Evaluation of Genomic Proximity Mapping for Detecting Genomic and Chromosomal Structural Variants in Constitutional...

Structural variants are critical to genetic diversity and disease, yet their detection remains challenging with conventional cytogenetic techniques, including karyotyping, fluorescence in situ hybridization, and chromosome microarray analysis. These methods often lack the resolution and sensitivity needed for comprehensive characterization of chromosomal aberrations. To address these limitations, we implemented genomic proximity mapping (GPM), a genome-wide chromosome conformation capture technology, in a clinical setting. Here, we applied GPM to a cohort of 123 individuals with constitutional disorders, achieving a 100% concordance in detecting 110 copy number variants (>25 kb) and 27 structural rearrangements, in addition to novel findings. GPM demonstrated unique advantages, such as resolving chromosomal rearrangements with precise (<5 kb) breakpoint resolution, maintaining robust performance with challenging samples, including formalin-fixed, paraffin-embedded tissues, and detecting mosaicism with high sensitivity. Furthermore, GPM reliably provided copy number and loss-of-heterozygosity profiles, streamlining workflows. GPM also uncovered 12 novel structural variants missed by standard methods, highlighting its superior detection capability. This analysis revealed that cases with more than two chromosomal rearrangements identified by traditional cytogenetics often harbor additional, cryptic rearrangements that remain undetected by standard-of-care methods. GPM represents a transformative tool for genomic diagnostics, offering a high-resolution, comprehensive approach to detecting genomic alterations. Its ability to address limitations of conventional cytogenetics methods positions GPM as a needed advance in the diagnosis, prognosis, and therapeutic management of genetic disorders.