Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology

Cancer is generally characterized by acquired genomic aberrations in a broad spectrum of types and sizes, ranging from single nucleotide variants to structural variants (SVs). At least 30% of cancers have a known pathogenic SV used in diagnosis or treatment stratification. However, research into the...

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Bibliographic Details
Published in:NPJ precision oncology 2021-03, Vol.5 (1), p.15-15, Article 15
Main Authors: van Belzen, Ianthe A. E. M., Schönhuth, Alexander, Kemmeren, Patrick, Hehir-Kwa, Jayne Y.
Format: Article
Language:English
Subjects:
631/114/2163
631/1647/2217
Cancer
Cancer Research
Classification
Datasets
Gene Therapy
Genomics
Human Genetics
Internal Medicine
Medicine
Medicine & Public Health
Mutation
Oncology
Pathogenesis
Review
Review Article
Targeted cancer therapy
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Summary:Cancer is generally characterized by acquired genomic aberrations in a broad spectrum of types and sizes, ranging from single nucleotide variants to structural variants (SVs). At least 30% of cancers have a known pathogenic SV used in diagnosis or treatment stratification. However, research into the role of SVs in cancer has been limited due to difficulties in detection. Biological and computational challenges confound SV detection in cancer samples, including intratumor heterogeneity, polyploidy, and distinguishing tumor-specific SVs from germline and somatic variants present in healthy cells. Classification of tumor-specific SVs is challenging due to inconsistencies in detected breakpoints, derived variant types and biological complexity of some rearrangements. Full-spectrum SV detection with high recall and precision requires integration of multiple algorithms and sequencing technologies to rescue variants that are difficult to resolve through individual methods. Here, we explore current strategies for integrating SV callsets and to enable the use of tumor-specific SVs in precision oncology.
ISSN:2397-768X
2397-768X
DOI:10.1038/s41698-021-00155-6