FV 943. Facilitating a Molecular Diagnosis as Soon as Possible: Diagnostic Exome in Neurometabolic Disorders

Background: Molecular diagnoses of inherited neurometabolic disorders are challenging given their genetic and clinical heterogeneity. Especially in infancy onset of inborn errors of metabolism an early identification is crucial for specific interventions, clinical management, and treatment decisions. Since July 2016 next-generation sequencing–based genetic testing is accepted in the German health system. However, its application as a first-line diagnostic tool is complicated by bureaucratic hurdles.

Objectives: Concerted efforts of researchers, clinicians, and managers are needed to promote the potential benefit of a systematic approach such as whole exome sequencing (WES)/genome sequencing.

Research Questions: We here report on the results of exome-based diagnostics of a cohort of 96 index cases with clinically suspected neurometabolic disorders to evaluate the diagnostic utility of WES.

Methods: Inclusion criteria were suspected neurometabolic disorders based on an insinuating disease course, pathologic neurometabolic work-up, suggestive cerebral MRI findings, and/or other characteristic organ affection. Coding genomic regions were enriched with a SureSelect Human All Exon Kit V6 (Agilent technologies) for subsequent sequencing as 2 × 125 bp/2 × 100 bp paired-end reads on an Illumina HiSeq2500/NovaSeq6000 system. Generated sequences were analyzed using the megSAP pipeline (https://github.com/imgag/megSAP). Clinical variant prioritization included different filtering steps (e.g., MAF < 0.1% in gnomAD, in-house database) and was conducted in parallel by at least two analyses according to an in-house standard operating procedure.

Results: In 84 cases, single exome analyses were performed as first-line diagnostics, in 13 cases trio or multisample exome analyses were conducted. In 44 (46%) cases, we identified likely pathogenic or pathogenic variants in genes that have been associated with mitochondrial diseases (25), other neurometabolic diseases (10), or other neurodevelopmental disorders (9).

In 16 (36%) cases, a targeted therapy was available; in 15 cases (33%), the firm diagnosis implicated a modification of clinical management. However, in 14 (31%) cases, the disorders were not amenable to targeted therapy or a specific clinical regimen.

In 29 cases (30%), we identified variants of unknown significance where follow-up studies for functional analyses are pending. Moreover, we newly identified five candidate genes affecting the mitochondrial function (three), selenoprotein metabolism (one), or posttranslational protein modification (one). However, 18 cases (19%) remain unsolved. Further ongoing investigations of the latter in a research setting include the additional trio analysis, full genome, and/or transcriptome sequencing.

Conclusion: WES is established as a potent first-line diagnostic tool for neurometabolic disorders. Although presenting with a wide phenotypic spectrum, WES facilitated a definite diagnosis in 46% and a possible diagnosis pending follow-up in 30% of the cases.