A national diagnostic framework for patients with ultra-rare disorders: molecular genetic findings using phenotypic and sequencing data

Abstract

Most individuals with rare diseases first contact primary care physicians. Although efficient diagnostic routines exist for a subset of rare diseases, ultra-rare entities often require expert clinical knowledge or comprehensive genetic diagnostics, which poses structural challenges to public healthcare systems. To address these challenges, a novel structured diagnostic concept based on the presence of multidisciplinary expertise at centers for rare diseases (CRDs) that have been established at German university hospitals in recent years, was evaluated in a prospective study (TRANSLATE-NAMSE). Between January 2018 and December 2020, 5652 patients were enrolled in the study and were comprehensively assessed by multidisciplinary teams (MDTs) at ten CRDs. Exome sequencing (ES) was initiated for 268 adult and 1309 pediatric patients and partially complemented by additional molecular tests. Conclusive diagnoses were established in 494 individuals, covering 400 diagnostic-grade genes, suggesting ultra-rare disorders were enriched in this cohort. In addition, we describe 56 novel gene-phenotype associations, mainly in individuals with neurodevelopmental delay. A subcohort of 211 individuals was analyzed with the artificial intelligence–based PEDIA protocol, which integrates next-generation phenotyping on medical imaging and sequencing data. With the entire cohort data, we developed a tool to predict the diagnostic yield from the clinical features of a patient if advanced molecular testing strategies are applied.

Next‐generation phenotyping contributing to the identification of a 4.7 kb deletion in KANSL1 causing Koolen‐de Vries syndrome

“…At re‐consultation 7 years later, the 15‐year‐old female was enrolled in a study protocol that involved NGP and trio exome sequencing (Krawitz, 2022). After analysis by GestaltMatcher, the computer‐assisted assessment of portrait images yielded high gestalt scores for KdVS (Figure 1).…”