Cancer phenotype development: A literature review

Pei Wang, Maryam Garza, Meredith Zozus

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

EHR-based, computable phenotypes can be leveraged by healthcare organizations and researchers to improve the cohort identification process. The ability to identify patient cohorts using aspects of care and outcomes based on clinical characteristics or diagnostic conditions and/or risk factors presents opportunities to researchers targeting specific populations for drug development and disease interventions. The objective of this review was to summarize the literature describing the development and use of phenotypes for cohort identification of cancer patients. A survey of the literature indexed in PubMed was performed to identify studies using EHR-based phenotypes for use in cancer studies. Specific search criteria were formulated by leveraging a phenotype identification guideline developed by the Phenotypes, Data Standards, and Data Quality Core of the NIH Health Care Systems Research Collaboratory. The final set of articles was examined further to identify 1) the cancer of interest and 2) the different approaches used for phenotype development, validation and implementation. The articles reviewed were specific to breast cancer, colorectal cancer, ovarian cancer, and lung cancer. The approaches taken for phenotype development and validation varied slightly among the relevant publications. Four studies relied on chart review, three utilized machine learning techniques, one took an ontological approach, and one utilized natural language processing (NLP).

Original languageEnglish (US)
Title of host publicationImproving Usability, Safety and Patient Outcomes with Health Information Technology
Subtitle of host publicationFrom Research to Practice
EditorsAlex Mu-Hsing Kuo, Andre Kushniruk, Francis Lau, Elizabeth M. Borycki, Gerry Bliss, Helen Monkman, Abdul Vahabpour Roudsari, John A. Bartle-Clar, Karen L. Courtney
PublisherIOS Press
Pages468-472
Number of pages5
ISBN (Electronic)9781614999508
DOIs
StatePublished - Jan 1 2019
Externally publishedYes

Publication series

NameStudies in Health Technology and Informatics
Volume257
ISSN (Print)0926-9630
ISSN (Electronic)1879-8365

Keywords

  • cancer phenotypes
  • computable phenotypes
  • electronic health records
  • phenotype development
  • secondary data use

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

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  • Cite this

    Wang, P., Garza, M., & Zozus, M. (2019). Cancer phenotype development: A literature review. In A. M-H. Kuo, A. Kushniruk, F. Lau, E. M. Borycki, G. Bliss, H. Monkman, A. V. Roudsari, J. A. Bartle-Clar, & K. L. Courtney (Eds.), Improving Usability, Safety and Patient Outcomes with Health Information Technology: From Research to Practice (pp. 468-472). (Studies in Health Technology and Informatics; Vol. 257). IOS Press. https://doi.org/10.3233/978-1-61499-951-5-468