# Optical Genome Mapping versus Whole-Genome Sequencing in the Clinical Diagnosis of Gynecologic Mesenchymal Tumors

## TL;DR

This study compares two genomic techniques for diagnosing gynecologic tumors, finding that each has strengths in detecting different types of genetic changes.

## Contribution

The study provides a direct technical comparison of OGM and WGS for mesenchymal tumor diagnosis, highlighting their relative strengths and weaknesses.

## Key findings

- OGM identified structural driver events in 80% of cases and showed high concordance with WGS for major CNAs and translocations.
- OGM resolved complex rearrangements not clearly defined by WGS, including specific fusion events.
- WGS uniquely detected clinically significant truncating translocations and fusions not identified by OGM.

## Abstract

Optical genome mapping (OGM) enables high-resolution detection of structural variants (SVs) and copy number aberrations (CNAs) using ultralong DNA molecules and minimal bioinformatics processing. Its diagnostic utility in solid tumors remains underexplored. Whole-genome sequencing (WGS) offers comprehensive variant detection but is resource intensive. This study presents a technical benchmarking of OGM versus WGS for mesenchymal tumors of the gynecologic tract. Twenty-five uterine mesenchymal tumors were prospectively analyzed using matched WGS, transcriptome sequencing, and OGM. Detected SVs, CNAs, and fusion genes were compared across platforms. OGM identified structural driver events in 80% of cases and demonstrated high concordance with WGS for major CNAs and translocations. In select cases, OGM resolved complex rearrangements not clearly defined by WGS, including a PLAG1::RERE fusion and an embedded inversion in a RAD51B::HMGA2 event. Conversely, WGS uniquely detected a truncating NF1 translocation and a TSC2::SENP3 fusion, both clinically significant. OGM is a technically robust platform for SV and CNA detection in mesenchymal tumors, and it may serve as an efficient alternative to sequencing-based cytogenomic approaches in selected clinical contexts, especially in tumors known to be driven by gross chromosomal rearrangements. WGS provides a comprehensive view of the cancer genome, suitable for tumors driven by single-nucleotide variants, SVs, and CNAs. The choice between platforms should be guided by clinical context, diagnostic needs, and available resources.