You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 37 Next »

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


  • red font - indicates potential for CT code lists
  • green font - links to other domains



The following shows the tabulated data as shown in the report for this study: 

Neutral Red Cytotoxicity Assay Results (Relative Absorbance Data)

Run-Port Number

Sample ID

Smoke Fraction

Replicate Number

Plate Number

Well Number

Relative Assay Plate Absorbance Readings

Cigarette Smoke Condensate (µg/mL)

SLS (µg/mL)

10

50

75

100

120

140

160

200

110

200

1-1

030001

A

1

1

1

100

83.0

56.7

29.5

13.0

8.57

4.44

1.76

13.7

0.547

1-1

030001

A

1

1

2

107

77.7

65.7

30.2

15.6

9.79

5.41

2.49

8.09

0.791

1-1

030001

A

1

1

3

98.6

77.4

57.7

35.8

8.09

7.36

3.22

0.791

6.38

0.061

1-1

030001

A

1

1

4

94.9

81.5

38.2

31.2

7.60

5.17

3.22

0.791

5.17

0.304

1-1

030001

A

1

1

5

111

78.1

64.5

32.9

8.82

5.90

2.74

1.28

10.3

0.547

1-1

030001

A

1

1

6

96.6

76.2

48.0

26.8

7.84

4.20

2.74

1.52

8.09

4.93

1-1

030001

A

1

1

7

105

77.9

58.2

28.3

8.09

4.68

1.76

0.547

8.57

1.76

1-1

030001

A

1

1

8

95.2

74.0

47.2

24.4

8.57

3.71

3.47

0.304

11.2

0.791

Average

101

78.2

54.5

29.9

9.70

6.17

3.37

1.19

8.94

1.22

Std. Dev.

6

2.9

9.4

3.6

2.95

2.19

1.12

0.72

2.72

1.58

Coeff. Var.

5.8

3.6

17.2

11.9

30.4

35.5

33.1

61.0

30.5

129.9

1-1

030001

A

1

2

1

93.4

74.0

56.0

35.1

11.8

8.70

5.10

1.98

5.34

1.02

1-1

030001

A

1

2

2

102

75.2

53.3

35.1

11.8

7.74

5.58

3.66

5.34

1.02

1-1

030001

A

1

2

3

107

79.0

55.0

26.5

10.1

6.06

3.66

1.74

7.02

0.780

1-1

030001

A

1

2

4

104

80.2

55.3

29.8

8.94

3.90

3.66

1.50

6.30

0.780

1-1

030001

A

1

2

5

101

75.7

54.1

26.7

4.86

4.38

1.26

1.02

6.30

1.02

1-1

030001

A

1

2

6

110

85.7

67.7

26.0

5.34

4.62

3.42

1.50

6.30

0.540

1-1

030001

A

1

2

7

104

77.8

64.9

27.7

8.22

3.18

2.46

1.02

6.30

0.780

1-1

030001

A

1

2

8

103

71.6

58.9

25.5

9.42

4.14

3.90

1.26

4.38

0.780

Average

103

77.4

58.1

29.0

8.82

5.34

3.63

1.71

5.91

0.840

Std. Dev.

5

4.4

5.3

4.0

2.63

1.97

1.37

0.86

0.83

0.170

Coeff. Var.

4.6

5.6

9.2

13.6

29.8

36.9

37.6

50.0

14.1

20.2

  • 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
  • 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)
    • needs to be allowed to vary down to the well level / result level
  • For the items highlighted in orange - what is the lowest level where this could vary?  e.g. at the level of a well in a 96-well plate, or a slide vs. assay level vs. product level
    • Smoke Regime needs to be allowed to vary down to the well level / result level
    • run - also at result level 
    • port - (smoking product on the machine, you assign a run number or port-number for multiple replicates depending on linear vs. rotary machines; machine bias), needs to be allowed to vary down to the well level / result level)
    • replicate - (e.g., multiple samples from one vial), could be a replicate per exposure (e.g., 3 plates, multiple analyses for exposure)
    • sample ID - typically a unique number assigned (at CRO) or supplied by sponsor - result level
    • Smoke fraction - result level (e.g.tpm particulate vs. gas gvp)

Row

STUDYID

ASSAYID

DOMAIN

TSSEQ

TSGRPID

TSPARMCD

TSPARM

TSVAL

TSVALNF

1123

ALL

TS1
GLPTYPGood Laboratory Practice TypeFDA
2123

ALL

TS2
GLPTYPGood Laboratory Practice TypeOECD
3123ALLTS1
STSTDTCStudy Start Date2022-05-25
4123ALLTS1
STITLEStudy 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


5123ALLTS1
SNDIGVERSEND Implementation Guide VersionTOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6123

ALL

TS1
SNDCTVERSEND Controlled Terminology VersionSEND Terminology 2021-09-30
7123ALLTS1
SSPONSORSponsor OrganizationExample Sponsor Inc.
8123ALLTS1
SPREFIDSponsor's Study Reference ID
NOT APPLICABLE
9123ALLTS11TSTFNAMTest Facility NameExample Tox Lab Name
10123

ALL

TS11TSTFLOCTest Facility Location10 Somewhere Street, Montgomery, AL 10000
11123ALLTS11TFCNTRYTest Facility CountryUSA
...123ALLTS11STDIRStudy DirectorDr. R. Smith

123ALLTS1
GLPFLGLP FlagY

123MNvitTS1
ASTDAssay StandardOECD Test No. 487 

123MNvitTS1
ASTDVAssay Standard Version2016-07-29

123MNvitTS1
SSTYPStudy TypeGENOTOXICITY IN VITRO

123MNvitTS1
SSSTYPStudy Sub TypeIn Vitro Micronucleus

123MNvitTS1
SPECIESSpeciesHomo Sapiens

123MNvitTS1
??Test System?TK6 Lymphoblastoid Suspension Cells

123NRUTS1
ASTDAssay StandardNIH Publication No. 07-4519

123NRUTS1
ASTDVAssay Standard Version2006-11

123NRUTS1
SSTYPStudy TypeGENOTOXICITY IN VITRO

123NRUTS1
SSSTYPStudy Sub TypeIn Vitro Neutral Red Uptake

123NRUTS1
SPECIESSpeciesSalmonella enterica 

123NRUTS1
??Test System??Normal Human Keratinocyte
  • 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.
RowSTUDYIDASSAYIDDOMAINSETCD
SET (what sponsor calls it)
TXSEQTXPARMCDTXPARMTXVAL
1123NRUTX1-1-A
(plate-col-row in the 96-well plate)
CSC-10
(through SLS-200)

PLATENUM. (e.g., 1 or 2)
1
2123NRUTX1-1-ACSC-10
WELLNUM (e.g., 1-A through 10-H)
Number representing the location of the well in the 96-well plate1-A 
3123NRUTX1-1-ACSC-10
INTRVNname of the intervention articleCigarette Smoke Condensate
4123NRUTX1-1-ACSC-10
ITVTYPE
(CT e.g, Product, positive control, negative control)
type of intervention articlePRODUCT
5123NRUTX1-1-ACSC-10
ITVCONCintervention concentration10
6123NRUTX1-1-ACSC-10
ITVCONCUintervention unitug/ml

123NRU
1

STRAINStrain/SubstrainSalmonella enterica enterica

123NRU
1

REGIMESmoking RegimeTraditional combustible 

123NRU
1

RUN

Assay run number (how is this different from REPNUM)

1


123NRU
1

PORTPort ID1

123NRU
1

SMPLIDSample ID030001

123NRU
1

SMKFRCSmoke FractionA

123NRU
1

REPNUMReplicate Number1
11123NRUTX1-1-BCSC-10
ITVCONCintervention concentration10
12123NRUTX1-1-BCSC-10
ITVCONCUintervention unitug/ml
...


...





123NRUTX1-10-HSLS-10
PLATENUMPlate number1  

123NRUTX1-10-HSLS-10
WELLNUMNumber representing the location of the well in the 96-well plate10-H

123NRUTX1-10-HSLS-10
INTRVNname of the intervention articlesodium laurel sulfate

123NRUTX1-10-HSLS-10
ITVTYPEtype of intervention articlePOSITIVE CONTROL

123NRUTX1-10-HSLS-10
ITVCONCintervention concentration200

123NRUTX1-10-HSLS-10
ITVCONCUintervention unitug/ml
...


...





123NRUTX2-10-HSLS-10
PLATENUMPlate number2

123NRUTX2-10-HSLS-10
WELLNUMNumber representing the location of the well in the 96-well plate10-H

123NRUTX2-10-HSLS-10
INTRVNname of the intervention articlesodium laurel sulfate

123NRUTX2-10-HSLS-10
ITVTYPEtype of intervention articlePOSITIVE CONTROL

123NRUTX2-10-HSLS-10
ITVCONCintervention concentration200

123NRUTX2-10-HSLS-10
ITVCONCUintervention unitug/ml

123MNvitTXA1

METACTMetabolic Activation  (should there be two parms? Presence, type)?+S9

123MNvitTXA1

TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range?  start/end, target and tolerance?, one text field not-analyzable)3

123MNvitTX






123MNvitTX


TRTDRTOLTreatment Duration Tolerance

123MNvitTX


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

123MNvitTX


INTRVNname of the intervention articleBleomycin or Cyclophosphamid A

123MNvitTX


ITVTYPEtype of intervention articlechoices of values:  product; negative control; positive control

123MNvitTXA1

ITVCONCConcentration of i a 0

123MNvitTXA1

ITVCONCUConcentration Unitug/ml










RowSTUDYIDASSAYIDDOMAINTXCDGTSEQGTTESTCDGTTESTGTCELLEV
(cells evaluated)
GTORRESGTORRESUGTSTRESCGTSTRESNGTSTRESUGTDTCGTNOMDYGTELTMGTTPTREF
1123NRUGT1-1-A1RELABSRelative Absorbance Reading
100ug/ml100100ug/ml



2123NRUGT1-1-B1RELABSRelative Absorbance Reading
107ug/ml100100ug/ml



3123NRUGT1-1-C1RELABSRelative Absorbance Reading
98.6ug/ml100100ug/ml



54123NRUGT1-1-D1RELABSRelative Absorbance Reading
94.9ug/ml100100ug/ml



6123NRUGT1-1-E1RELABSRelative Absorbance Reading
111







7123NRUGT1-1-F1RELABSRelative Absorbance Reading
96.9







8123NRUGT1-1-G1RELABSRelative Absorbance Reading
105







9123NRUGT1-1-H1RELABSRelative Absorbance Reading
95.2







10123NRUGT1-2-A1RELABSRelative Absorbance Reading

83.0









11123NRUGT1-2-B1RELABSRelative Absorbance Reading
77.7







...


...












80123NRUGT1-10-H1RELABSRelative Absorbance Reading
0.791







...


...












160123NRUGT2-10-H1RELABSRelative Absorbance Reading
0.780







1123MNvitGTA21RICCRelative Increase in Cell Count13415.7%15.715.7%2022-05-25


2123MNvitGTA22RCCRelative Cell Count13413.0%13.013.0%2022-05-25


3123MNvitGTA23RPDRelative Population Doubling1347.9%7.97.9%2022-05-25


4123MNvitGTA24MNCELLSMicronucleated Cells326620Cells2020Cells2022-05-25


5123MNvitGTA25MNCELLSMicronucleated Cells219017Cells1717Cells2022-05-25


6123MNvitGTA26MNCELLSMicronucleated Cells275813Cells1313Cells2022-05-25


7123MNvitGTA27MNCELLSMicronucleated Cells271421Cells2121Cells2022-05-25


8123MNvitGTA28AVGRELAverage Relative MN Frequency
0.66%0.660.66%2022-05-25


9123MNvitGTA11RICCRelative Increase in Cell Count1540%00%2022-05-25


10123MNvitGTA12RCCRelative Cell Count1540%00%2022-05-25


11123MNvitGTA13RPDRelative Population Doubling1540%00%2022-05-25


12123MNvitGTA14MNCELLSMicronucleated Cells326615Cells1515Cells2022-05-25


13123MNvitGTA15MNCELLSMicronucleated Cells219013Cells1313Cells2022-05-25


14123MNvitGTA16MNCELLSMicronucleated Cells275817Cells1717Cells2022-05-25


15123MNvitGTA17MNCELLSMicronucleated Cells271412Cells1212Cells2022-05-25


16123MNvitGTA18AVGRELAverage Relative MN Frequency
0.57%0.570.57%2022-05-25


Below this line are domains we currently do not see a use for



(Do we need this? a single element (treatment)?)

RowSTUDYIDASSAYIDDOMAINETCDELEMENT

(Do we need this? one arm for each trial set?)

RowSTUDYIDASSAYIDDOMAINARMCDARMTAETORDETCDELEMENT

Not needed.

RowSTUDYIDDOMAINENID (Entity ID)RICCRCCRPDSum of cell ev.Cells with MNSMKFID (Smoke Fraction)

REPLCTID

(Replicate Number)

PLATEID (Plate ID)

COLID

(Column number)

ROWID (Row  number)
SETCD (Set Code, TX)RFSTDTCRFENDTCRFXSTDTCRFXENDTCRFCSTDTCRFCENDTCARMCD
  • No labels