Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jsteinmetz Type: design-issue | Status: assigned Priority: major| Milestone: survey-redcap-als Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63, 245 Blocking: | -+ Changes (by dconnolly): * cc: gpc-dev@… (removed) * cc: jsteinmetz (added) * owner: badagarla = jsteinmetz Comment: ''I promoted the issue with living situation etc. (comment:31) to its own ticket: #245.'' -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:36 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: badagarla Type: design-issue | Status: assigned Priority: major| Milestone: survey-redcap-als Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Changes (by dconnolly): * owner: jhe = badagarla Comment: Bhargav, have you been involved in any discussions of living situation, occupation, and years of education? (ref comment:31) -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:33 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: badagarla Type: design-issue | Status: assigned Priority: major| Milestone: survey-redcap-als Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by badagarla): Replying to [comment:33 dconnolly]: No, I have not been a part of that discussion. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:34 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: survey-redcap-als Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by dconnolly): In section 5.0 Data management and case report forms of the protocol (attached to #208): The following EMR data will be included for analysis: age, gender, race, ethnicity, living situation, occupation, and years of education. I don't know where living situation, occupation, and years of education are expected to come from. They're not on the current survey draft, and they're not in any of the currently planned GPC ontologies. In section 6.0 Biostatistical Approach: Outcome Measures, Data Analysis and Power: ... Basic descriptive statistics will be used to describe the overall ALS clinic cohort: including basic demographics (age, gender, race, ethnicity, living situation, occupation, years of education) and functional burden as identified by survey response (clinical diagnosis, and functional status). -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:31 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: survey-redcap-als Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by jhe): Wendy sent a report on ALS comobidities and complications to John on Friday Feb 06, 2015. John provided the list of ICD-9 codes comorbidities related to Charlson comobidity index and Jeff provided the list of ICD-9 codes for more ALS relevant comobidities and complications (Wendy and Siya together completed the work). Cohort characterization for ALS cohort will stop for now to focus on the Breast cancer cohort. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:32 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: survey-redcap-als Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Changes (by dconnolly): * milestone: cohort-char1 = survey-redcap-als -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:30 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by jhe): Due to travel and other meetings, John, Jeff, Scott, and Wendy finally met all together on 21st (Scott and Wendy met on Nov 7, Scott, Wendy, and John met on Nov 14). The major issue for ALS cohort characterization is to identify variables needed. We went through a list Jeff made in October but many of them do not identify enough records. At the meeting, we decoded to use ICD9 code to identify variables for comobidities. John provided a list of ICD9 codes for creating charlson comobidity code and Jeff will find ICD 9 codes for other variables. Identifing medications remains an issue. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:26 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by jhe): Replying to [comment:23 dconnolly]: We found the problem list under diagnosesclinical(O2 EMR), but there seems to have no content in it. Replying to [comment:21 jhe]: [...] 2. Jeff mentioned that there is “problem list” in O2 that is easier for identifying comorbidities. Are they in Heron? If yes, where they are? Yes, the problem list is a collection of modifiers in the Diagnosis Hierarchy: - Problem status - Active - Deleted - Resolved p.s. thanks for the notes; more on meds separately -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:27 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Changes (by jhe): * cc: skoertner@… (added) -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:25 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by dconnolly): Replying to [comment:21 jhe]: [...] 2.Jeff mentioned that there is “problem list” in O2 that is easier for identifying comorbidities. Are they in Heron? If yes, where they are? Yes, the problem list is a collection of modifiers in the Diagnosis Hierarchy: - Problem status - Active - Deleted - Resolved p.s. thanks for the notes; more on meds separately -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:23 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by ngraham): Replying to [comment:21 jhe]: 1.Do medications in Heron include physician’s prescription data or they are KU pharmacy’s fulfilling prescriptions data? If the clinician orders the medication in Epic/O2, it should be in HERON. I'm not sure if this is the same as the prescription workflow or not. If you query based on medication(s) in HERON (without specifying a modifier) you should be including patients who ever had an order recorded in the Epic system for the selected medication(s) whether or not a dispense was recorded. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:24 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
Hubert and Mike are currently testing out the problem list extracts to SNOMED CT (can also obtain ICD-9-CM) for our load of SNOMED diagnoses. They will share soon and can demo on GPC-DEV call if interested. UNMC medication data not tested yet but we have outpatient prescriptions (med orders) as well as dispense histories received from Surescripts during ambulatory clinical encounters. To the best of my knowledge, inpatients med orders are also available but we have not started work on the extracts for those yet Jim James R. Campbell MD campb...@unmc.edu Office: 402-559-7505 Secretary: 402-559-7299 Pager: 402-888-1230 On Oct 11, 2014, at 1:13 AM, GPC Informatics d...@madmode.com wrote: #31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by jhe): Oct 10: we had a 2.5 hours meeting discussing variables from Jeff’s list. Most of items connected with a small number of patients and some of the items pulled a lot of things out by searching key words. We had discussions on what should be used for pulling data. Jeff thought many of the numbers are much lower than what he saw in clinic, for example, only 261 out of 1905 patients took Riluzole that is the only FDA approved medication for ALS. So, there is a big question of whether Heron have all the data from O2. If not, then that is a really serious problem for using Heron for research. If all O2 data is in Heron, then we need to figure out how we can pull them out. During the meeting, two key questions came up: 1. Do medications in Heron include physician’s prescription data or they are KU pharmacy’s fulfilling prescriptions data? 2. Jeff mentioned that there is “problem list” in O2 that is easier for identifying comorbidities. Are they in Heron? If yes, where they are? Can anybody from the medicalinformatics team answer these? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:21 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev 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. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by jhe): Drs Jeffrey Statland, John Chen, Scott Koertner, and Wendy He had a meeting this afternoon, discussing the progress of the ALS cohort characterization and future steps. Jeff gave a lot insignts on what would be interesting information for this patient population. He will come up with a list of prioritized variables for data query. Besides demographics, stand of care will be the focus of the list. Some trivial notes Demographic variables (of particular interest): occupation (employed or not) Livng situation (along or live with others, marital status) (found this variable in Heron but not many patients have the information) Economic status (may come from insurance information) Standar of care Medication (Only one FDA approved medication for ALS, but there are many medicaitons for specific symptoms, such as drooling, muscle spasm. Device: bipap Found ALSFRS in flowsheet and Pba (pseudo bulbar) score. Jeff will find out when the clinic started using these scales. Others Jeff thougt that the 1900+ ALS cases in Heron is more than expected. (more than half of them are dead though. But the 800 alive ones are also more than expected based on the patients seen in the clinic) John mentioned that a patient need to have at least 2 ALS outpatient encounters be be qualified as a ALS patients (this may reduce the patient volumn) Jeff mentioned that it is important to find out what happended to patients before they were diagnozed with ALS (This is regarded as research question that we can work on later) Although there is no specific diagnosis date for ALS in Heron. It would be interesting to show the distribition of the time difference between first ALS encounter and time of death. The expected median is 3 years. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:20 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Changes (by dconnolly): * cc: gchen2@… (added) -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:19 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: dconnolly Type: design-issue | Status: assigned Priority: major| Milestone: data-domains2 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Changes (by dconnolly): * cc: campbell, rwaitman (removed) * cc: gpc-dev@…, tshireman (added) Comment: Replying to [comment:12 dconnolly]: ... I'm not entirely sure that it's entirely free of sensitive details, so I'm not sure how to share it more widely. I made a new folder in the PCORNet Central desktop and put my work there: [https://pcornet.centraldesktop.com/c4gpc/folder/4029536/#folder:4029536 Methods Core Cohort Characterization] Wendy, you might want to share your work there too. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:13 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: tshireman Type: design-issue | Status: assigned Priority: major| Milestone: data-domains2 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Changes (by dconnolly): * owner: dconnolly = tshireman Comment: Dr. Shireman, In the July 14 MethodsCore call we talked about having you attend the next ALS call to discuss things like what **physical exam** from section 6 of the [wiki:WikiStart#GPCProposal GPC proposal] mean (cf. comment:11). For the call in details, see: - [http://www.mail-archive.com/gpc-als@listserv.kumc.edu/msg00047.html ALS call July 25 11am] Kieran, Russ plans to attend, as well as several others from the DevTeams: Phillip Reeder, Jim !McClay, someone from Wisconsin, Glenn Bushee. I wonder how to get this on the agenda. I'll try you by phone. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:14 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
