Farr Institute London Short Courses


Phenotyping methods for linked EHRs - CALIBER

Primary and Secondary care records are increasingly being linked for use in research. These data, however, are collected as part of routine care or for administrative purposes and a significant amount of work is required to build robust and accurate definitions of clinical concepts that can used to identify cases for further study.

In this course we present the basic theory behind the extraction of phenotype data from combined data resources such as CALIBER.

Learning Objectives

Through this practical course, participants will:

  • become familiar with two contemporary primary and secondary data sources (CPRD and HES);
  • learn what types of EHR data are collected and the different ways in which data are recorded;
  • understand how to combine linked EHR data sources to define disease cases. 

Outline Timetable

Time Session Led by
09:00-09:30 Registration and coffee  
09:30-10:30 Phenotyping electronic health records for research - theory Arturo Gonzalez-Izquierdo
10:30-10:45 Case study: Phenotyping Cancer Costantinos Parisinos
10:45-11:00 Coffee  
11:00-11:45 Phenotyping Reumathoid Arthritis Mar Pujades-Rodriguez
11:45-12:15 Practical
Arturo Gonzalez-Izquierdo
12:15-13:15 Lunch  
13:15-14:15 Practical Arturo Gonzalez-Izquierdo
14:15-15:15 Validating phenotypes across linked data sources Mar Pujades-Rodriguez
15:15-15:30 Case study: Phenotyping myocardial infarction (UK Biobank) Ghazaleh Fatemifar
15:30-15:45 Coffee  
15:45-16:00 Case study: Symptoms and signs Hannah Evans
16:00-16:45 Alternative methods - next generation phenotyping Spiros Denaxas
16:45-17:00 Q&A session Arturo Gonzalez-Izquierdo

Course Team

Dr Arturo Gonzalez-Izquierdo (Lead Tutor)
Dr Mar Pujades-Rodriguez (Lead Tutor)
Dr Spiros Denaxas
Ms Hannah Evans
Dr Ghazaleh Fatemifar
Dr Constantinos Parisinos