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 genomic mapping (OGM) surpasses short read sequencing in detecting large (>500bp) 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 6.5mg 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 utility of the system at 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.

Next-generation cytogenetics: Comprehensive assessment of 52 hematological malignancy genomes by optical genome mapping

“…The latter is now available within the most recent update of the Bionano software (Figure S10), as should be an ISCN-compatible nomenclature for OGM aberrations as suggested by us (Table S16) and others. 47 While we could show 100% sensitivity for detecting the previously known clinically relevant aberrations, we could also provide analytical validity on the basis of an in-depth technical comparison. As such, a comparison between OGM and FISH resulted in 100% sensitivity and specificity.…”

Clinical Validation and Diagnostic Utility of Optical Genome Mapping in Prenatal Diagnostic Testing

“…The isodicentric Y chromosomes were called upon manual interrogation, while the isodicentric X chromosome showed a complex CNV profile with inverted maps (inverted duplications called by the software), from which the isodicentric chromosome X was inferred ( Figure 4 ). Notably, the isodicentric Y chromosome exhibits a characteristic mapping profile, which has been recently reported by Mantere et al, and can be visualized in the SV view of the software [ 20 ]. Consistent with the previous report, the three isodicentric Y chromosomes showed a genome map pattern where the maps were completely absent from the q arm starting from Yq11.222 compared to other XY samples.…”

“…Also, an independent coverage-based algorithm detects large CNVs and aneuploidies (similar to CMAs). Recently, several investigators have shown that OGM is 100% concordant when compared to standard-of-care (SOC) technologies in several settings including postnatal [ 18 ], hematological neoplasms [ 19 ], and solid tumors [ 20 ] in either a single site or multi-site studies. We have previously discussed the potential utility of OGM in prenatal diagnostic testing [ 21 ], but the application of the technology for a large-scale evaluation in a clinical setting for prenatal application remained elusive.…”

Inferring functions of coding and non-coding genes using epigenomic patterns and deciphering the effect of combinatorics of transcription factors binding at promoters

“…Supplementary Table 2 Intersection of predicted genes with mice disease-gene sets. GO_COVALENT_CHROMATIN_MO DIFICATION AC087623.3 [13] Supplementary References…”