8325064
Ames
SetSTM
STM
1
TRIAL SET
2
8325064
Ames
SetA
A
STM
2
EXPERIMENTAL UNIT/TRIAL SET
3
8325064
Ames
SetA
1_1
A
3
OBSERVATIONAL UNIT
4
8325064
Ames
SetA
1_2
A
3
OBSERVATIONAL UNIT
5
8325064
Ames
SetA
1_3
A
3
OBSERVATIONAL UNIT
6
8325064
Ames
SetA
1_4
A
3
OBSERVATIONAL UNIT
7
8325064
Ames
SetA
1_5
A
3
OBSERVATIONAL UNIT
8
8325064
Ames
SetF
F
STM
2
EXPERIMENTAL UNIT/TRIAL SET
9
8325064
Ames
SetF
6_1
F
3
OBSERVATIONAL UNIT
10
8325064
Ames
SetF
6_2
F
3
OBSERVATIONAL UNIT
11
8325064
Ames
SetF
6_3
F
3
OBSERVATIONAL UNIT
12
8325064
Ames
SetG
G
STM
2
EXPERIMENTAL UNIT/TRIAL SET
13
8325064
Ames
SetG
7_1
G
3
OBSERVATIONAL UNIT
14
8325064
Ames
SetG
7_2
G
3
OBSERVATIONAL UNIT
15
8325064
Ames
SetG
7_3
G
3
OBSERVATIONAL UNIT
16
8325064
Ames
SetG
R
STM
2
EXPERIMENTAL UNIT/TRIAL SET
17
8325064
Ames
SetR
18_1
R
3
OBSERVATIONAL UNIT
18
8325064
Ames
SetR
18_2
R
3
OBSERVATIONAL UNIT
19
8325064
Ames
SetR
18_3
R
3
OBSERVATIONAL UNIT
$warningHtml
Dataset Wrapper Debug Message
Please add a row column to your dataset.
Rows 1-5:
Show the number of revertant colonies per plate collected for each of five observational units GTREFID=1_1 through 1_5 (see description in the relref dataset).
Rows 6, 7:
Show summary values collected (MEAN, STANDARD DEVIATION) for GTREFID=A that apply to the entire trial set, SetA, as indicated by LEVEL=1 and LVLDESC=TRIAL SET for this REFID as shown in the relref dataset.
Rows 8-13:
Revertent colonies were counted for each of three plates/observational units (GTREFID=6_1 through 6_3) and each value is associated with a record to show a postfix code of "V" = "Very thin background bacterial lawn"
Rows 14-16:
Show summary values collected (MEAN, STANDARD DEVIATION, and FOLD INCREASE) for GTREFID=F that apply to the entire trial set, SetF, as indicated by LEVEL=1 and LVLDESC=TRIAL SET for this REFID in the relref dataset.
Rows 17-19:
Show three plates/observational units (GTREFID=5_1 through 5_3) where no revertant colonies were counted due to too much cytotoxicity and a postfix code of "T".
Rows 20-22:
Show the number of revertant colonies per plate collected for each of three observational units (GTREFID=18_1 through 18_3).
Rows 23-25:
Show summary values collected (MEAN, STANDARD DEVIATION, and FOLD INCREASE) for GTREFID=R that apply to the entire trial set, SetR, as indicated by LEVEL=1 and LVLDESC=TRIAL SET for this REFID in the relref dataset.