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Dataset2

hi1style	yellow
hi1	column ISBDAGNT
tableid	IS table 1

Row	STUDYID	DOMAIN	USUBJID	SPDEVID	ISSEQ	ISTESTCD	ISTEST	ISTSTCND	ISCNDAGT	ISORRES	ISORRESU	ISSTRESC	ISSTRESN	ISSTRESU	ISSPEC	ISMETHOD	ISDTC
1	ABC	IS	ABC-01-203	ABC001	1	IFNG	Interferon Gamma	WITHOUT STIMULATING AGENT		2.17	IU/mL	2.17	2.17	IU/mL	SERUM	ELISA/Other Method	2013-08-26
2	ABC	IS	ABC-01-203	ABC001	2	IFNG	Interferon Gamma	WITH STIMULATING AGENT	Study Drug, 20 mg	6.2	IU/mL	6.2	6.2	IU/mL	SERUM	ELISA/Other Method	2013-08-26
3	ABC	IS	ABC-01-203	ABC001	3	IFNG	Interferon Gamma	WITH STIMULATING AGENT	Study Drug, 40 mg	15.8	IU/mL	15.8	15.8	IU/mL	SERUM	ELISA/Other Method	2013-08-26
4	ABC	IS	ABC-01-203	ABC001	4	IFNG	Interferon Gamma	WITH STIMULATING AGENT	Other Test Agent, 5 mg	3.33	IU/mL	3.33	3.33	IU/mL	SERUM	ELISA/Other Method	2013-08-26
5	ABC	IS	ABC-01-203	ABC001	5	IFNG	Interferon Gamma	WITH STIMULATING AGENT	Other Test Agent, 15 mg	7.22	IU/mL	7.22	7.22	IU/mL	SERUM	ELISA/Other Method	2013-08-26

Background Information:

This was sent to the lab team for discussion and we decided that the INF-y response tests should be modeled in IS (as agreed to with the same TB TAUG INF-y response tests here: https://wiki.cdisc.org/x/azXFBg).
Craig mentioned that there are NO other variables to capture the units and dosing concentrations for the test agents that are added to the samples. In fact, this is a gap in the CDISC model that we lack variables (or a domain) to help mapping in vitro drug/non-drug exposure data. The EX/EC and AG domains are used for mapping in vivo drug and non-drug agents exposure data (respectively) in SDTM. These domains have variables for mapping dosing concentrations and units, but we can NOT use EX/EC/AG for in vitro exposure data (Diane W confirmed). In light of this, one option is to pre-coordinate the concentrations and dosing units of the added agents into the ISCNAGT (test condition agent) variable, see the texts in red in the above example.
- This is a problem because a single CDISC variable should be designed for a single meaning and a single purpose. The Test Condition Agent variable is used for the name/identity of the added study/control drugs or other materials. I think we would be breaking rules to also include the concentration and unit in this variable as well.
While brain storming Stefan's use-case, I remembered that in the MS domain, there are MSAGENT (Agent Name), MSCONC (Agent Concentration), MSCONCU (Agent Concentration Units) variables that were added back in SDTMIG v3.2 to represent the study and control drugs used for microbial resistance testing. The 3 variables, MSAGENT, MSCONC, and MSCONCU are used to map the name of the study/control drugs, their concentrations and units respectively. Basically, for these MS tests, you dump study drugs, likely an antibiotic (at varying concentrations) on a plate to see if the bacteria would be resistant or susceptible for the drug by measuring a few specific outputs. Below is a MS example from IG3.4 to show how the 3 variables are used together with the MSTESTs:

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title	ms.xpt
Name	ms

Rowcaps

Rows 1-4:	Show the minimum inhibitory concentration and the interpretation result reported from Central Lab ABC from a sample that was tested for susceptibility to the sponsor drug and amoxicillin, using an epsilometer test method.
Rows 5-6:	Show that Local Lab XYZ found that the sample was susceptible to the sponsor drug at a concentration of 0.5 ug/dL and resistant to amoxicillin at a concentration of 0.5 ug/dL.
Rows 7-10:	Show the diameter of the zone of inhibition and the interpretation result reported from Local Lab XYZ from a sample that was tested for susceptibility to the sponsor drug and amoxicillin using a disk diffusion test method.

Dataset2

Row	STUDYID	DOMAIN	USUBJID	NHOID	MSGRPID	MSSEQ	MSREFID	MSLNKGRP	MSTESTCD	MSTEST	MSAGENT	MSCONC	MSCONCU	MSORRES	MSORRESU	MSSTRESC	MSSTRESN	MSSTRESU	MSNAM	MSMETHOD	MSDTC
1	ABC	MS	ABC-001-002	ENTEROCOCCUS FAECALIS	1	1	SPEC01	1	MIC	Minimum Inhibitory Concentration	Sponsor Drug			0.25	ug/dL	0.25	0.25	ug/dL	CENTRAL LAB ABC	EPSILOMETER	2005-06-19T08:00
2	ABC	MS	ABC-001-002	ENTEROCOCCUS FAECALIS	1	2	SPEC01	1	MICROSUS	Microbial Susceptibility	Sponsor Drug			SUSCEPTIBLE		SUSCEPTIBLE			CENTRAL LAB ABC	EPSILOMETER	2005-06-19T08:00
3	ABC	MS	ABC-001-002	ENTEROCOCCUS FAECALIS	2	3	SPEC01	1	MIC	Minimum Inhibitory Concentration	Amoxicillin			1	ug/dL	1	1	ug/dL	CENTRAL LAB ABC	EPSILOMETER	2005-06-19T08:00
4	ABC	MS	ABC-001-002	ENTEROCOCCUS FAECALIS	2	4	SPEC01	1	MICROSUS	Microbial Susceptibility	Amoxicillin			RESISTANT		RESISTANT			CENTRAL LAB ABC	EPSILOMETER	2005-06-19T08:00
5	ABC	MS	ABC-001-002	ENTEROCOCCUS FAECALIS		5	SPEC01	2	MICROSUS	Microbial Susceptibility	Sponsor Drug	0.5	ug/dL	SUSCEPTIBLE		SUSCEPTIBLE			LOCAL LAB XYZ	MACRO BROTH DILUTION	2005-06-19T08:00
6	ABC	MS	ABC-001-002	ENTEROCOCCUS FAECALIS		6	SPEC01	2	MICROSUS	Microbial Susceptibility	Amoxicillin	0.5	ug/dL	RESISTANT		RESISTANT			LOCAL LAB XYZ	MACRO BROTH DILUTION	2005-06-19T08:00
7	ABC	MS	ABC-001-002	ENTEROCOCCUS FAECALIS	3	7	SPEC01	2	DIAZOINH	Diameter of the Zone of Inhibition	Sponsor Drug			23	mm	23	23	mm	LOCAL LAB XYZ	DISK DIFFUSION	2005-06-26T08:00
8	ABC	MS	ABC-001-002	ENTEROCOCCUS FAECALIS	3	8	SPEC01	2	MICROSUS	Microbial Susceptibility	Sponsor Drug			SUSCEPTIBLE		SUSCEPTIBLE			LOCAL LAB XYZ	DISK DIFFUSION	2005-06-26T08:00
9	ABC	MS	ABC-001-002	ENTEROCOCCUS FAECALIS	4	9	SPEC01	2	DIAZOINH	Diameter of the Zone of Inhibition	Amoxicillin			25	mm		25	mm	LOCAL LAB XYZ	DISK DIFFUSION	2005-06-26T08:00
10	ABC	MS	ABC-001-002	ENTEROCOCCUS FAECALIS	4	10	SPEC01	2	MICROSUS	Microbial Susceptibility	Amoxicillin			RESISTANT		RESISTANT			LOCAL LAB XYZ	DISK DIFFUSION	2005-06-26T08:00

PowerPoint Illustration for the in vitro testing exposure data problem:

View file

name	in vitro Testing & Induced Responses.pptx
height	250

Questions/Discussion Needed:

I want to run this by the team to see if we can take advantage of the existing standard variables? Do we also have "duplicate variables" in different domains that serve the same purpose?

Are we using the Test Condition Agent (ISCNDAGT) variable the same as the Agent Name (MSAGENT)? Do we use them for the same purpose?
- They both are used to map the name of the thing/entity (e.g. study/control drug, stimulating test materials like TB antigens, etc) that are added to a sample to "induce" a response.
- The "induced" response can be stimulatory (in immune response) or inhibitory (in bacterial resistance response).
If yes, do we need to merge these two variables? Seeing as we are making changes for IG4.0, this might be worth considering, and will need multiple team's review and approval.
- This also means there would be one less standard variable out there (as people complain that there are too many new variables in IG3.4).
As a separate conversation, can we extend the use of the standard variables --CONC (Agent Concentration), --CONCU (Agent Concentration Units) to the other specimen-based domains? For mapping concentration and unit of the in vitro exposure agents? There are now use-cases needing these variables in IS, MS and CP. Right now --CONC and --CONCU are limited to MS only. They also only qualify --AGENT.
- This way we can take advantage of existing standard variables, instead of creating new ones.
- This also means we don't need to tell users to pre-coordinate unit and dosing concentration of the exposure agent into the same variable - which would be breaking rules.

Team Final Recommendations/Decisions:

1.We need a variable to map the added agent: drug, diagnostic agents, other substances (used to induce a in vitro response). Sometimes this is all we need, and the dataset stops here.

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- MSCONCU works but this is limited to MS.
- Expand it to other specimen-domains, no need to create new variable. – Yes, we agree to extend --CONCU to other domains. Meanwhile people can use it as a NSV for their respective domains if they are using IG3.2-3.4. We may aim for IG4.0 for this change. If ISMT/GGG agrees, we need to update the variable Role, Notes and Definition so that it qualifies --CNDAGT as well. Also CONCU is already a standard variable, we can just take advantage of it.

If we extend CONC and CONCU to other specimen domains...

Here is a mock example of Stefan's data using --CONC and --CONCU:

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Key

Background Information:

PowerPoint Illustration for the in vitro testing exposure data problem:

Questions/Discussion Needed:

Team Final Recommendations/Decisions:

If we extend CONC and CONCU to other specimen domains...