Whole-Genome Sequencing is a Viable Replacement for Chromosomal Microarray and Fragile X PCR Testing

Developmental disabilities and congenital anomalies are common pediatric conditions that often require extensive genetic testing to determine an underlying cause. Traditionally, chromosomal microarrays (CMA) and Fragile X testing have served as first-tier diagnostics, but these tests are limited in scope and often necessitate follow-up sequencing assays. Whole Genome Sequencing (WGS) offers a single, comprehensive assay capable of detecting a broad spectrum of genetic variation, including single nucleotide variants (SNVs), insertions and deletions (INDELs), copy number variants (CNVs), structural variants (SVs), loss of heterozygosity (LOH), and tandem repeat alterations. In this study, we evaluated whether WGS could replace CMA and serve as a more effective first-tier test. WGS achieved a 97.28% concordance with CMA for clinically relevant CNVs and LOH, while also offering more accurate breakpoint resolution and broader data point coverage. Notably, 4 out of 5 discordant cases (80%) were due to WGS providing more accurate breakpoint resolution. WGS covered over 97% of clinically relevant regions for CNV detection, compared to < 3% with CMA. To address the interpretive burden associated with the increased CNV calls, we implemented a cohort-based occurrence filter that successfully prioritized potential pathogenic events without sacrificing clinical sensitivity. Additionally, we assessed the feasibility of Fragile X screening from WGS data using a custom PCR confirmation logic built on Expansion Hunter output. This approach accurately excluded normal-range alleles and flagged indeterminate or expanded alleles for follow-up PCR confirmation. Our results support the use of WGS as a scalable and comprehensive diagnostic platform capable of consolidating multiple traditional assays. By streamlining workflows and enhancing clinical resolution, WGS offers a compelling alternative to the current diagnostic paradigm for patients with suspected genetic disorders.