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CSTE National ELR Workgroup

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Becky Lampkins, Manager, Surveillance/Informatics Program at CSTEMegan Toe, CSTEScott Troppy, Surveillance Epidemiologist at MA DPHMeredith Lichtenstein, CSTEAmy Drake, NMJohn RobertsNancy Barrett, Epi 4/PH Informatics SpecialistErin Holt, TDHRita Altamore, EpidemiologistDavid DiCesareJason HallWalter Kemper, ELR Coordinator, NC DHHS Div of Public HealthJulie LuepkeCarmen Pugh, Labcorp Manager State Reporting at LabCorpTom Safranek +399 others
Posted by Nancy Barrett ·

Capture of Ct values in HL7

hi,
I've been asked to now have labs doing SARS-CoV-2 sequencing to report the Ct values. How are folks capturing that in HL7 that is not NTE?

thanks

Comments & Events

Annie Fine, CSTE Annie Fine
Curious who asked you Nancy. We are having discussions about this topic very soon with APHL and CDC. Also I know that Florida and TX have gone or are going in direction of having CT values reported. My thought was that it could go into the "quantitative result" field but not sure if that will work. There are still conflicting thoughts about this among APHL, CDC lab, CDC epi and others. I know when I was at NYC DOHMH we wanted these reported, and stll do (obviously only from those labs that do have the values).  thx!
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Nancy Barrett, Epi 4/PH Informatics Specialist Nancy Barrett, Epi 4/PH Informatics Specialist
Lynn Sosa our Deputy State Epi is leading our covid-19 surveillance response and she said it was requested - I'm assuming by one of the bodies you mentioned.  We are putting this request into our state contracts with sequencing labs.

There are several Cycle Threshold # LOINCs to chose from; I'm going to ask the labs to use the most generic one: 
  | 94746-5  | SARS-CoV-2 (COVID-19) RNA [Cycle Threshold #] in Unspecified specimen by NAA with probe detection

Although we can take any of the others. 
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Riki Merrick, Terminologist at APHL Riki Merrick, Terminologist at APHL
These should be additional OBX segments with the most specific LOINC for the target they are capturing - just know that for many of the tests you have been getting only 1 OBX you will now get 3 or 4, as many have more than one target. You should also consider taking the Ct value for the internal control (though some labs may not want to report that one out). And not every lab has Ct values in their LIMS, so might require some development work for those labs.

Riki
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Nancy Barrett, Epi 4/PH Informatics Specialist Nancy Barrett, Epi 4/PH Informatics Specialist
yup, I've been asked to get that also (internal control) - these are labs under state contract and many are outside of the usual lab part that is testing for covid or a research arm.

Riki - can we get a new LOINC that is a Qn or mixed value type for not using PLR codes for lineage reporting? so we don't violate LOINC rules :-)
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Riki Merrick, Terminologist at APHL Riki Merrick, Terminologist at APHL
I am not sure what you are asking for - you mean ORDQN? there is NO quantitative part in the lineage reporting, so not likely.
and the ST for lineage reporting would not fit into the QN part anyway - that should be NM or SN datatype (DT, TS and TM would not apply here) - I could ask for a narrative term, though not sure that we really want that - Regenstrief calls these nominal, because theoretically there is only a limited number (though very large) of possible answers

RIki
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Nancy Barrett, Epi 4/PH Informatics Specialist Nancy Barrett, Epi 4/PH Informatics Specialist
Riki there is a narrative LOINC already. Just need to be as flexible as possible so we can capture all results in a timely manner. no worries. Sometimes HL7 is not the best method, but we are working with both HL7 and csv. Thanks for all of your work on this!
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