Single-Molecule Sequencing Reveals Structural Variants in Cancer Genomes
DOI:
https://doi.org/10.5281/zenodo.22688251Keywords:
long-read sequencing, structural variants, cancer genomics, nanopore sequencing, chromothripsis, optical genome mapping, extrachromosomal DNAAbstract
Structural variants -- deletions, duplications, inversions, translocations and more complex rearrangements
spanning kilobases to whole chromosome arms -- drive oncogenesis through mechanisms that point mutations
cannot easily replicate, including gene fusion, enhancer hijacking and large-scale copy-number amplification of
oncogenes, yet they have historically been the class of cancer genomic variation most difficult to detect reliably.
Short-read sequencing, the workhorse of clinical and research cancer genomics for over a decade, struggles
specifically with the repetitive, low-complexity and structurally rearranged regions of the genome in which many
clinically important structural variants occur, producing systematic false negatives that are increasingly well
documented. This review synthesises the current evidence on how single-molecule long-read sequencing
platforms -- Oxford Nanopore and Pacific Biosciences HiFi sequencing, together with the complementary
technology of optical genome mapping -- have changed the practical and conceptual landscape of structural
variant detection in cancer genomes. We summarise the technical basis for long reads' improved sensitivity in
repetitive and structurally complex regions, review comparative benchmarking studies quantifying the sensitivity
gap relative to short-read calling across variant size classes, and discuss the application of these technologies to
specific cancer biology questions including chromothripsis reconstruction, extrachromosomal DNA
characterisation, and detection of complex oncogene amplicons that short-read approaches under-resolve. We
also address the practical barriers -- cost, input DNA quality requirements, computational infrastructure and clinical
validation pathways -- that currently limit routine adoption of long-read sequencing in clinical cancer genomics,
and we outline the comparative evidence base for optical genome mapping as a lower-cost, more clinically mature
complement to sequencing-based structural variant detection. We conclude that single-molecule and
mapping-based technologies have moved from a research curiosity to a demonstrably superior tool for a specific
and clinically consequential subset of structural variant classes, and that the principal remaining barriers to
broader adoption are now more operational than technical.
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