Genetic testing knowledge base (GTKB) towards individualized genetic test recommendation - An experimental study

Qian Zhu, Hongfang Liu, Christopher G. Chute, Matthew Ferber

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

The gap between a large growing number of genetic tests and a suboptimal clinical workflow of incorporating these tests into regular clinical practice poses barriers to effective reliance on advanced genetic technologies to improve quality of healthcare. A promising solution to encourage and assist physicians to incorporate genetic tests in their clinical practice is an intelligent genetic test recommendation system for 1) providing a comprehensive view of genetic tests as education resources; 2) recommending the most appropriate genetic tests to patients based on clinical evidence. In this paper, we introduce a genetic testing knowledge base, called GTKB, which was designed to support further individualized genetic test recommendation. More specifically, we extracted clinical characteristics identified from Electronic Health Records (EHRs) that have been used as phenotypic information for linked archived biological material to accelerate research in individualized medicine, and well-documented public genetic testing resources including Genetic Testing Registry (GTR) and published genetic testing guidelines (GTG) to construct a genetic test orientated knowledge base, ultimately supporting genetic test recommendation. An experimental study for 'wilson disease mutation screen test' has been conducted to demonstrate the identification of salient clinical characteristics and the process of incorporating EHR derived phenotypes into the GTKB construction.

Original languageEnglish (US)
Title of host publicationProceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
EditorsHuiru Zheng, Xiaohua Tony Hu, Yadong Wang, Jin-Kao Hao, David Gilbert, Daniel Berrar, Kwang-Hyun Cho, Werner Dubitzky
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages574-577
Number of pages4
ISBN (Electronic)9781479956692
DOIs
StatePublished - Dec 29 2014
Event2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014 - Belfast, United Kingdom
Duration: Nov 2 2014Nov 5 2014

Publication series

NameProceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014

Other

Other2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
CountryUnited Kingdom
CityBelfast
Period11/2/1411/5/14

Keywords

  • Genetic test
  • Individualized medicine
  • electronic health record
  • wilson disease

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

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  • Cite this

    Zhu, Q., Liu, H., Chute, C. G., & Ferber, M. (2014). Genetic testing knowledge base (GTKB) towards individualized genetic test recommendation - An experimental study. In H. Zheng, X. T. Hu, Y. Wang, J-K. Hao, D. Gilbert, D. Berrar, K-H. Cho, & W. Dubitzky (Eds.), Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014 (pp. 574-577). [6999223] (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2014.6999223