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| Dataset2 |
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| hi1style | yellow |
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| hi1 | column ISBDAGNT |
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| tableid | IS table 1 |
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| Row | STUDYID | DOMAIN | USUBJID | SPDEVID | ISSEQ | ISTESTCD | ISTEST | ISTSTCND | ISCNDAGT | ISORRES | ISORRESU | ISSTRESC | ISSTRESN | ISSTRESU | ISSPEC | ISMETHOD | ISDTC |
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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 |
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- 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 said 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). These domains have variables for mapping dosing concentrations and units, but we can't use them for in vitro exposure data. Craig said he would pre-coordinate the concentrations and 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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| Rowcaps |
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| 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 |
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| Row | STUDYID | DOMAIN | USUBJID | NHOID | MSGRPID | MSSEQ | MSREFID | MSLNKGRP | MSTESTCD | MSTEST | MSAGENT | MSCONC | MSCONCU | MSORRES | MSORRESU | MSSTRESC | MSSTRESN | MSSTRESU | MSNAM | MSMETHOD | MSDTC |
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| 1 | ABC | MS | ABC-001-002 | ENTEROCOCCUS FAECALIS | 1 | 1 | SPEC01 | 1 | MIC | Minimum Inhibitory Concentration | Sponsor Drug |
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| 0.25 | ug/dL | 0.25 | 0.25 | ug/dL | CENTRAL LAB ABC | EPSILOMETER | 2005-06-19T08:00 |
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| 2 | ABC | MS | ABC-001-002 | ENTEROCOCCUS FAECALIS | 1 | 2 | SPEC01 | 1 | MICROSUS | Microbial Susceptibility | Sponsor Drug |
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| SUSCEPTIBLE |
| SUSCEPTIBLE |
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| CENTRAL LAB ABC | EPSILOMETER | 2005-06-19T08:00 |
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| 3 | ABC | MS | ABC-001-002 | ENTEROCOCCUS FAECALIS | 2 | 3 | SPEC01 | 1 | MIC | Minimum Inhibitory Concentration | Amoxicillin |
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| 1 | ug/dL | 1 | 1 | ug/dL | CENTRAL LAB ABC | EPSILOMETER | 2005-06-19T08:00 |
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| 4 | ABC | MS | ABC-001-002 | ENTEROCOCCUS FAECALIS | 2 | 4 | SPEC01 | 1 | MICROSUS | Microbial Susceptibility | Amoxicillin |
|
| RESISTANT |
| RESISTANT |
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| CENTRAL LAB ABC | EPSILOMETER | 2005-06-19T08:00 |
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| 5 | ABC | MS | ABC-001-002 | ENTEROCOCCUS FAECALIS |
| 5 | SPEC01 | 2 | MICROSUS | Microbial Susceptibility | Sponsor Drug | 0.5 | ug/dL | SUSCEPTIBLE |
| SUSCEPTIBLE |
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| LOCAL LAB XYZ | MACRO BROTH DILUTION | 2005-06-19T08:00 |
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| 6 | ABC | MS | ABC-001-002 | ENTEROCOCCUS FAECALIS |
| 6 | SPEC01 | 2 | MICROSUS | Microbial Susceptibility | Amoxicillin | 0.5 | ug/dL | RESISTANT |
| RESISTANT |
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| LOCAL LAB XYZ | MACRO BROTH DILUTION | 2005-06-19T08:00 |
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| 7 | ABC | MS | ABC-001-002 | ENTEROCOCCUS FAECALIS | 3 | 7 | SPEC01 | 2 | DIAZOINH | Diameter of the Zone of Inhibition | Sponsor Drug |
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| 23 | mm | 23 | 23 | mm | LOCAL LAB XYZ | DISK DIFFUSION | 2005-06-26T08:00 |
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| 8 | ABC | MS | ABC-001-002 | ENTEROCOCCUS FAECALIS | 3 | 8 | SPEC01 | 2 | MICROSUS | Microbial Susceptibility | Sponsor Drug |
|
| SUSCEPTIBLE |
| SUSCEPTIBLE |
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| LOCAL LAB XYZ | DISK DIFFUSION | 2005-06-26T08:00 |
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| 9 | ABC | MS | ABC-001-002 | ENTEROCOCCUS FAECALIS | 4 | 9 | SPEC01 | 2 | DIAZOINH | Diameter of the Zone of Inhibition | Amoxicillin |
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| 25 | mm |
| 25 | mm | LOCAL LAB XYZ | DISK DIFFUSION | 2005-06-26T08:00 |
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| 10 | ABC | MS | ABC-001-002 | ENTEROCOCCUS FAECALIS | 4 | 10 | SPEC01 | 2 | MICROSUS | Microbial Susceptibility | Amoxicillin |
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| RESISTANT |
| RESISTANT |
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| LOCAL LAB XYZ | DISK DIFFUSION | 2005-06-26T08:00 |
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PowerPoint Illustration for the in vitro testing exposure data problem:
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| name | in vitro Testing & Induced Responses.pptx |
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| height | 250 |
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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.
Recommendations:
- We can tell Stefan to use --CONC and --CONCU for exposure agent concentration and unit, and add them to the IS domain as NSVs, because IG3.2 and SDTM 2.0 still limit these variables to the MS domain only. Meanwhile, we work on getting these variables officially added to the other domains for IG4.0 or a later version of the IG (IS, CP, maybe GF too).
- Or we tell Stefan to pre-coordinate all that information into the Test Condition Agent (ISCNDAGT) variable, or create his own NSV for concentration and unit of the agent.
- Other thoughts? Other ways forward?
...