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bsshstudyathon2021's Introduction

BSSH Studyathon 8th September 2021, Oxford

An international study characterising patients undergoing surgery for wrist arthritis and its outcomes

There are 3 elements to this studyathon:

  1. Appraising the literature for what is already known within systematic review (led by researchers from NDORMS, University of Oxford and University of Leeds)
  2. Assessing the outcomes of proximal row carpectomy - patient reported pain and hand function (led by Xpert clinics and Erasmus MC)
  3. Characterising the patients proceeding to intervention for wrist arthritis, and assessing the serious adverse events associated with intervention (led by the OHDSI community)

All 3 parts aim to contribute equally address the central research question

3. OHDSI study- Characterisation

Study Status: Started

  • Analytics use case(s): Characterization
  • Study type: Clinical Application
  • Tags: OHDSI
  • Study lead: Jenny Lane
  • Study lead forums tag: jenniferlane
  • Study start date: 1st July 2021
  • Study end date: 1st October 2021
  • Protocol: attached
  • Publications: ** **
  • Results explorer:

If you are undertaking cohort diagnostics for the first time, you may need set up your environment using the instructions given in the HADES installation guide. To run the study you will need to load the package, enter the RProj, and build it. Once built, you will need to open the extras/CodeToRun.R file and enter your database connection details, where you want to save your results locally, and so on (see instructions in the file). In this same file you can then run the study, view the results locally in a shiny application, and share your results.

Requirements

Please note prior to running (and as detailed in the file Extas/CodetoRun.R), you may also need to install packages in order for packages to run including:

- devtools
- dplyr
- ggplot2
- SqlRender
- DatabaseConnector
- parallel
- rJava  
From github:  
- OHDSI/[email protected]
- OHDSI/[email protected]
- OHDSI/[email protected]
- edward-burn/CohortDiagnostics; branch = DiagAi

Note, we suggest using the branch of cohort diagnostics from the edward-burn account rather than the OHDSI one so as to ensure consistency in results set (the OHDSI cohort diagnostics package continues to be developed - the version on Ed´s github is just a recent fork from the main OHDSI repo).

Sharing Results

The output is contained in a .ZIP file within the Outputfolder, in the Export directory. We recommend centres review the blinded results in their personal shiny app prior to sharing within OHDSI. We then invite centres to share the results with us via the SFTP server. To share these via the OHDSI SFTP you will need a key file which you will need to be sent separately. To get this please contact [email protected].

We look forward to working with you!

bsshstudyathon2021's People

Contributors

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Stargazers

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Watchers

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bsshstudyathon2021's Issues

Cohort definition: Crystalline deposition (gout, pseudogout)

Persons in secondary target cohorts:
For cohorts by disease aetiology: Crystalline deposition (gout, pseudogout)
● have a record of a first surgery for wrist arthritis (index event)
● have a record of gout or pseudogout any time prior to and including the date of the index event

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

Consolidate Results

  • UCSF (Rohit)
  • JHMI (Mary Grace/Paul)
  • Columbia (Thomas)
  • CPRD (Jenny)
  • IQVIA (TBD)

Retrieve Features from Prior OHDSI Studies

Cohort-based Medical outcomes:
● Acute kidney injury (AKI) diagnosis during hospitalization
● Acute kidney injury (AKI) using diagnosis codes and change in measurements during hospitalization
● Acute myocardial infarction events
● Angina during hospitalization
● Bleeding during hospitalization
● Bradycardia or heart block during hospitalization
● Cardiac arrhythmia during hospitalization
● Cardiovascular-related mortality
● Death
● Deep vein thrombosis events
● Renal/Dialysis during hospitalization
● Heart failure during hospitalization
● Hemorrhagic stroke (intracerebral bleeding) events
● Hospitalization episodes
● Intensive services during hospitalization
● Ischemic stroke events
● Mechanical ventilation during hospitalization
● Persons with chest pain or angina
● Pneumonia during hospitalization
● Pneumonia episodes
● Pulmonary Embolism events
● Sepsis during hospitalization
● Stroke (ischemic or hemorrhagic) events
● Supraventricular arrythymia during hospitalization
● Total cardiovascular disease events
● Transient ischemic attack events
● Venous thromboembolic (pulmonary embolism and deep vein thrombosis) events
● Ventricular arrhythmia or cardiac arrest during hospitalization

Create Surgical Outcome Cohort Definitions

Create a cohort definitions for:

  • Wound infection requiring antibiotics
  • Wound infection requiring surgical management
  • Deep surgical site infection including septic arthritis
  • Neurovascular injury
  • Tendon injury
  • Fracture
  • Prominent metalwork
  • Reoperation
  • Non-union

Cohort definition: SNAC

Persons in secondary target cohorts:
For cohorts by disease aetiology: SNAC
● have a record of a first surgery for wrist arthritis (index event)
● have a record of SNAC any time prior to and including the date of the index event

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

make discussion points following editorial presentation

what would bring the most interesting discussion after Dr Graham's presentation:

Is the question appropriate?
How we show that we're not interested in data mining?
Statistical significance?
How do we confirm this is clinically relevant work?
How do we best discuss limitations?

Going forward, what data would be most useful in order to augment routinely collected data

Cohort definition: Radial styloidectomy

Persons in secondary target cohorts:
For cohorts by surgical intervention: Radial styloidectomy
● have a record of a first Radial styloidectomy (index event)

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

Cohort definition: PRC

Persons in secondary target cohorts:
For cohorts by surgical intervention: PRC (proximal row carpectomy)
● have a record of a first proximal row carpectomy (index event)

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

Cohort definition: wrist arthroplasty

Persons in secondary target cohorts:
For cohorts by surgical intervention: wrist arthroplasty
● have a record of any form of wrist arthroplasty (including total wrist and pyrocarbon interposition if identifiable) (index event)

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

Cohort definition: Total wrist fusion

Persons in secondary target cohorts:
For cohorts by surgical intervention: Total Wrist fusion
● have a record of a first wrist fusion (index event)

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

Cohort definition: Wrist (AIN/ PIN) denervation

Persons in secondary target cohorts:
For cohorts by surgical intervention: Wrist (AIN/ PIN) denervation
● have a record of a first wrist denervation (index event)

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

Implement Post-Index Features in CohortDiagnostics

Post-index characteristics
These features will be described in two different time windows: at index date (day 0) and in the 30 days from index date (0 to 30 days). As time elapses, additional windows of time will be investigated (eg. in the 90 days from index date [0 to 90 days]) and where possible for some surgical outcomes up to 1 and 5 years following surgery. The characteristics will include:

Concept-based:
● Condition groups (SNOMED + descendants), >=1 occurrence during the interval
● Drug era start groups (ATC/RxNorm + descendants), >=1 drug era start during the interval

Cohort-based Medical outcomes: (See #17)
Cohort-based Surgical outcomes: (See #18)

Implement Stratifications in CohortDiagnostics

Each target cohort will be analysed in full and stratified on factors based on the following pre-index characteristics, all stratum are pending meeting minimum reportable cell counts (as specified by data owners) and where possible, may include:
● Follow-up time: overall, with full 30 days follow-up, without full 30 days follow-up
● Sex (Male vs. Female)
● Those with another type of specified hand surgery prior to index procedure (eg denervation prior to arthrodesis)
● All reportable age groups as well as specifically:
○ Young age ( Age >=35)
○ Elderly (Age >= 65). If sample size allows, results will be reported stratified in the following age categories: 65-84 years, and >=85 years, or in finer age strata (65-69, 70-74, 75-79, 80-84, >=85 years)

Cohort definition: Idiopathic

Persons in secondary target cohorts:
For cohorts by disease aetiology: Idiopathic
● have a record of a first surgery for wrist arthritis (index event)
● have a record of Kienbocks or Preisers disease any time prior to and including the date of the index event

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

Cohort definition: SLAC

Persons in secondary target cohorts:
For cohorts by disease aetiology: SLAC
● have a record of a first surgery for wrist arthritis (index event)
● have a record of SLAC any time prior to and including the date of the index event

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

Execute Package

  • UCSF (Rohit)
  • JHMI (Mary Grace/Paul)
  • Columbia (Thomas)
  • CPRD (Jenny)
  • IQVIA (TBD)

Refine target cohort: wrist arthritis

Persons in the main target cohort for all surgically managed wrist arthritis will:
● have a record of a first surgery for wrist arthritis (index event)

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

Implement Pre-Index Features in CohortDiagnostics

Pre-index characteristics
These features will be described as assessed in two different time windows: the last 30 days (-1 to -30 days) and the year (-1 to -365 days) pre-index:
Demographics:

  • Age: calculated as year of cohort start date – year of birth and with 5 year groupings
  • Sex
  • Race
    -Measures of comorbidity (such as Charlson comorbidity index or isolated comorbidities of interest)
    Concept-based:
  • Condition groups (SNOMED + descendants), >=1 occurrence during the interval
  • Drug era groups (ATC/RxNorm + descendants), >=1 day during the interval which overlaps with at least 1 drug era
    Cohort-based: (to be added if relevant from lists)

Cohort definition: PWA

Persons in secondary target cohorts:
For cohorts by surgical intervention: PWA – partial wrist arthrodesis (will capture RSL, RL, other midcarpal fusions)
● have a record of a first partial wrist arthrodesis (index event)

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

Cohort definition: Rheumatoid arthritis

Persons in secondary target cohorts:
For cohorts by disease aetiology: Rheumatoid arthritis
● have a record of a first surgery for wrist arthritis (index event)
● have a record of rheumatoid arthritis any time prior to and including the date of the index event

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

Cohort definition: wrist arthroscopy

Persons in secondary target cohorts:
For cohorts by surgical intervention: wrist arthroscopy
● have a record of wrist arthroscopy (index event)
● have a record of SLAC, SNAC, Kienbocks disease, Preisers disease, Rheumatoid arthritis or crystalline deposition any time prior to and including the date of index event

  • Initial draft of cohort
  • Run on sites
  • Modifications per site or clinical input

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