Integrating Genetic Data into Electronic Health Records: Medical Geneticists' Perspectives

Ayatollahi, Haleh; Hosseini, Seyedeh Fatemeh; Hemmat, Morteza

doi:10.4258/hir.2019.25.4.289

Cited by 16 publications

(14 citation statements)

References 19 publications

(55 reference statements)

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“…Therefore, genetic testing, especially next generation sequencing, is an established test method in clinical managements (40,41). Integrating genetic and clinical data enhances the care quality for the patients as well as their families (40)(41)(42)(43).…”

Section: Discussionmentioning

confidence: 99%

Late-Onset Ornithine Transcarbamylase Deficiency and Variable Phenotypes in Vietnamese Females With OTC Mutations

Nguyen

et al. 2020

Front. Pediatr.

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Background: Ornithine transcarbamylase deficiency (OTCD) is an X-linked recessive disorder and the most common error of the urea cycle, caused by the mutations in the OTC gene. Due to X-inactivation, 15-20% of female carriers present symptoms of OTCD at late onset. Early diagnosis of OTCD by molecular analysis in females is highly desirable. The aim of the study was to identify the mutations in two unrelated Vietnamese girls suspected with OTCD and the carriers in their families for definitive diagnosis and proper counseling. Case Presentation: Two patients presented with an acute encephalopathy at the first admission. Biochemical tests revealed hyperammonemia, hyperlactatemia, elevated glutamine level, elevated transaminase, elevated urinary orotic and uracil acid levels, and disorder of prothrombin time. Brain magnetic resonance imaging indicated cerebral edema. Based on the clinical and laboratory results, the two patients were diagnosed with urea cycle disorders. Therefore, the two patients were managed by stopping feeding, with infused glucose, l-carnitine, l-arginine, and sodium benzoate, and with hemofiltration. The two patients were alert and recovered with normal blood ammonia levels after 72 h of treatment. The family history of patient 1 showed that her brother died at 4 days of age due to a coma and dyspnea, while her parents were asymptomatic. Variable phenotypes were observed in three generations of the patient 2's family, including asymptomatic (mother), affected female adults dying at the first symptom (grandmother and aunt), and affected males dying in the first week of life (uncle, cousin, and siblings). Whole-exome sequencing showed two mutations in the OTC gene, including one novel missense mutation, c.365A>T, in the patient 1 and one previously reported splicing mutation, c.717+1G>A, in the patient 2. The two mutations are evaluated as likely pathogenic and pathogenic, respectively, according to the recommendations of the American College of Medical Genetics and Genomics (ACMG). Genetic analyses in the families indicated the mothers were heterozygous. Nguyen et al. Vietnamese Females With OTC Mutations Conclusion: Clinical, biochemical, and molecular findings accurately diagnosed the two patients with late-onset OTCD. Our results explained the genetic causes and proposed the risk in the patients' families, which could be useful for genetic counseling and monitoring in prenatal diagnosis.

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Section: Discussionmentioning

confidence: 99%

Late-Onset Ornithine Transcarbamylase Deficiency and Variable Phenotypes in Vietnamese Females With OTC Mutations

Nguyen

et al. 2020

Front. Pediatr.

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“…The structured analysis of the documents consists of the object's type, and explanation of its attributes and related methods are conducted in this step; • Proposing an accessible object-oriented design for a typical blood bank's inventory management process considering user requirements and information collected during the previous steps. This step is conducted through objectoriented programming [18] using unified modeling language (UML) [19,20].…”

Section: Methodsmentioning

confidence: 99%

“…Proposing an accessible object-oriented design for a typical blood bank’s inventory management process considering user requirements and information collected during the previous steps. This step is conducted through object-oriented programming [ 18 ] using unified modeling language (UML) [ 19 , 20 ].…”

Section: Case Descriptionmentioning

confidence: 99%

Dynamic Demand-Centered Process-Oriented Data Model for Inventory Management of Hemovigilance Systems

2021

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The variation of demand, limited supply, and perishability of blood products results in a high degree of uncertainty and complexity in hemovigilance systems [1]. The effective management of blood products in this segment of the blood supply chain plays a crucial role in decreasing unnecessary costs, wastage, and shortages [2]. One of the primary concerns of blood banks, as an essential part of the blood transfusion chain, is identifying and separating the system's activities and components. Hence, user requirements should be recognized to organize the resources and functions that

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“…The remaining 92% (73/80) of requirements can be found in Multimedia Appendix 1 requirements. The first requirement, DP-01, was mentioned in 18 publications [10,12,34,39,40,46,[48][49][50][51][52][53][54][55][56][57][58][59] and, therefore, the most cited requirement of this study. It describes the need to map data to international terminology standards such as SNOMED-CT, LOINC, ICD, ATC, ICD-O, CPT, and RxNorm as part of processing.…”

Section: Data Processingmentioning

confidence: 99%

Functional Requirements for Medical Data Integration into Knowledge Management Environments: Requirements Elicitation Approach Based on Systematic Literature Analysis

Kinast¹,

Ulrich²,

Bergh³

et al. 2023

J Med Internet Res

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Background In patient care, data are historically generated and stored in heterogeneous databases that are domain specific and often noninteroperable or isolated. As the amount of health data increases, the number of isolated data silos is also expected to grow, limiting the accessibility of the collected data. Medical informatics is developing ways to move from siloed data to a more harmonized arrangement in information architectures. This paradigm shift will allow future research to integrate medical data at various levels and from various sources. Currently, comprehensive requirements engineering is working on data integration projects in both patient care– and research-oriented contexts, and it is significantly contributing to the success of such projects. In addition to various stakeholder-based methods, document-based requirement elicitation is a valid method for improving the scope and quality of requirements. Objective Our main objective was to provide a general catalog of functional requirements for integrating medical data into knowledge management environments. We aimed to identify where integration projects intersect to derive consistent and representative functional requirements from the literature. On the basis of these findings, we identified which functional requirements for data integration exist in the literature and thus provide a general catalog of requirements. Methods This work began by conducting a literature-based requirement elicitation based on a broad requirement engineering approach. Thus, in the first step, we performed a web-based systematic literature review to identify published articles that dealt with the requirements for medical data integration. We identified and analyzed the available literature by applying the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. In the second step, we screened the results for functional requirements using the requirements engineering method of document analysis and derived the requirements into a uniform requirement syntax. Finally, we classified the elicited requirements into a category scheme that represents the data life cycle. Results Our 2-step requirements elicitation approach yielded 821 articles, of which 61 (7.4%) were included in the requirement elicitation process. There, we identified 220 requirements, which were covered by 314 references. We assigned the requirements to different data life cycle categories as follows: 25% (55/220) to data acquisition, 35.9% (79/220) to data processing, 12.7% (28/220) to data storage, 9.1% (20/220) to data analysis, 6.4% (14/220) to metadata management, 2.3% (5/220) to data lineage, 3.2% (7/220) to data traceability, and 5.5% (12/220) to data security. Conclusions The aim of this study was to present a cross-section of functional data integration–related requirements defined in the literature by other researchers. The aim was achieved with 220 distinct requirements from 61 publications. We concluded that scientific publications are, in principle, a reliable source of information for functional requirements with respect to medical data integration. Finally, we provide a broad catalog to support other scientists in the requirement elicitation phase.

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Integrating Genetic Data into Electronic Health Records: Medical Geneticists' Perspectives

Cited by 16 publications

References 19 publications

Late-Onset Ornithine Transcarbamylase Deficiency and Variable Phenotypes in Vietnamese Females With OTC Mutations

Late-Onset Ornithine Transcarbamylase Deficiency and Variable Phenotypes in Vietnamese Females With OTC Mutations

Dynamic Demand-Centered Process-Oriented Data Model for Inventory Management of Hemovigilance Systems

Functional Requirements for Medical Data Integration into Knowledge Management Environments: Requirements Elicitation Approach Based on Systematic Literature Analysis

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