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A comparison of genomic laboratory reports and observations that may enhance their clinical utility for providers and patients.

ABSTRACT: PURPOSE:To assess clinical chromosomal microarray (CMA) genomic testing reports for the following: (a) usage of reporting elements consistent with 2011 ACMG guidelines and other elements identified in the primary literature, (b) information quality, and (c) readability. METHODS:We retrospectively analyzed genomic testing reports from 2011 to 2016 provided to, or by our laboratory to aid in clinical detection and interpretation of copy number variants. Analysis was restricted to the following sections: interpretation, recommendations, limitations, and citations. Analysis included descriptive characteristics, reporting elements, reading difficulty using the Simple Measure of Gobbledygook (SMOG), and quality ratings using a subset of questions adapted from the DISCERN-Genetics questionnaire. RESULTS:The analysis included 44 unique reports from 26 laboratories comprising four groups: specialty laboratories (SL; N = 9), reference laboratories (RL; N = 12), hospital laboratories (HL; N = 10), and university-based laboratories (UL; N = 13). There were 23 abnormal/pathogenic reports and 21 of uncertain/unknown significance. Nine laboratories did not include one or more pieces of information based on ACMG guidelines; only one of ten laboratories reported condition-specific management/treatment information when available and relevant. Average quality ratings and readability scores were not significantly different between laboratory types or result classification. CONCLUSIONS:Reporting practices for most report elements varied widely; however, readability and quality did not differ significantly between laboratory types. Management and treatment information, even for well-known conditions, are rarely included. Effectively communicating test results may be improved if certain reporting elements are incorporated. Recommendations to improve laboratory reports are provided.

SUBMITTER: Davis KW

PROVIDER: S-EPMC6625363 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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A comparison of genomic laboratory reports and observations that may enhance their clinical utility for providers and patients.

Davis Kyle Walter KW Hamby Erby Lori L Fiallos Katie K Martin Megan M Wassman Edward Robert ER

Molecular genetics & genomic medicine 20190521 7

<h4>Purpose</h4>To assess clinical chromosomal microarray (CMA) genomic testing reports for the following: (a) usage of reporting elements consistent with 2011 ACMG guidelines and other elements identified in the primary literature, (b) information quality, and (c) readability.<h4>Methods</h4>We retrospectively analyzed genomic testing reports from 2011 to 2016 provided to, or by our laboratory to aid in clinical detection and interpretation of copy number variants. Analysis was restricted to th ...[more]

PMID: 31115190

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Project description:BACKGROUND:Interprofessional collaboration is increasingly important in healthcare, but interprofessional education (IPE) faces challenges, such as different study programmes with varied schedules and campuses. These challenges can be met, in part, by using web-based virtual patients (VPs) as a tool in IPE. However, demands for relevant patient presentations and clinical practice increase when VPs are used by students from different programmes. The aim of this study was to improve the presentation of professional perspectives regarding nurses and physicians and their collaboration in order to increase the clinical authenticity of existing VPs. METHODS:Clinical observations were conducted to gain familiarity with the context. Semi-structured interviews were performed with individual nurses and physicians with experience of patients with leg ulcers. The interviews were recorded, transcribed and analysed using thematic analysis. RESULTS:The clinical observations exposed a lack of interprofessional collaboration in practice with regard to patients with leg ulcers. The interview analysis resulted in two themes: Clinical care and Organizational structure. The theme Clinical care included nursing with a holistic approach to the patient and awareness of the patient's well-being, including nutrition and home situation. The theme Organizational structure revealed a lack of teamwork in primary care. The interviewees stressed learning together and sharing responsibility, and they emphasised the importance of implementing interprofessional learning in the education of nurses and physicians in order to stimulate future teamwork. The VP should offer a broad medical history so that healthcare students are made aware of how a disease can affect the patient's social situation, and thereby illustrate the importance of interprofessional collaboration. The information should also be comprehensive and clear, leading to a diagnosis, so the student can gain clinical knowledge and build a foundation for discussion of treatment. CONCLUSIONS:Interviews and observations in clinical practice can be used to enhance authenticity in VPs for interprofessional learning. A thorough look at authentic clinical environments can enrich and improve educational settings using VPs, and it can highlight the challenges students can encounter in clinical care of the patient and in an organisation with regard to interprofessional collaboration.

Project description:The mechanisms leading to the vancomycin-intermediate Staphylococcus aureus (VISA) phenotype are incompletely understood. In an effort to identify VISA determinants, clinical hVISA strain MM66 and its 1st-step VISA mutants were compared. S. aureus microarrays, array data analysis protocols (NIAID's Pathogen Functional Genomics Resource Center), as well as comparative genomic sequencing (CGS) were utilized to determine VISA transcriptome alterations and mutations that define the MM66 VISA mechanism. In addition, whole cell autolysis, antimicrobial susceptibility tests, growth in the presence of salt, coagulase and hemolysis assays were performed to confirm VISA transcriptional alterations. Overall, 2 MM66 VISA demonstrated 85 up-regulated and 8 down-regulated genes in common. SAMMD (Staphylococcus aureus Microarray Metadatabase) analysis identified a significant differential gene expression overlap between the global stress response regulator sigB-controlled genes in MM66-3 and MM66-4. CGS analysis on a MM66 VISA revealed two mutations in: a sensory box histidine kinase (yycG) and a putative adenine phosphoribosyltransferase (apt). The yycFG two-component system has been reported to regulate whole cell autolysis and MM66 VISA demonstrated reduced whole cell autolysis. Five ssaA homologues (putative amidases) and a gene that expresses a bifunctional autolysin (atlA) controlled by YycFG were downregulated in MM66 VISA. One MM66 VISA mutant demonstrated drastic downregulation of a gene cluster (betA, gbsA, betB, and cudT) required for the osmoprotective response of S. aureus and MM66 VISA mutants demonstrated reduced growth in high salt media compared to MM66. Virulence genes were also downregulated (coa, hla, hlb, hlgA, hlgB, and hlgC) in 2 MM66 VISA mutants which also demonstrated reduced coagulase and hemolytic activities compared to MM66. pur operon genes were also upregulated in MM66 VISA and it is interesting that we have also found an apt mutation, since Apt activity can be inhibited by high AMP levels and reduces the conversion of AMP into adenine. Conclusion: Mutations in yycG and apt allow hVISA to acquire the VISA phenotype and yycFG is involved with altered autolytic activity in MM66 VISA.

Project description:ImportanceClinical genomic tests that examine the DNA sequence of large numbers of genes are commonly used in the diagnosis and management of epilepsy in pediatric patients. The permanence of genomic test result interpretations is not known.ObjectiveTo investigate the value of reinterpreting previously reported genomic test results.Design, setting, and participantsThis study retrospectively reviewed and reinterpreted genomic test results from July 1, 2012, to August 31, 2015, for pediatric patients who previously underwent genomic epilepsy testing at a single tertiary care pediatric health care facility. Reinterpretation of previously reported variants was conducted in May 2017.Main outcomes and measuresPatient reports from clinical genomic epilepsy tests were reviewed, and all reported genetic variants were reinterpreted using 2015 consensus standards and guidelines for interpreting hereditary genetic variants. Three classification tiers were used in the reinterpretation: pathogenic or likely pathogenic variant, variant of uncertain significance (VUS), or benign or likely benign variant.ResultsA total of 309 patients had genomic epilepsy tests performed (mean [SD] age, 5.6 [0.8] years; 163 [52.8%] male), and 185 patients had a genetic variant reported. The reported variants resulted in 61 patients with and 124 patients without a genetic diagnosis (VUS variants only). On reinterpretation of all reported variants, 67 of the 185 patients (36.2%) had a change in variant classification. Of the 67 patients with a genetic variant change in interpretation, 21 (31.3%) experienced a change in diagnosis. During the 5 years of the study, 19 of 61 patients (31.1%) with a genetic diagnosis and 48 of 124 patients (38.7%) with undiagnosed conditions (VUS only) had their results reclassified. Review of genomic reports issued during the final 2 years of the study identified reclassification of variants in 4 of 16 patients (25.0%) with a pathogenic or likely pathogenic variant and 11 of 41 patients (26.8%) with a VUS.Conclusions and relevanceThe identified high rate of reinterpretation in this study suggests that interpretation of genomic test results has rapidly evolved during the past 5 years. These findings suggest that reinterpretation of genomic test results should be performed at least every 2 years.

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A comparison of genomic laboratory reports and observations that may enhance their clinical utility for providers and patients.

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A comparison of genomic laboratory reports and observations that may enhance their clinical utility for providers and patients.

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