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Poster presented at SAPC 2013 at SAPC conference, Nottingham on 3/07/2013. David A. Springate, Evangelos Kontopantelis, David Reeves Primary Care Research group, Centre for Biostatistics, University of Manchester Publications in healthcare research using electronic medical records (EMR) databases are increasing at an exponential rate. Because of the amount of data available in large EMR databases, it has been suggested that they may be able to provide results of equal validity to randomised controlled trials. EMR studies rely on clinical codes (such as Read codes) to provide standardised and expressive means for medical professionals to record clinical information. The validity of these studies is dependent on (among other things) the validity of the clinical codes that are used to define the population of interest and their disease conditions. Clinical codes should be held to scrutiny in the same way as other methods since if the inclusion/exclusion criteria for a given condition is invalid then so will be the rest of the study. Also, it should be possible to replicate a given study (e.g. in a different EMR database) based on the information provided in the original paper, not possible if the lists of clinical code definitions are not provided. Furthermore, access to historical code-lists allows researchers and clinicians to make incremental improvements to disease and other definitions, building on and avoiding unnecessary replication of previous work There is currently no obligation to publish clinical code lists and no centralised repository to hold them. Consequently, the vast majority of database studies do not publish their clinical codes and as such are impossible to be fully validated or replicated. To illustrate this, we looked at 45 UK case-control EMR database studies indexed on PubMed and found that only five had any record of any clinical codes in their methodology sections. Of these five, only two published code lists in online appendices and only one provided a full set of codes that would allow for proper replication of the study. We have built an online repository where researchers can deposit their clinical codes at the time of publication in a standardised way, as well as download historical code lists from previous studies. We have uploaded a complete set of Read codes for all versions of the Quality and Outcomes Framework and encourage all code lists published by major medical organisations to be deposited. Reproducibility and validity of EMR database studies would be greatly aided if deposition of all clinical codes was a prerequisite for publication of all future database studies. The ability to build on code lists from historical studies during the development of new code lists will also ease a considerable bottleneck in database study design, removing the need for a huge deal of “reinventing of the wheel” each time a new EMR-based study is undertaken.

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Page 1: Improving validity and reproducibility of primary care database studies: An online clinical codes repository

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Funded by the National Institute for Health Research (NIHR) School for Primary Care Research.

This is a summary of independent research funded by the NIHR. The views expressed are those

of the authors and not necessarily those of the NHS, the NIHR or the Department of Health.

Background

Centre for Primary Care: www.population-health.manchester.ac.uk/primarycare

Centre for Biostatistics: www.population-health.manchester.ac.uk/biostatistics

For example, in 45 UK PCD case-control studies into diabetes:

Only 5 reported ANY clinical codes in the paper

Only 2 published lists of codes in an online appendix

Only 1 Provided a full set of code lists for the study

So, in 44 out of 45 studies, given the original paper, there is no

way of independently assessing the validity of how diseases,

exposures, treatments or outcomes were defined or of

replicating the research.

1. Shephard et al. Family Practice 2011; 28:4

2. Brookhart et al. Medical Care 2010; 48:6

3. Jordon et al. Family Practice 2004; 21:4.

4. Smeeth et al. Family Practice 2006; 23:5

• All historical code-lists

published on

clinicalcodes.org are freely

downloadable

• The repository will host the

full set of Read codes from

all versions of the Quality

and Outcomes Framework

(QOF) from 2004 – 2012

• Other clinical codes (e.g.

SNOMED, ICD-10) can

also be deposited

• Can also be used to host

database-specific coding

information (e.g. CPRD

consultation types)

• Codes from other

Electronic medical record

database studies can also

be hosted

The repository would be most effective if…

• Deposition of all clinical codes was a prerequisite for publication of all

future PCD studies

• Funding bodies included deposition as a pre-condition for funding

• Authors of historical PCD studies were encouraged to deposit their

codes post-publication

We are working to automate up/download via an API

Challenges

Improving validity and reproducibility

of primary care database studies:

An online clinical codes repository

University of Manchester Centre for Primary Care / Centre for Biostatistics

David A. Springate, Evangelos Kontopantelis, David Reeves and Ivan Olier

Knowledge of the clinical codes used in a PCD study is critical to

determining its validity because…

1. The ways in which populations, diseases, exposures, treatments and

outcomes are defined through code lists can have a large impact on the

results

2. If a code list for a study is unavailable, that study is impossible to

properly validate or replicate

However, there is currently no…

• Obligation on researchers to publish clinical codes lists by journals or

research councils

• Centralised repository to hold archived clinical code lists

This means that the vast majority of published PCD studies do not

publish their clinical codes and so are impossible to properly validate.

The problem

We are developing an online repository where researchers can freely

deposit their lists of clinical codes at the time of publication in a

standardised way, along with links to the original paper and meta-data on

the codes used.

www.ClinicalCodes.org

• Clinical codes can be held to scrutiny and peer-review in the same way

as any other research methods

• Replication of previously published studies (e.g. in different databases) is

facilitated

• Access to historical code-lists allows researchers and clinicians to make

incremental improvements to disease (and other) definitions, building on

and avoiding unnecessary replication of previous work

• Clinical code lists can become a resource for future research in their own

right (e.g. tracking disease definitions through time)

Advantages

[email protected]

www.clinicalcodes.org – online from July 2013

@medcodes – follow us to keep up with updates to the repository

Contact and references

• Large Primary Care Databases (eg CPRD, Qresearch, THIN) are

increasingly used to address a wide range of research questions1

• Much research has been done into establishing the validity of statistical

analysis of PCD data, e.g. the role of confounding variables2, GP

recording quality3 and selection bias4

• BUT PCDs also rely on clinical codes (such as Read codes) to provide

standardised means for medical professionals to record clinical

information. The validity of PCD studies depends upon the validity of the

clinical codes used to define the population of interest, their disease

conditions, exposures, treatments and outcomes

New primary care

database (PCD) studies

are being published at an

exponential rate