Singleton rapid long-read genome sequencing as first tier genetic test for critically Ill children with suspected genetic diseases.

Abstract

Timely genetic testing is crucial for diagnosing pediatric patients in the intensive care units (ICUs) without known etiology. We aim to explore the benefits of singleton rapid long-read genome sequencing (rLR-GS) in critically ill children admitted to ICU with a suspected genetic etiology. Children younger than 18 years of age admitted to the ICU with a suspected genetic etiology at two tertiary hospitals in Thailand from August 2023 to May 2024 were included. rLR-GS was performed. The value of a molecular diagnosis for changing patient management outcomes was assessed. Eighteen patients were recruited. Singleton rLR-GS identified seventeen likely pathogenic (LP) or pathogenic (P) variants, resulting in the diagnosis of eleven distinct genetic disorders with autosomal recessive, autosomal dominant, and mitochondrial inheritance patterns. This yielded a diagnostic rate of 61% (11/18) with a median turnaround time of nine days. Specifically, rLR-GS identified three pathogenic structural variants (SVs), including large deletions of 19 kb, 2.4 kb, and 10.1 kb. Additionally, it provided phasing information for the two variants in each of the six patients with autosomal recessive disorders. Furthermore, the identification of two SVs and the phasing information led to the reclassification of three single nucleotide variants (SNV), one in each patient, from variants of unknown significance (VUS) to LP. The application of rLR-GS resulted in significant changes in the management of all eleven patients. This proof-of-concept study demonstrated the utility of singleton rLR-GS as a first-tier diagnostic approach for critically ill patients with unknown causes.