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Refining the structure and content of clinical genomic reports.

ABSTRACT: To effectively articulate the results of exome and genome sequencing we refined the structure and content of molecular test reports. To communicate results of a randomized control trial aimed at the evaluation of exome sequencing for clinical medicine, we developed a structured narrative report. With feedback from genetics and non-genetics professionals, we developed separate indication-specific and incidental findings reports. Standard test report elements were supplemented with research study-specific language, which highlighted the limitations of exome sequencing and provided detailed, structured results, and interpretations. The report format we developed to communicate research results can easily be transformed for clinical use by removal of research-specific statements and disclaimers. The development of clinical reports for exome sequencing has shown that accurate and open communication between the clinician and laboratory is ideally an ongoing process to address the increasing complexity of molecular genetic testing.

SUBMITTER: Dorschner MO

PROVIDER: S-EPMC4077592 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature

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Refining the structure and content of clinical genomic reports.

Dorschner Michael O MO Amendola Laura M LM Shirts Brian H BH Kiedrowski Lesli L Salama Joseph J Gordon Adam S AS Fullerton Stephanie M SM Tarczy-Hornoch Peter P Byers Peter H PH Jarvik Gail P GP

American journal of medical genetics. Part C, Seminars in medical genetics 20140310 1

To effectively articulate the results of exome and genome sequencing we refined the structure and content of molecular test reports. To communicate results of a randomized control trial aimed at the evaluation of exome sequencing for clinical medicine, we developed a structured narrative report. With feedback from genetics and non-genetics professionals, we developed separate indication-specific and incidental findings reports. Standard test report elements were supplemented with research study- ...[more]

PMID: 24616401

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Project description:BackgroundTo implement standardized machine-processable clinical sequencing reports in an electronic health record (EHR) system, the International Organization for Standardization Technical Specification (ISO/TS) 20428 international standard was proposed for a structured template. However, there are no standard implementation guidelines for data items from the proposed standard at the clinical site and no guidelines or references for implementing gene sequencing data results for clinical use. This is a significant challenge for implementation and application of these standards at individual sites.ObjectiveThis study examines the field utilization of genetic test reports by designing the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) for genomic data elements based on the ISO/TS 20428 standard published as the standard for genomic test reports. The goal of this pilot is to facilitate the reporting and viewing of genomic data for clinical applications. FHIR Genomics resources predominantly focus on transmitting or representing sequencing data, which is of less clinical value.MethodsIn this study, we describe the practical implementation of ISO/TS 20428 using HL7 FHIR Genomics implementation guidance to efficiently deliver the required genomic sequencing results to clinicians through an EHR system.ResultsWe successfully administered a structured genomic sequencing report in a tertiary hospital in Korea based on international standards. In total, 90 FHIR resources were used. Among 41 resources for the required fields, 26 were reused and 15 were extended. For the optional fields, 28 were reused and 21 were extended.ConclusionsTo share and apply genomic sequencing data in both clinical practice and translational research, it is essential to identify the applicability of the standard-based information system in a practical setting. This prototyping work shows that reporting data from clinical genomics sequencing can be effectively implemented into an EHR system using the existing ISO/TS 20428 standard and FHIR resources.

Project description:Rupture of abdominal aortic aneurysm (AAA) is associated with high mortality rates. Risk of rupture is multi-factorial involving AAA geometric configuration, vessel tortuosity, and the presence of intraluminal pathology. Fluid structure interaction (FSI) simulations were conducted in patient based computed tomography scans reconstructed geometries in order to monitor aneurysmal disease progression from normal aortas to non-ruptured and contained ruptured AAA (rAAA), and the AAA risk of rupture was assessed. Three groups of 8 subjects each were studied: 8 normal and 16 pathological (8 non-ruptured and 8 rAAA). The AAA anatomical structures segmented included the blood lumen, intraluminal thrombus (ILT), vessel wall, and embedded calcifications. The vessel wall was described with anisotropic material model that was matched to experimental measurements of AAA tissue specimens. A statistical model for estimating the local wall strength distribution was employed to generate a map of a rupture potential index (RPI), representing the ratio between the local stress and local strength distribution. The FSI simulations followed a clear trend of increasing wall stresses from normal to pathological cases. The maximal stresses were observed in the areas where the ILT was not present, indicating a potential protective effect of the ILT. Statistically significant differences were observed between the peak systolic stress and the peak stress at the mean arterial pressure between the three groups. For the ruptured aneurysms, where the geometry of intact aneurysm was reconstructed, results of the FSI simulations clearly depicted maximum wall stress at the a priori known location of rupture. The RPI mapping indicated several distinct regions of high RPI coinciding with the actual location of rupture. The FSI methodology demonstrates that the aneurysmal disease can be described by numerical simulations, as indicated by a clear trend of increasing aortic wall stresses in the studied groups, (normal aortas, AAAs and rAAAs). Ultimately, the results demonstrate that FSI wall stress mapping and RPI can be used as a tool for predicting the potential rupture of an AAA by predicting the actual rupture location, complementing current clinical practice by offering a predictive diagnostic tool for deciding whether to intervene surgically or spare the patient from an unnecessary risky operation.

Project description:BACKGROUND: The objective of the study was to analyse the evolution of Bordetella pertussis population and the influence of herd immunity in different areas of the world where newborns and infants are highly vaccinated. METHODOLOGY: The analysis was performed using DNA microarray on 15 isolates, PCR on 111 isolates as well as GS-FLX sequencing technology on 3 isolates and the B. pertussis reference strain, Tohama I. PRINCIPAL FINDINGS: Our analyses demonstrate that the current circulating isolates are continuing to lose genetic material as compared to isolates circulating during the pre-vaccine era whatever the area of the world considered. The lost genetic material does not seem to be important for virulence. Our study confirms that the use of whole cell vaccines has led to the control of isolates that were similar to vaccine strains. GS-FLX sequencing technology shows that current isolates did not acquire any additional material when compared with vaccine strains or with isolates of the pre-vaccine era and that the sequenced strain Tohama I is not representative of the isolates. Furthermore, this technology allowed us to observe that the number of Insertion Sequence elements contained in the genome of the isolates is temporally increasing or varying between isolates. CONCLUSIONS: B. pertussis adaptation to humans is still in progress by losing genetic material via Insertion Sequence elements. Furthermore, recent isolates did not acquire any additional material when compared with vaccine strains or with isolates of the pre-vaccine era. Herd immunity, following intensive vaccination of infants and children with whole cell vaccines, has controlled isolates similar to the vaccine strains without modifying significantly the virulence of the isolates. With the replacement of whole cell vaccines by subunit vaccines, containing only few bacterial antigens targeting the virulence of the bacterium, one could hypothesize the circulation of isolates expressing less or modified vaccine antigens.

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Refining the structure and content of clinical genomic reports.

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Refining the structure and content of clinical genomic reports.

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