Optical Genome Mapping for Oncology Applications

Abstract

Optical genome mapping (OGM) is a next‐generation cytogenomic technology that has the potential to replace standard‐of‐care technologies used in the genetic workup of various malignancies. The ability to detect various classes of structural variations that include copy number variations, deletions, duplications, balanced and unbalanced events (insertions, inversions, and translocation) and complex genomic rearrangements in a single assay and analysis demonstrates the utility of the technology in tumor research and clinical application. Herein, we provide the methodological details for performing OGM and pre‐ and post‐analytical quality control (QC) checks and describe critical steps that should be performed with caution, probable causes for specific QC failures, and potential method modifications that could be implemented as part of troubleshooting. The protocol description and troubleshooting guide should help new and current users of the technology to improve or troubleshoot the problems (if any) in their workflow. © 2023 Wiley Periodicals LLC.Basic Protocol: Optical genome mapping

Optical Genome Mapping for Applications in Repeat Expansion Disorders

“…If storage is necessary, cells can be stored either as dry pellets (1.5 million cells) or mixed with 40 μl of stabilizing buffer at −80°C. If stored as dry pellets, the stabilizing buffer should be added immediately atop the pellet before it thaws (Koppikar et al, 2023;Sahajpal et al, 2023).…”

“…Basic Protocol 1 describes the standard UHMW DNA extraction and subsequent DNA labeling and staining methods for OGM purposes as recommended by Bionano Genomics. Therefore, versions of Basic Protocol 1 (with slight variations depending on the cell types covered) have also been published in previous Current Protocols manuscripts that describe methods using Bionano OGM (Koppikar et al, 2023;Sahajpal et al, 2023). In addition, future Current Protocols manuscripts describing the Bionano OGM method will contain the same Basic Protocol 1 (Broeckel, 2024;Kanagal-Shamanna, 2024).…”

“…Under optimal conditions, peripheral blood should be collected using EDTA tubes and stored at 4°C for a maximum of 4 days. For later analysis, aliquots of 650 μl should be preserved in screw-cap vials at −80°C (Koppikar et al, 2023;Sahajpal et al, 2023).…”