Hi,
I didn't perform the query at UNMC, but our (UNMC's) result appears to have the
following set of concept-codes in the exported observation_fact table (1 LOINC
code):
ICD9CM:279.06
ICD9CM:473.0
ICD9CM:473.9
ICD9CM:486
LOINC:2465-3
Jay Pedersen, M.A.
Department of Pathology/Microbiology
University of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE 68198-5900
402-559-9487 (office)
402-739-3496 (mobile)
________________________________________
From: gpc-dev-boun...@listserv.kumc.edu [gpc-dev-boun...@listserv.kumc.edu] on
behalf of gpc-dev-requ...@listserv.kumc.edu [gpc-dev-requ...@listserv.kumc.edu]
Sent: Thursday, July 07, 2016 1:00 PM
To: gpc-dev@listserv.kumc.edu
Subject: Gpc-dev Digest, Vol 29, Issue 15
Send Gpc-dev mailing list submissions to
gpc-dev@listserv.kumc.edu
To subscribe or unsubscribe via the World Wide Web, visit
http://listserv.kumc.edu/mailman/listinfo/gpc-dev
or, via email, send a message with subject or body 'help' to
gpc-dev-requ...@listserv.kumc.edu
You can reach the person managing the list at
gpc-dev-ow...@listserv.kumc.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Gpc-dev digest..."
Today's Topics:
1. RE: GPC DEID Data Request: Immunoglobulin G Levels and the
pattern of infection (Tamara McMahon)
----------------------------------------------------------------------
Message: 1
Date: Thu, 7 Jul 2016 18:00:02 +0000
From: Tamara McMahon <tmcma...@kumc.edu>
To: "'Verhagen, Laurel A'" <verhagen.lau...@mcrf.mfldclin.edu>,
"Campbell, Walter S" <wcamp...@unmc.edu>, "Campbell, James R"
<campb...@unmc.edu>
Cc: "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>
Subject: RE: GPC DEID Data Request: Immunoglobulin G Levels and the
pattern of infection
Message-ID:
<6b28166ee734b445a714dd10b07839f362e58...@exmail3.kumc.edu>
Content-Type: text/plain; charset="utf-8"
Hi,
The researcher has specific ICD9 codes, but no specific IgG LOINC codes.
Regarding diagnosis, please limit the diagnosis to the ICD9s codes supplied in
the query. Regarding labs, you can localize the query to obtain the necessary
IgG codes.
Thank you,
Tamara
From: Verhagen, Laurel A [mailto:verhagen.lau...@mcrf.mfldclin.edu]
Sent: Thursday, July 07, 2016 11:48 AM
To: Campbell, Walter S <wcamp...@unmc.edu>; Campbell, James R
<campb...@unmc.edu>
Cc: Sravani Chandaka <schand...@kumc.edu>; Tamara McMahon <tmcma...@kumc.edu>;
gpc-dev@listserv.kumc.edu; Gardner, Bret J <bret.gard...@unmc.edu>; McClay,
James C <jmcc...@unmc.edu>
Subject: RE: GPC DEID Data Request: Immunoglobulin G Levels and the pattern of
infection
Hi all,
UNMC ? thanks so much for your assistance in this discussion.
I think at this point, direction should be coming from the requestor and/or
KUMC, as the facilitator of the requests. A main question that has not been
addressed is whether sites are allowed to localize the query. Again the
specifications appear to be vague and the babel example seems to be incorrect,
based on Jim Campbell?s review.
Have any other DROC-approved sites (KUMC, IU, UIOWA, MCW, Marshfield, MU, UNMC,
UTHSCSA) submitted data for this request? If so, how did you address the Ig G
requirement?
Thanks,
Laurel
From: Campbell, Walter S [mailto:wcamp...@unmc.edu]
Sent: Thursday, July 07, 2016 10:51 AM
To: Campbell, James R; Verhagen, Laurel A
Cc: Sravani Chandaka (schand...@kumc.edu<mailto:schand...@kumc.edu>); Tamara
McMahon; gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>; Gardner,
Bret J; McClay, James C
Subject: RE: GPC DEID Data Request: Immunoglobulin G Levels and the pattern of
infection
Hi Laurel,
I am out this week, as well. How quickly do you need this information? I can
get it to you on Monday if that is not too late. Otherwise, I can task one of
the "minions" to get it sooner.
Please advise.
W. Scott Campbell, PhD, MBA
Assistant Professor
Director of Public Health Laboratory Informatics and
Pathology Laboratory Informatics
Department of Pathology/Microbiology
University of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE 68198-5900
402-559-9593 (office)
402-350-7851 (mobile)
________________________________
From: Campbell, James R
Sent: Wednesday, July 06, 2016 2:34 PM
To: Verhagen, Laurel A; Campbell, Walter S
Cc: Sravani Chandaka (schand...@kumc.edu<mailto:schand...@kumc.edu>); Tamara
McMahon; gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>; Gardner,
Bret J; McClay, James C
Subject: Re: GPC DEID Data Request: Immunoglobulin G Levels and the pattern of
infection
Laurel
Glad to do so! I am looking out over Loch Ness on a fair Scottish eve as I
type and so am directing Scott Campbell to organize the UNMC minions and send a
list of LOINC codes that would be appropriate to the query. I have no RELMA
access in my current situation but would otherwise be happy to reply.
Scott, please work with Bret and Jay to prepare a value set for Laurel and
GPC-DEV to use for this query.
Jim
James R. Campbell MD
campb...@unmc.edu<mailto:campb...@unmc.edu>
Office: 402-559-7505
Secretary: 402-559-7299
Pager: 402-888-1230
On Jul 6, 2016, at 12:34 PM, Verhagen, Laurel A
<verhagen.lau...@mcrf.mfldclin.edu<mailto:verhagen.lau...@mcrf.mfldclin.edu>>
wrote:
Jim,
Thanks for your expertise! Is it possible to share the LOINC codes used at UNMC
for this request?
Laurel
From: Campbell, James R [mailto:campb...@unmc.edu]
Sent: Wednesday, July 06, 2016 12:01 PM
To: Verhagen, Laurel A
Cc: Sravani Chandaka (schand...@kumc.edu<mailto:schand...@kumc.edu>); Tamara
McMahon; gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>
Subject: Re: GPC DEID Data Request: Immunoglobulin G Levels and the pattern of
infection
Laurel
The LOINC parts code (LP14672-2) is only valid as a defining 'atom' in LOINC
and should be ignored for retrieving valid IgG levels from your lab data. I
assume this was a simple misinterpretation of the meaning of the LOINC part.
Jim
James R. Campbell MD
campb...@unmc.edu<mailto:campb...@unmc.edu>
Office: 402-559-7505
Secretary: 402-559-7299
Pager: 402-888-1230
On Jul 5, 2016, at 4:24 PM, Verhagen, Laurel A
<verhagen.lau...@mcrf.mfldclin.edu<mailto:verhagen.lau...@mcrf.mfldclin.edu>>
wrote:
Hi Sravani and Tamara,
I?m wondering if one of you can help answer a question related to the PI
CONNECT query.
The Cohort definition doesn?t specify coding for the IgG levels. Marshfield
doesn?t populate LP14672-7, which is used in the sample query on babel.
Is it appropriate to substitute another test? If so, does the PI want to
provide a list of approved codes or can this be localized without PI
involvement?
I do have data for LOINC
2465-3<https://urldefense.proofpoint.com/v2/url?u=http-3A__s.details.loinc.org_LOINC_2465-2D3.html-3Fsections-3DComprehensive&d=CwMGaQ&c=KNVzINr6WAqWApikNSnyDeOu0ck0iFwcrMz92MxUhIs&r=A2PXk2ZGVGBzoEOQMwrrbqse0CnDMUgS4P3-3HOTSAwE8Vfvoc1Wm0NCYFbuU-_5&m=K46w4rQwaUJuGxCIYEtVubiGOtWo53CRIGSeaPr-Ftw&s=ocg6T0ZpCjvNLbTsVKIRadFm-9n4_0LyZyDIiRV_36Q&e=>
IgG [Mass/?volume] in Serum or Plasma, as well as several panels that contain
the component:
MEMBER OF THESE PANELS
34550-4 Immunoglobulin panel [Mass/?volume] -
Serum
47289-4 IgG and IgG subclass panel [Mass/?volume]
- Serum
55121-8 Multiple sclerosis panel - Serum and CSF
55295-0 Protein electrophoresis and
Immunoglobulins panel - Serum
We also have a couple of CPT codes that might be relevant ? 82784, 82787.
Looking for guidance on how to proceed?or whether Marshfield would be out,
because we?re missing LP14672-7.
Thanks,
Laurel
From:
gpc-honest-brokers-boun...@listserv.kumc.edu<mailto:gpc-honest-brokers-boun...@listserv.kumc.edu>
[mailto:gpc-honest-brokers-boun...@listserv.kumc.edu] On Behalf Of Tamara
McMahon
Sent: Friday, June 17, 2016 1:54 PM
To:
gpc-honest-brok...@listserv.kumc.edu<mailto:gpc-honest-brok...@listserv.kumc.edu>;
gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>
Subject: GPC DEID Data Request: Immunoglobulin G Levels and the pattern of
infection
All,
The GPC received a de-identified data request from Dr. Kate Sullivan of the
PI-CONNECT PPRN. This query contains labs and diagnosis (ICD-9 codes). The
query is located on Babel at Shared\PI-Connect\PIConnect[6-17-2016]. Attached
is a description of the search and output criteria. The stratification does
not need to be included in the query.
Data files should be created using the data builder. You can read about the
data builder output and how it is
made<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_wiki_BuilderSaga-23builder-2Dsql-2Dguide&d=CwMFAg&c=KNVzINr6WAqWApikNSnyDeOu0ck0iFwcrMz92MxUhIs&r=A2PXk2ZGVGBzoEOQMwrrbqse0CnDMUgS4P3-3HOTSAwE8Vfvoc1Wm0NCYFbuU-_5&m=1s3q4ZJyND4-iDjqR8VdH3Q5iMWtjrMQmY0D8x20n1A&s=g2vp7MaK6nOY0kvXVBsVaiC0zWtpZ5XEPpL6CVHAqFc&e=>
and about the data
summary<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_wiki_BuilderSaga-23DataSummary&d=CwMFAg&c=KNVzINr6WAqWApikNSnyDeOu0ck0iFwcrMz92MxUhIs&r=A2PXk2ZGVGBzoEOQMwrrbqse0CnDMUgS4P3-3HOTSAwE8Vfvoc1Wm0NCYFbuU-_5&m=1s3q4ZJyND4-iDjqR8VdH3Q5iMWtjrMQmY0D8x20n1A&s=coDOqgi-3PrCK_xu38j5D9EZvZtg0VNiIOIXpPSWtHs&e=>.
Submit the data via this
survey<https://urldefense.proofpoint.com/v2/url?u=https-3A__redcap.gpcnetwork.org_surveys_-3Fs-3DN9MEMP84HX&d=CwMFAg&c=KNVzINr6WAqWApikNSnyDeOu0ck0iFwcrMz92MxUhIs&r=A2PXk2ZGVGBzoEOQMwrrbqse0CnDMUgS4P3-3HOTSAwE8Vfvoc1Wm0NCYFbuU-_5&m=1s3q4ZJyND4-iDjqR8VdH3Q5iMWtjrMQmY0D8x20n1A&s=mzY4n_a86rCyjUkVkfh3f5FJPAe4HS3OY3KfQOQf83Q&e=>.
Note: I am unavailable next week but will be on the GPC-Dev call 6/28 to
discuss any questions about this query or data request.
The following institutions have DROC approval and can submit their data at any
time.
KUMC
Indiana
Iowa
MCW
Marshfield
Missouri
Nebraska
UTHSC-SA
The following sites do not have DROC approval yet. Please do not submit until
approval is in place for your institution.
Minnesota
UTSW
Wisconsin
The following sites are not required to run the query.
CMH
Each site that provides data will be reimbursed $500.
Regards,
Tamara McMahon
Director, Engineering & Product Experience
Medical Informatics, University of Kansas Medical Center
________________________________
The contents of this message may contain private, protected and/or privileged
information. If you received this message in error, you should destroy the
e-mail message and any attachments or copies, and you are prohibited from
retaining, distributing, disclosing or using any information contained within.
Please contact the sender and advise of the erroneous delivery by return e-mail
or telephone. Thank you for your cooperation.
_______________________________________________
Gpc-dev mailing list
Gpc-dev@listserv.kumc.edu<mailto:Gpc-dev@listserv.kumc.edu>
http://listserv.kumc.edu/mailman/listinfo/gpc-dev<https://urldefense.proofpoint.com/v2/url?u=http-3A__listserv.kumc.edu_mailman_listinfo_gpc-2Ddev&d=CwMGaQ&c=KNVzINr6WAqWApikNSnyDeOu0ck0iFwcrMz92MxUhIs&r=A2PXk2ZGVGBzoEOQMwrrbqse0CnDMUgS4P3-3HOTSAwE8Vfvoc1Wm0NCYFbuU-_5&m=K46w4rQwaUJuGxCIYEtVubiGOtWo53CRIGSeaPr-Ftw&s=gMn6Yw805WgvNKX8iYHlDPacAnFXjZiThEc5YfJ_oi4&e=>
The information in this e-mail may be privileged and confidential, intended
only for the use of the addressee(s) above. Any unauthorized use or disclosure
of this information is prohibited. If you have received this e-mail by mistake,
please delete it and immediately contact the sender.
________________________________
The contents of this message may contain private, protected and/or privileged
information. If you received this message in error, you should destroy the
e-mail message and any attachments or copies, and you are prohibited from
retaining, distributing, disclosing or using any information contained within.
Please contact the sender and advise of the erroneous delivery by return e-mail
or telephone. Thank you for your cooperation.
________________________________
The contents of this message may contain private, protected and/or privileged
information. If you received this message in error, you should destroy the
e-mail message and any attachments or copies, and you are prohibited from
retaining, distributing, disclosing or using any information contained within.
Please contact the sender and advise of the erroneous delivery by return e-mail
or telephone. Thank you for your cooperation.
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
<http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20160707/d1dabcae/attachment.html>
------------------------------
_______________________________________________
Gpc-dev mailing list
Gpc-dev@listserv.kumc.edu
http://listserv.kumc.edu/mailman/listinfo/gpc-dev
End of Gpc-dev Digest, Vol 29, Issue 15
***************************************
_______________________________________________
Gpc-dev mailing list
Gpc-dev@listserv.kumc.edu
http://listserv.kumc.edu/mailman/listinfo/gpc-dev
