Page History
Request | Notes | Status | Fixed/Updated/Removed from SDTMIG v4.0? | ||||||||||||||
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This is sponsor inquiry. How do you model pre-specified ANA tests? | Question about how to model ANA data that are collected, and therefore should be molded differently from the example that's shown in the SDTMIG 3.4. |
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2023-03-24: Added to SDTMIG v4.0. |
User Inquiry:
"I wanted to revisit this discussion on ANA pattern reporting. We also deal with testing labs where they pre-coordinate the pattern result into the test name and perform a call of whether the pattern is observed or not. For example, the 'test' the lab performs evaluates each staining pattern as listed below:
...
Then, the result for each of these tests is 'POSITIVE' or 'NEGATIVE', affirming presence or identity of the specific pattern in question. "
Our recommendation:
In cases like these and the study is submitting under SDTMIG v3.4, should we simply add each of these patterns as sponsor-extended ISTEST/TESTCD terms? Or, would it be acceptable that these remain in LB (MI is also another possible consideration...)?
Our Recommendations and Rationales:
For modeling Open-ended Findings Question vs. Prespecified Findings Question, analogy can be drawn from the MB domain modeling principles. For modeling pre-specified finding findings vs open-ended findings in MB, the approach has been:
- When asking an open-ended “what bug do you have in the culture” question, MBTEST = Microbial Organism Identification; MBORRES = Name of the Microorg (from the Microorg codelist).
- When asking for a pre-specified finding “do you have this particular named bug in the culture” type question, MBTEST = Name of the specific Microorg, MBORRES = positive/negative, present/absent.
The MB example is to illustrate that the result of result of an open-ended findings question becomes the test or a test test or a test qualifier for the pre-specified findings questionfindings question. This modeling principle applies consistently in IS as well.
Therefore for the pre-specified ANA Stain Pattern tests,
...
Open-ended findings modeling: What ANA stain pattern antinuclear antibody staining pattern(s) do you observe in the specimen? (This is the IS Example 10 in the SDTMIG v3.4)
Con: This approach would only allow people to report the positive findings - ANA patterns that have been observed and reported as results. Patterns that are not observed will not be reported.
Supporting LOINC codes:
- https://loinc.org/14722-3/ Presence
- https://loinc.org/29953-7/ Titer
https://loinc.org/14611-8/ Pattern
Example title IS Example 1 Dataset wrap Name
...
IS Dataset2 Row
STUDYID
DOMAIN
USUBJID
ISSEQ
ISREFID
ISGRPID
ISTESTCD
ISTEST
ISBDAGNT
ISTSTDTL
ISTSTOPO
ISORRES
ISORRESU
ISSTRESC
ISSTRESN
ISSTRESU
ISSPEC
ISMETHOD
VISITNUM
VISIT
ISDTC
1 XYZ IS XYZ1234 1 19283746 1 ATAB Autoantibody NUCLEAR AUTOANTIGENS SCREEN POSITIVE POSITIVE SERUM FLUORESCENT IMMUNOASSAY 1 SCREENING 2018-06-20 2 XYZ IS XYZ1234 2 19283746 1a ATAB Autoantibody NUCLEAR AUTOANTIGENS QUANTIFY 1:340 340 340 titer SERUM FLUORESCENT IMMUNOASSAY 1 SCREENING 2018-06-20 3 XYZ IS XYZ1234 3 19283746 1a ATAB Autoantibody NUCLEAR AUTOANTIGENS STAINING PATTERN
CYTOPLASMIC,
SPECKLED PATTERNCYTOPLASMIC, SPECKLED PATTERN SERUM FLUORESCENT IMMUNOASSAY 1 SCREENING 2018-06-20 4 XYZ IS XYZ1234 4 19283746 1b ATAB Autoantibody NUCLEAR AUTOANTIGENS QUANTIFY 1:170 170 170 titer SERUM FLUORESCENT IMMUNOASSAY 1 SCREENING 2018-06-20 5 XYZ IS XYZ1234 5 19283746 1b ATAB Autoantibody NUCLEAR AUTOANTIGENS STAINING PATTERN NUCLEAR, NUCLEOLAR PATTERN NUCLEAR, NUCLEOLAR PATTERN SERUM FLUORESCENT IMMUNOASSAY 1 SCREENING 2018-06-20 6 XYZ IS XYZ1007 1 19283746 1 ATAB Autoantibody NUCLEAR AUTOANTIGENS SCREEN NEGATIVE NEGATIVE SERUM FLUORESCENT IMMUNOASSAY 1 SCREENING 2018-06-20
Pre-specified findings modeling: Do you observe nuclear centromere /ANA pattern? Do you observe cytoplasmic speckled ANA pattern? etc.
Pro:
- This approach allows the users to report both the "specific, pre-specified" positive and negative patterns, if interested.
- This is also almost a 1:1 mapping to LOINC codes.
- Consistent modeling approach across specimen-based domains.
Supporting LOINC Codes:
- https://loinc.org/53994-0/ Presence
https://loinc.org/96921-2/ Titer
Example title IS Example 2 Dataset wrap Name
...
IS Dataset2 Row
STUDYID
DOMAIN
USUBJID
ISSEQ
ISREFID
ISGRPID
ISTESTCD
ISTEST
ISBDAGNT
ISTSTDTL
ISTSTOPO
ISORRES
ISORRESU
ISSTRESC
ISSTRESN
ISSTRESU
ISSPEC
ISMETHOD
VISITNUM
VISIT
ISDTC
1 XYZ IS XYZ1234 1 19283746 1 ATAB Autoantibody NUCLEAR AUTOANTIGENS CYTOPLASMIC, SPECKLED PATTERN SCREEN POSITIVE POSITIVE SERUM FLUORESCENT IMMUNOASSAY 1 SCREENING 2018-06-20 2 XYZ IS XYZ1234 2 19283746 1 ATAB Autoantibody NUCLEAR AUTOANTIGENS CYTOPLASMIC, SPECKLED PATTERN QUANTIFY 1:170 170 170 titer SERUM FLUORESCENT IMMUNOASSAY 1 SCREENING 2018-06-20 3 XYZ IS XYZ1234 1 19283746 2 ATAB Autoantibody NUCLEAR AUTOANTIGENS NUCLEAR, NUCLEOLAR PATTERN
SCREEN POSITIVE POSITIVE SERUM FLUORESCENT IMMUNOASSAY 1 SCREENING 2018-06-20 4 XYZ IS XYZ1234 2 19283746 2 ATAB Autoantibody NUCLEAR AUTOANTIGENS NUCLEAR, NUCLEOLAR PATTERN
QUANTIFY 1:340 340 340 titer SERUM FLUORESCENT IMMUNOASSAY 1 SCREENING 2018-06-20 5 XYZ IS XYZ1234 1 19283746 ATAB Autoantibody NUCLEAR AUTOANTIGENS NUCLEAR, CENTROMERE PATTERN
SCREEN NEGATIVE NEGATIVE SERUM FLUORESCENT IMMUNOASSAY 1 SCREENING 2018-06-20
Decision Decisions and Additional Notes/Action Items: colour Status
- Team is happy with both approaches, this "reciprocal" modeling approach provides flexibility and allows sponsors to accommodate different data collection schemas. It is also highly consistent with LOINC, both example have LOINC codes corroboration.
- Jordan to enter this into the CDISC Example Library.already added this one to the SDTMIG v4.0.
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