Identification of Somatic Structural Variants in Solid Tumors by Optical Genome Mapping

Abstract

Genomic structural variants comprise a significant fraction of somatic mutations driving cancer onset and progression. However, such variants are not readily revealed by standard next-generation sequencing. Optical genome mapping (OGM) surpasses short-read sequencing in detecting large (>500 bp) and complex structural variants (SVs) but requires isolation of ultra-high-molecular-weight DNA from the tissue of interest. We have successfully applied a protocol involving a paramagnetic nanobind disc to a wide range of solid tumors. Using as little as 6.5 mg of input tumor tissue, we show successful extraction of high-molecular-weight genomic DNA that provides a high genomic map rate and effective coverage by optical mapping. We demonstrate the system’s utility in identifying somatic SVs affecting functional and cancer-related genes for each sample. Duplicate/triplicate analysis of select samples shows intra-sample reliability but also intra-sample heterogeneity. We also demonstrate that simply filtering SVs based on a GRCh38 human control database provides high positive and negative predictive values for true somatic variants. Our results indicate that the solid tissue DNA extraction protocol, OGM and SV analysis can be applied to a wide variety of solid tumors to capture SVs across the entire genome with functional importance in cancer prognosis and treatment.

Optical Genome Mapping: Clinical Validation and Diagnostic Utility for Enhanced Cytogenomic Analysis of Hematological Neoplasms

“…Additionally, we analyzed each genome for all clinically relevant SVs, and report findings as “concordant” to previous SOC results and “additional findings” that were not reported with SOC methods ( Supplementary file 1) . Although detailed investigation and confirmation of these additional findings remain beyond the scope of this manuscript, we have provided all clinically reportable SVs in Supplementary file 1 to assist future discoveries and consider these findings as likely true events, consistent with previous reports [ 16 , 17 ].…”

“…The variants from the two algorithms are simultaneously visualized in a unique analysis tool for ease of interpretation, variant classification, and reporting (Bionano access 1.6 software). Recently, the technology has gained enormous traction and has been evaluated in several settings, including prenatal [ 14 ], postnatal [ 15 ], hematological neoplasms [ 16 ], and solid tumors [ 17 ], demonstrating 100% clinical concordance with traditional cytogenetic analysis. However, the literature lacks any clinical validation studies, which are critical for comprehensive evaluation and clinical implementation.…”

Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing

“…More complex events, known as chromoanagenesis, combine a cascade of chromosomal rearrangements 1 . Over the past few years, structural variants and complex genomic rearrangements have been implicated in various phenotypes: cancer 2 , 3 , rare disorders 4 – 9 and common diseases 10 in humans, reproduction traits in pigs 11 , virulence traits in plant pathogenic fungi 12 , local adaptation in maize 13 , and behavior in Caenorhabditis elegans ( C. elegans ) 14 . However, the technologies and methods used to identify SVs and complex rearrangements are still multifaceted and no approach has yet been recognized as standard.…”

Signal-based optical map alignment

“…These images are then processed into label coordinates per DNA molecule, typically ranging from 100kb up to several Mb. This data can then either be used to scaffold existing sequence-based assemblies [ 12 – 15 ], or directly assembled into consensus optical maps which can help detect structural variation [ 16 – 19 ].…”