Simultaneous detection of small and large variants enhances the diagnosis of rare diseases using full genome sequencing

Despite advances in exome and genome sequencing, many patients with suspected genetic disorders remain undiagnosed due to limitations in detecting complex structural variants. This study aimed to evaluate the diagnostic yield and clinical utility of Full-Genome Analysis (FGA), an integrated approach that combines short-read whole-genome sequencing (WGS), 10x Genomics linked-read sequencing, and Bionano optical genome mapping (OGM). Twenty-nine patients with unclear or inconclusive genetic diagnoses after standard testing were analyzed using an in-house FGA pipeline capable of simultaneously detecting single nucleotide variants (SNVs), copy number variants (CNVs), and structural variants (SVs). FGA established molecular diagnoses in 12 of 29 patients (41.4%), identifying nine pathogenic SNVs, three CNVs, and two complex SVs. Two CNVs were missed by chromosomal microarray, and both SVs were undetectable by short-read WES or WGS. Representative cases demonstrated that integrating OGM and linked-read sequencing improved detection of compound heterozygous variants and cryptic rearrangements that conventional methods failed to resolve. FGA substantially improved the diagnostic yield in patients with unresolved genetic disorders after conventional testing. Its ability to comprehensively detect small and large genomic variants within a single workflow highlights its potential as a next-generation diagnostic platform for rare disease evaluation.