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Predictive value of genomic screening: cross-sectional study of cystic fibrosis in 50,788 electronic health records.

ABSTRACT: Doubts have been raised about the value of DNA-based screening for low-prevalence monogenic conditions following reports of testing this approach using available electronic health record (EHR) as the sole phenotyping source. We hypothesized that a better model for EHR-focused examination of DNA-based screening is Cystic Fibrosis (CF) since the diagnosis is proactively sought within the healthcare system. We reviewed CFTR variants in 50,778 exomes. In 24 cases with bi-allelic pathogenic CFTR variants, there were 21 true-positives. We considered three cases "potential" false-positives due to limitations in available EHR phenotype data. This genomic screening exhibited a positive predictive value of 87.5%, negative predictive value of 99.9%, sensitivity of 95.5%, and a specificity of 99.9%. Despite EHR-based phenotyping limitations in three cases, the presence or absence of pathogenic CFTR variants has strong predictive value for CF diagnosis when EHR data is used as the sole phenotyping source. Accurate ascertainment of the predictive value of DNA-based screening requires condition-specific phenotyping beyond available EHR data.

SUBMITTER: Sugunaraj JP

PROVIDER: S-EPMC6726623 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Predictive value of genomic screening: cross-sectional study of cystic fibrosis in 50,788 electronic health records.

Sugunaraj J P JP Brosius H M HM Murray M F MF Manickam K K Stamm J A JA Carey D J DJ Mirshahi U L UL

NPJ genomic medicine 20190904

Doubts have been raised about the value of DNA-based screening for low-prevalence monogenic conditions following reports of testing this approach using available electronic health record (EHR) as the sole phenotyping source. We hypothesized that a better model for EHR-focused examination of DNA-based screening is Cystic Fibrosis (CF) since the diagnosis is proactively sought within the healthcare system. We reviewed <i>CFTR</i> variants in 50,778 exomes. In 24 cases with bi-allelic pathogenic <i ...[more]

PMID: 31508243

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Project description:BackgroundElectronic personal health records (ePHRs) are secure Web-based tools that enable individuals to access, manage, and share their medical records. England recently introduced a nationwide ePHR called Patient Online. As with ePHRs in other countries, adoption rates of Patient Online remain low. Understanding factors affecting patients' ePHR use is important to increase adoption rates and improve the implementation success of ePHRs.ObjectiveThis study aimed to examine factors associated with patients' use of ePHRs in England.MethodsThe unified theory of acceptance and use of technology was adapted to the use of ePHRs. To empirically examine the adapted model, a cross-sectional survey of a convenience sample was carried out in 4 general practices in West Yorkshire, England. Factors associated with the use of ePHRs were explored using structural equation modeling.ResultsOf 800 eligible patients invited to take part in the survey, 624 (78.0%) returned a valid questionnaire. Behavioral intention (BI) was significantly influenced by performance expectancy (PE; beta=.57, P<.001), effort expectancy (EE; beta=.16, P<.001), and perceived privacy and security (PPS; beta=.24, P<.001). The path from social influence to BI was not significant (beta=.03, P=.18). Facilitating conditions (FC) and BI significantly influenced use behavior (UB; beta=.25, P<.001 and beta=.53, P<.001, respectively). PE significantly mediated the effect of EE and PPS on BI (beta=.19, P<.001 and beta=.28, P=.001, respectively). Age significantly moderated 3 paths: PE→BI, EE→BI, and FC→UB. Sex significantly moderated only the relationship between PE and BI. A total of 2 paths were significantly moderated by education and internet access: EE→BI and FC→UB. Income moderated the relationship between FC and UB. The adapted model accounted for 51% of the variance in PE, 76% of the variance in BI, and 48% of the variance in UB.ConclusionsThis study identified the main factors that affect patients' use of ePHRs in England, which should be taken into account for the successful implementation of these systems. For example, developers of ePHRs should involve patients in the process of designing the system to consider functions and features that fit patients' preferences and skills to ensure systems are useful and easy to use. The proposed model accounted for 48% of the variance in UB, indicating the existence of other, as yet unidentified, factors that influence the adoption of ePHRs. Future studies should confirm the effect of the factors included in this model and identify additional factors.

Project description:To compare online and paper-based screening for depression and anxiety in adults with cystic fibrosis (CF).Cross-sectional study in CF clinics in Ireland and through the Cystic Fibrosis Ireland online community.160 adult patients aged 18 or above were recruited. Of these, 147 were included in the analysis; 83 online and 64 paper-based. The remaining 13 were excluded because of incomplete data.Depression and anxiety were measured using the Hospital Anxiety and Depression Scale (HADS). Data on pulmonary function (forced expiratory volume in 1 s %) and body mass index were self-reported based on clinical assessments. Sociodemographic data were collected.Compared with the paper-based participants, the online participants were more likely to be female (61.7% vs 48.4%), older (mean 32.2 vs 28.2 years) and were more likely to be married (32.5% vs 15.6%), living with their spouse or partner (42.5% vs 22.6%) and working either full time (33.7% vs 15.9%) or part time (30.1%vs 17.5%). The prevalence rates of elevated anxiety and depression were not significantly different (P=0.71 and P=0.56). HADS anxiety and depression scores were not statistically different between online (P=0.83) and paper-based (P=0.92) participants based on Mann-Whitney U test. A significant negative correlation was found between depression and pulmonary function (r=-0.39, P=0.01) and anxiety and pulmonary function (r=-0.36, P=0.02). Based on Cronbach's alpha, there were no statistically significant differences between the online and paper-based participants on the internal consistency of the HADS anxiety (P=0.073) and depression (P=0.378) scales.Our findings suggest that online and paper-based screening for depression and anxiety in adult patients with CF yield comparable findings on prevalence rates and scores, associations with health and internal consistency of subscales. This study highlights that online screening offers an alternative method to paper-based screening. Further research with a larger sample and assessment of measurement equivalence between online and paper based screening is needed to confirm our results.

Dataset Information

Predictive value of genomic screening: cross-sectional study of cystic fibrosis in 50,788 electronic health records.

Publications

Predictive value of genomic screening: cross-sectional study of cystic fibrosis in 50,788 electronic health records.

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