High-resolution structural variant detection and validation via nanopore long-read whole-genome sequencing | LC26

Abstract
The diagnostic odyssey for rare genetic disorders often involves some order of workflow of karyotyping, chromosomal microarray, and exome sequencing. However, these traditional methods frequently struggle with complex genomic architectures and balanced rearrangements. This study aimed to demonstrate the diagnostic utility of Oxford Nanopore Technologies (ONT)-based long-read whole-genome sequencing (LR-WGS) in pediatric cases with known or suspected structural abnormalities, particularly those unresolved by conventional methods. Five pediatric patients with clinically suspected chromosomal disorders were analyzed. Genomic DNA extracted from peripheral blood underwent LR-WGS on the ONT PromethION platform. Structural variant calling and breakpoint mapping were performed using an integrated bioinformatics workflow combining Guppy, Sniffles2, and visualization in Integrative Genomics Viewer (IGV). In four cases, LR-WGS confirmed large deletions detected previously by microarray or karyotyping, including a 15 Mb 8q23q24.22 deletion (Langer-Giedion syndrome), an 8 Mb 22q13 deletion (Phelan-McDermid syndrome), and 22q11.2 deletions (DiGeorge syndrome). Breakpoint resolution and phasing provided added interpretative value. In a previously unsolved case, LR-WGS identified a pathogenic 16.8 Mb 4q12q13.2 deletion and a 3.4 Mb 19q13.32q13.33 duplication undetectable by earlier tests. In conclusion, these cases underscore that ONT’s LR-WGS offers a comprehensive, "all-in-one" assay capable of detecting large structural variants (SVs) with superior sensitivity. By bridging the gap between cytogenetics and high-resolution genomics, LR-WGS acts as a critical failsafe for technical limitations in traditional pipelines, significantly increasing diagnostic yield in rare disease. Further work: ongoing efforts aim to integrate LR-WGS into first-tier diagnostics to streamline rare disease workflows and improve turnaround times.

Biography
Chanatjit Cheawsamoot utilizes long-read whole-genome sequencing to resolve the complex molecular drivers of rare diseases, significantly improving diagnostic yields in previously unsolved cases. Beyond variant discovery, she leverages precision genome editing and patient-derived induced pluripotent stem cells (iPSC) models, including 3D tissues and organoids, to interrogate disease pathogenesis. She is dedicated to bridging foundational genetic discovery with the development of precision therapies to improve patient outcomes.