Developing automated methods for disease subtyping in UK Biobank: an exemplar study on stroke.

Kristiina Rannikmae, Honghan Wu, Steven Tominey, William N Whiteley, Naomi Allen, Cathie L M Sudlow

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Background: Better phenotyping of routinely collected coded data would be useful for research and health improvement. For example, the precision of coded data for hemorrhagic stroke (intracerebral hemorrhage [ICH] and subarachnoid hemorrhage [SAH]) may be as poor as <50%. This work aimed to investigate the feasibility and added value of automated methods applied to clinical radiology reports to improve stroke subtyping. Methods: From a sub-population of 17,249 Scottish UK Biobank participants, we ascertained those with an incident stroke code in hospital, death record or primary care administrative data by September 2015, and ≥1 clinical brain scan report. We used a combination of natural language processing and clinical knowledge inference on brain scan reports to assign a stroke subtype (ischemic vs ICH vs SAH) for each participant and assessed performance by precision and recall at entity and patient levels. Results: Of 225 participants with an incident stroke code, 207 had a relevant brain scan report and were included in this study. Entity level precision and recall ranged from 78% to 100%. Automated methods showed precision and recall at patient level that were very good for ICH (both 89%), good for SAH (both 82%), but, as expected, lower for ischemic stroke (73%, and 64%, respectively), suggesting coded data remains the preferred method for identifying the latter stroke subtype. Conclusions: Our automated method applied to radiology reports provides a feasible, scalable and accurate solution to improve disease subtyping when used in conjunction with administrative coded health data. Future research should validate these findings in a different population setting.
Original languageEnglish
JournalBmc medical informatics and decision making
Publication statusPublished - 15 Jun 2021

Keywords / Materials (for Non-textual outputs)

  • NLP
  • Stroke
  • disease subtyping
  • Brain scan
  • Natural Language Processing


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