M. Tuberculosis Spoligotype

Where it is mentioned in the SDTMIG 3.4: OI Assumptions

Reference Reading:

https://www.cdc.gov/tb/programs/genotyping/chap3/3_cdclab_2description.htm
https://www.researchgate.net/figure/Spoligotype-patterns-of-mycobacterial-isolates-recovered-from-tuberculosis-lesions-in_fig2_45287894
https://www.heartlandntbc.org/assets/products/clinicians_lab_guide.pdf, Page 69 sample report

http://www.pasteur-guadeloupe.fr:8081/SITVIT2/

Based on the CDC article, you get four types of results from a spoligotyping assay:

1. Original band pattern: the black/white spacer sequence bands (black band means presence of a spacer and white means absence of a spacer) - there are 43 know spacers in this direct repeat (DR) region in the DNA of M. tuberculosis.
2. Binary Code
3. 14+1 Grouping Result
4. Octal Designation Result

What you report, again, based on CDC, is the 4th one, Octal designation number, such as 000000000003771, or 777777777760771.
There is no actual example in the SDTMIG v3.4 so I don't know how this is reported. Is it important to map the words "Octal Designation" somewhere? How about the other 3?
I searched on http://www.pasteur-guadeloupe.fr:8081/SITVITDemo/index.jsp, and this website gives output in both the Binary Code and Octal Designation. I initially thought these would be TSTDTL, but they are result types. Because all you get from the hybridization assay is the banding patterns on the membrane. The other 3 results you have to "covert/translate" from the banding patterns. So maybe we could use the result type variable, RESTYP - currently not in OI, will need to be added. However if all you need to report is just that Octal number, then we just need to create a new OIPARM = Spoligotype and forget about the result types for now.

Additional Information:

Email from Kelly Stinson (TB SME): but what I can tell you is on a previous clinical trial, rather than capturing the detailed results of each spoligo pattern, we captured the bigger question we wanted answered by spoligo: do the two isolates match, or are they different, such that it represents either a new MTB infection or potential lab error? - Phil, this is comparing a new TB infection to a previously identified TB strain from the same patient. If the two isolates match, it means your drug/treatment didn't work, if they don't match, it means either a new infection or lab error. This is measuring new against baseline. But yes, you would need to store the original strain's spoligotype pattern somewhere in order to do that comparison.

Decision:

Team decided to create the OIPARM only for now and when there are clear requests or uses-cases where one needs to distinguish the different type of spoligotype results, we can then consider adding RESTYP to OI.