Incorporation of personal Single Nucleotide Polymorphism (SNP) data into a national level electronic health record for disease risk assessment, part 2: The incorporation of SNP into the national health information system of Turkey

Beyan T., AYDIN SON Y.

Journal of Medical Internet Research, vol.16, no.8, 2014 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 16 Issue: 8
  • Publication Date: 2014
  • Doi Number: 10.2196/medinform.3555
  • Journal Name: Journal of Medical Internet Research
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Emerging Sources Citation Index (ESCI), Scopus
  • Keywords: health information systems, clinical decision support systems, disease risk model, electronic health record, epigenetics, personalized medicine, single nucleotide polymorphism
  • Middle East Technical University Affiliated: Yes


©Timur Beyan, Yeşim Aydin Son.Background: A personalized medicine approach provides opportunities for predictive and preventive medicine. Using genomic, clinical, environmental, and behavioral data, the tracking and management of individual wellness is possible. A prolific way to carry this personalized approach into routine practices can be accomplished by integrating clinical interpretations of genomic variations into electronic medical record (EMR)s/electronic health record (EHR)s systems. Today, various central EHR infrastructures have been constituted in many countries of the world, including Turkey. Objective: As an initial attempt to develop a sophisticated infrastructure, we have concentrated on incorporating the personal single nucleotide polymorphism (SNP) data into the National Health Information System of Turkey (NHIS-T) for disease risk assessment, and evaluated the performance of various predictive models for prostate cancer cases. We present our work as a miniseries containing three parts: (1) an overview of requirements, (2) the incorporation of SNP into the NHIS-T, and (3) an evaluation of SNP data incorporated into the NHIS-T for prostate cancer. Methods: For the second article of this miniseries, we have analyzed the existing NHIS-T and proposed the possible extensional architectures. In light of the literature survey and characteristics of NHIS-T, we have proposed and argued opportunities and obstacles for a SNP incorporated NHIS-T. A prototype with complementary capabilities (knowledge base and end-user applications) for these architectures has been designed and developed. Results: In the proposed architectures, the clinically relevant personal SNP (CR-SNP) and clinicogenomic associations are shared between central repositories and end-users via the NHIS-T infrastructure. To produce these files, we need to develop a national level clinicogenomic knowledge base. Regarding clinicogenomic decision support, we planned to complete interpretation of these associations on the end-user applications. This approach gives us the flexibility to add/update envirobehavioral parameters and family health history that will be monitored or collected by end users. Conclusions: Our results emphasized that even though the existing NHIS-T messaging infrastructure supports the integration of SNP data and clinicogenomic association, it is critical to develop a national level, accredited knowledge base and better end-user systems for the interpretation of genomic, clinical, and envirobehavioral parameters.