CAPICE:a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations

Exome sequencing is now mainstream in clinical practice. However, identification of pathogenic Mendelian variants remains time-consuming, in part, because the limited accuracy of current computational prediction methods requires manual classification by experts. Here we introduce CAPICE, a new machine-learning-based method for prioritizing pathogenic variants, including SNVs and short InDels. CAPICE outperforms the best general (CADD, GAVIN) and consequence-type-specific (REVEL, ClinPred) computational prediction methods, for both rare and ultra-rare variants. CAPICE is easily added to diagnostic pipelines as pre-computed score file or command-line software, or using online MOLGENIS web service with API. Download CAPICE for free and open-source (LGPLv3) at https://github.com/molgenis/capice.

Clusters of medical specialties around patients with multimorbidity – employing fuzzy c-means clustering to explore multidisciplinary collaboration

Abstract Background Hospital care organization, structured around medical specialties and focused on the separate treatment of individual organ systems, is challenged by the increasing prevalence of multimorbidity. To support the hospitals’ realization of multidisciplinary care, we hypothesized that using machine learning on clinical data helps to identify groups of medical specialties who are simultaneously involved in hospital care for patients with multimorbidity. Methods We conducted a cross-sectional study of patients in a Dutch general hospital and used a fuzzy c-means clustering algorithm for the analysis. We explored the patients’ membership degrees in each cluster to identify subgroups of medical specialties that provide care to the same patients with multimorbidity. We used retrospectively collected electronic health record data from 2017. We extracted data from 22,133 patients aged ≥18 years who had received outpatient clinical care for two or more chronic and/ or oncological diagnoses. Results We found six clusters of medical specialties and identified 22 subgroups. The clusters were labeled based on the specialties that most characterized them: 1. dermatology/ plastic surgery, 2. six specialties (gynecology/ rheumatology/ orthopedic surgery/ urology/ gastroenterology/ otorhinolaryngology), 3. pulmonology, 4. internal medicine/ cardiology/ geriatrics, 5. neurology/ physiatry (rehabilitation)/ anesthesiology, and 6. internal medicine. Most patients had a full or dominant membership to one of these clusters of medical specialties (11 subgroups), whereas fewer patients had a membership to two clusters. The prevalence of specific diagnosis groups, patient characteristics, and healthcare utilization differed between subgroups. Conclusion Our study shows that clusters and subgroups of medical specialties simultaneously involved in hospital care for patients with multimorbidity can be identified with fuzzy c-means cluster analysis using clinical data. Clusters and subgroups differed regarding the involved medical specialties, diagnoses, patient characteristics, and healthcare utilization. With this strategy, hospitals and medical specialists can further analyze which subgroups are target populations that might benefit from improved multidisciplinary collaboration