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

Abstract

BackgroundA 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.ObjectiveAs 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.MethodsFor 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.ResultsIn 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.ConclusionsOur 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.

Incorporation of Personal Single Nucleotide Polymorphism (SNP) Data into a National Level Electronic Health Record for Disease Risk Assessment, Part 3: An Evaluation of SNP Incorporated National Health Information System of Turkey for Prostate Cancer

“…In envirobehavioral and clinical evaluation, it was found that patient “03-huD889CC” had previously been diagnosed with syphilis. In prior publications, syphilis has been reported as a risk factor for prostate cancer [ 2 ]. The healthy individuals, who had a higher risk than controls, namely “06-hu56B3B6”, had basal cell carcinoma, and “21-huAC827A” had hypogonadism, that is a low level of testosterone.…”

“…The healthy individuals, who had a higher risk than controls, namely “06-hu56B3B6”, had basal cell carcinoma, and “21-huAC827A” had hypogonadism, that is a low level of testosterone. And both of these clinical conditions are known to decrease the prostate cancer risk [ 1 , 2 ]. Also, “06-hu56B3B6” and “17-huA720D3” used several risky, protective drugs and supplements regarding prostate cancer risk.…”

“…The need for a structured knowledge base, decision support approaches, systems for reporting, and risk assessment are addressed as well. Next, the NHIS-T system is overviewed, and architectural extensions to the NHIS-T for the integration of the SNP data are proposed [ 2 ]. Additionally, we have presented our design and developmental process for the complementary components of this system, for example, a knowledge base, Clinicogenomic Knowledge Base, (ClinGenKB), and end-user application, Clinicogenomic Web Application, (ClinGenWeb).…”

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

“…In this work, as an initial attempt to develop a sophisticated infrastructure, we focused to incorporate the personal SNP data into NHIS-T for disease risk assessment, and evaluated the performance of various predictive models for prostate cancer cases. We presented our work as three parts: (1) a literature review for requirements, (2) the incorporation of SNP into the NHIS-T [ 18 ], and (3) an evaluation of SNP incorporated into NHIS-T for prostate cancer [ 19 ]. In this part, the scientific literature was reviewed, and the requirements were extracted regarding SNP data integrated EMRs/EHRs.…”

An ancillary genomics system to support the return of pharmacogenomic results

“…Many institutions have adopted genetic testing as part of clinical care, with some exploring how computable representations of genetic and genomic results in the electronic health record (EHR) can facilitate clinical decision support (CDS). [1][2][3][4][5][6][7][8] However, despite established standards for the computable representation of these results, 9 this level of integration has not seen wide adoption outside of the research setting. 10,11 Genetic test results are generally returned as a plain-text representation of the interpretation report and transmitted using the Health Level 7 (HL7) v2 standard, or more commonly as PDFs that must be scanned from a fax or downloaded from an external laboratory portal.…”