Journal Article

Reanalysis of exome negative patients with rare disease: a pragmatic workflow for diagnostic applications

Kamsteeg, Erik-Jan, Pfundt, Rolph, Hofste, Tom, Galbany, Jordi Corominas, de Wijs, Ilse, Yntema, Helger G., Derks, Ronny, Schieving, Jolanda H., Vissers, Lisenka E. L. M., van den Heuvel, Simone, Schobers, Gaby, Pennings, Maartje, Nelen, Marcel, Gilissen, Christian, Willemsen, Michèl A. A. P., Wieskamp, Nienke, Brunner, Han G., Kleefstra, Tjitske

2022

Overview

Background Approximately two third of patients with a rare genetic disease remain undiagnosed after exome sequencing (ES). As part of our post-test counseling procedures, patients without a conclusive diagnosis are advised to recontact their referring clinician to discuss new diagnostic opportunities in due time. We performed a systematic study of genetically undiagnosed patients 5 years after their initial negative ES report to determine the efficiency of diverse reanalysis strategies. Methods We revisited a cohort of 150 pediatric neurology patients originally enrolled at Radboud University Medical Center, of whom 103 initially remained genetically undiagnosed. We monitored uptake of physician-initiated routine clinical and/or genetic re-evaluation (ad hoc re-evaluation) and performed systematic reanalysis, including ES-based resequencing, of all genetically undiagnosed patients (systematic re-evaluation). Results Ad hoc re-evaluation was initiated for 45 of 103 patients and yielded 18 diagnoses (including 1 non-genetic). Subsequent systematic re-evaluation identified another 14 diagnoses, increasing the diagnostic yield in our cohort from 31% (47/150) to 53% (79/150). New genetic diagnoses were established by reclassification of previously identified variants (10%, 3/31), reanalysis with enhanced bioinformatic pipelines (19%, 6/31), improved coverage after resequencing (29%, 9/31), and new disease-gene associations (42%, 13/31). Crucially, our systematic study also showed that 11 of the 14 further conclusive genetic diagnoses were made in patients without a genetic diagnosis that did not recontact their referring clinician. Conclusions We find that upon re-evaluation of undiagnosed patients, both reanalysis of existing ES data as well as resequencing strategies are needed to identify additional genetic diagnoses. Importantly, not all patients are routinely re-evaluated in clinical care, prolonging their diagnostic trajectory, unless systematic reanalysis is facilitated. We have translated our observations into considerations for systematic and ad hoc reanalysis in routine genetic care.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Bioinformatics / Biomedical and Life Sciences / Biomedicine / Cancer Research / Diagnosis / Diagnostic implementation of recommended ACMG guideline / Diagnostic tests / Genetic disorders / Genetic screening / Genotype & phenotype / Human Genetics / Longitudinal follow-up of systematic cohort / Medical centers / Medical research / Medicine, Experimental / Medicine/Public Health / Metabolomics / Neurology / NGS-based resequencing / Patients / Pediatric neurology / Pediatrics / Rare disease / Rare diseases / Reclassification / Systematic reanalysis / Systems Biology