Incorporation of personal single nucleotide polymorphism (SNP) data into a national level electronic health record for disease risk assessment, part 1: An overview of requirements

Beyan T., AYDIN SON Y.

Journal of Medical Internet Research, vol.16, no.7, 2014 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 16 Issue: 7
  • Publication Date: 2014
  • Doi Number: 10.2196/medinform.3169
  • 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, INDIVIDUAL GENETIC RISK, SYSTEMATIC METAANALYSES, ASSOCIATION, PREDICTION, ARTICLE, INFORMATION, KNOWLEDGE, VARIANTS, MEDICINE, GENOMICS
  • Middle East Technical University Affiliated: Yes


Personalized medicine approaches provide opportunities for predictive and preventive medicine. Using genomic, clinical, environmental, and behavioral data, 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 records (EMRs)/electronic health records (EHRs). Today, various central EHR infrastructures have been constituted in many countries of the world including Turkey. Objective: The objective of this study was to concentrate on incorporating the personal single nucleotide polymorphism (SNP) data into the National Health Information System of Turkey (NHIS-T) for disease risk assessment, and evaluate 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 incorporated NHIS-T for prostate cancer. Methods: For the first article of this miniseries, the scientific literature is reviewed and the requirements of SNP data integration into EMRs/EHRs are extracted and presented. Results: In the literature, basic requirements of genomic-enabled EMRs/EHRs are listed as incorporating genotype data and its clinical interpretation into EMRs/EHRs, developing accurate and accessible clinicogenomic interpretation resources (knowledge bases), interpreting and reinterpreting of variant data, and immersing of clinicogenomic information into the medical decision processes. In this section, we have analyzed these requirements under the subtitles of terminology standards, interoperability standards, clinicogenomic knowledge bases, defining clinical significance, and clinicogenomic decision support. Conclusions: In order to integrate structured genotype and phenotype data into any system, there is a need to determine data components, terminology standards, and identifiers of clinicogenomic information. Also, we need to determine interoperability standards to share information between different information systems of stakeholders, and develop decision support capability to interpret genomic variations based on the knowledge bases via different assessment approaches.