Nat. However, on the one hand, the current algorithms exhibited different performances in detecting different types and sizes of SVs; on the other hand, the whole-genome/exome sequencing for detecting SVs is costly, and only a portion of SVs . Genet. These merging approaches can yield different outcomes as shown by how only a small segment of the deletion overlaps between tools and not all breakpoints could be matched. Background: Structural variations (SVs) are common genetic alterations in the human genome that could cause different phenotypes and diseases, including cancer. c Identification of tumor-specific SVs (red) requires tumor-normal differential analysis of reads or events. BMC Cancer Identification of Somatic Structural Variants in Solid Tumors by Sanborn, A. L. et al. However, alignment uncertainty is inherent to short-read sequencing data. At present, only SVclone uses SVs to estimate intra-tumor heterogeneity due to the complexities of calculating variant AF for SVs43. This Perspective discusses how the folding of the 3D genome, and differences in its folding across cell types, affect observed SV rates in different cancer types as well as how SVs can impact cancer cell fitness. Structural variations (SVs) affect more of the cancer genome than any other type of somatic genetic alteration but difficulties in detecting and interpreting them have limited our understanding. Yi, K. & Ju, Y. S. Patterns and mechanisms of structural variations in human cancer. 6, 3139 (2020). Biotechnol. Cell 35, 359367 (1983). Nature 499, 214218 (2013). Nat. Pathol. Zheng, G. X. Y. et al. Nat. In addition, 10 can report variants in repeat-rich regions not accessible by standard short-read IL sequencing79,80. Split reads (SR) span breakpoints and can only be partially aligned. We propose cuteSV, a sensitive, fast, and scalable long-read-based SV detection approach. Cell 169, 780791 (2017). SR can detect small variants with base-pair resolution, especially those smaller than the size of the read. Nat. Characterizing and measuring bias in sequence data. 2, 2140 (2018). Chromothripsis from DNA damage in micronuclei. Specialized somatic SV detection tools such as Lancet and Varlociraptor account for challenges specific to the identification of TSSVs (Box 2)31,40. PubMed Central Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat. 28, 266274 (2018). 52, 891897 (2020). SVscape: Article Med. EMBO J. et al. Clin. Meyerson: The first wave of variants that researchers noticed were those that affect proteins in some clear way, such as a translocation that leads to a fusion gene, or translocations that bring strong promoters in front of oncogenes. Protein complexes including CCCTC binding factor (CTCF) and cohesin that contribute to organizing the 3D structure of the genome. & Bafna, V. The elusive evidence for chromothripsis. This refers to the rate at which SVs form rather than the rate at which they are observed after undergoing evolutionary selection. Genomes for kids: the scope of pathogenic mutations in pediatric cancer revealed by comprehensive DNA and RNA sequencing. Driver fusions and their implications in the development and treatment of human cancers. Science 351, 14541458 (2016). SV may be copy number neutral or it may involve duplications, deletions, and complex rearrangements. PubMed 10, 1784 (2019). Cho, S. W. et al. 20, 97 (2019). Chromosome Res. 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CTCF binding polarity determines chromatin looping. Barrett, T. et al. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. 1, 20 (2018). 18, 188 (2017). Dixon, J. R. et al. Shi, J. et al. 1. volume5, Articlenumber:15 (2021) PubMedGoogle Scholar. Structural variants (SVs) that alter three-dimensional (3D) genome organization can lead to enhancer-promoter rewiring and human disease, particularly in the context of cancer 3. Nature 578, 129136 (2020). Assessing the performance of the Oxford Nanopore Technologies MinION. An, J. et al. USA 101, 1136811373 (2004). Rev. Characterizing the major structural variant alleles of the human genome. Adjusting the filtering threshold based on an estimated contamination fraction is a balance between precision and sensitivity for detecting low-AF variants. Cold Spring Harb. However, research into the role of SVs in cancer has been limited due to difficulties in detection. Microhomology-mediated end-joining errors typically result in deletions. PacBio and ONT generate reads of ~10+ kb versus ~250bp from IL; the longer reads reduce alignment ambiguity and do not have a GC bias, resulting in improved coverage of dark regions in the genome55. The latest generation of SV detection algorithms that combine multiple read-alignment patterns can detect SVs across a broad range of types and sizes. 12, 16921697 (2002). Strong association of de novo copy number mutations with autism. Ma, Z. S., Li, L., Ye, C., Peng, M. & Zhang, Y.-P. Genet. 384, 924935 (2021). Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements. Pan-cancer analysis of whole genomes. CAS & Belmont, A. S. Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression. Continuous improvements in algorithms for base calling and error correction have increased the accuracy of these platforms58,59. Intersection of callsets identifies the SVs with support from multiple algorithms or technologies. Genom. Lematre, C. et al. 37, 973982 (2019). Nat. Ther. Article Engreitz, J. M., Agarwala, V. & Mirny, L. A. Three-dimensional genome architecture influences partner selection for chromosomal translocations in human disease. 353, 133144 (2005). A hybrid approach for de novo human genome sequence assembly and phasing. Cohesins functionally associate with CTCF on mammalian chromosome arms. Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma. Commun. DPs are best suited for detecting large SVs such as inter-chromosomal translocations or inversions. High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Tsao, M.-S. et al. CAS Genomic instability in cancer genomes results in more breakpoints and more complex SVs compared to germline variation46. Harewood, L. et al. In a pediatric pan-cancer cohort of 128 patients, we identified 155 high confidence tumor-specific gene fusions and their underlying structural variants (SVs). Lancet is specialized in the detection of somatic SNVs, insertions (<200bp) and deletions (<400bp) from short-read WGS data using local (micro-)assembly and re-alignment to the reference40. Structural alterations driving castration-resistant prostate cancer revealed by linked-read genome sequencing. Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing. ISSN 1474-1768 (online) Chiang, C. et al. 27, 200218 (2019). Nanopore sequencing and assembly of a human genome with ultra-long reads. Sima, J. et al. Rev. Biotechnol. Genomic structural variation is the variation in structure of an organism's chromosome.It consists of many kinds of variation in the genome of one species, and usually includes microscopic and submicroscopic types, such as deletions, duplications, copy-number variants, insertions, inversions and translocations.Originally, a structure variation affects a sequence length about 1kb to 3Mb, which . Mol. Biochem. Kster, J., Dijkstra, L. J., Marschall, T. & Schnhuth, A. Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery. Aymard, F. et al. Nat. Zhou, B. et al. Google Scholar. In parallel, the reference genome continues to evolve, resulting in improved alignments and fewer false-positive variants in studies which adopted GRCh38 (hg38) compared to GRCh37 (hg19)8,21,22,23. PubMed Central Rev.Cancer Biol. Cancer Discov. Genome-wide somatic variant calling using localized colored de Bruijn graphs. 344, 10311037 (2001). Cell Syst. 49, 692699 (2017). Cancer Center, Daping Hospital, Army Medical University, Chongqing, China; Chromothripsis is a catastrophic event involving numerous chromosomal rearrangements in confined genomic regions of one or a few chromosomes, causing complex effects on cells via the extensive structural variation. Structural variants drive context-dependent oncogene activation in cancer Clinical cancer sequencing also increasingly aims to detect SVs, leading to a widespread necessity to interpret their biological and clinical relevance. Cell Biol. Structural variations (SVs) affect more of the cancer genome than any other type of somatic genetic alteration but difficulties in detecting and interpreting them have limited our understanding. 24, 390400 (2014). Google Scholar. Alternatively, short reads can be used for error correction by aligning them to the long reads, but this approach only improves accuracy of genomic regions accessible to IL sequencing55,61. 50, 98 (2018). Google Scholar. Fudenberg, G., Kelley, D. R. & Pollard, K. S. Predicting 3D genome folding from DNA sequence with Akita. Li, Y. et al. MAVIS: merging, annotation, validation, and illustration of structural variants. Biol. Wittler, R., Marschall, T., Schnhuth, A. Chromosome structural variation is a vital driver of oncogenesis and progression in both solid tumors and hematopoietic malignancies [ 1 ]. Article Gene-centric approaches based on unions seem the most applicable. Structural variants (SVs) can contribute to oncogenesis through a variety of mechanisms. Sci. The emerging role of epigenetic therapeutics in immuno-oncology. PubMed Central Rhoads, A. Pleasance, E. D. et al. After overlapping variants are merged, integration of SV callsets from multiple algorithms can either be performed by taking the union or intersection (Fig. Bioinformatics 31, 2741 (2015). 47, 598606 (2015). 65, 310 (2019). Vogelstein, B. Commun Biol. Sarni, D. et al. Open Access Initial sequencing and analysis of the human genome. Currently, many tools are actively developed to detect SVs from alignment of ONT and PacBio data (Table 2). Rev. Jain, M. et al. Lin, K., Smit, S., Bonnema, G., Sanchez-Perez, G. & de Ridder, D. Making the difference: integrating structural variation detection tools. Structural variants (SVs) that alter three-dimensional (3D) genome organization can lead to enhancer-promoter rewiring and human disease, particularly in the context of cancer 3. Rev. Detection Quant. Brief. AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications. 14, R51 (2013). Fungtammasan, A., Walsh, E., Chiaromonte, F., Eckert, K. A. 21, 7187 (2020). Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. NanoVar: accurate characterization of patients genomic structural variants using low-depth nanopore sequencing. Third, we highlight the impact that long-read sequencing can have on somatic SV detection. Cell 144, 2740 (2011). Nat. Recent studies have shown SV to be associated with many human diseases. 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. 1, 210 (2015). Zhang, X. et al. de Wit, E. et al. N. Engl. Typically paired tumor-normal samples are used to classify SVs as either germline, mosaic-normal or tumor-specific variants15. Each platform has its own scope of variant detection. (2020). Similarities and differences between variants called with human reference genome HG19 or HG38. Nat. Evol. Although most studies comparing SV algorithms focus on germline SVs, these findings were recently also confirmed for somatic SV detection26. Pfister, S. X. et al. The majority of SV tools operate under a diploid genome assumption. Nat. Long-read SV detection algorithms are either based on de novo assembly or read-alignment to a reference genome. Topper, M. J., Vaz, M., Marrone, K. A., Brahmer, J. R. & Baylin, S. B. PLoS ONE 7, e44196 (2012). (2020). Nat. For example, sequencing lung cancer cell lines with PromethION detected both known cancer-driver SNVs and revealed large previously unknown genomic rearrangements, including an 8Mb amplification of MYC57. Nat. Mifsud, B. et al. Genet. Long-Read Whole-Genome Sequencing Using a Nanopore Sequencer - Springer Advances in sequencing technologies have increased the number of SVs identified per genome from ~2,12,5k in the 1000 genomes project to more than 27k in recent multi-platform sequencing efforts3,4,12. Stratton, M. R., Campbell, P. J. Google Scholar. LUMPY has a probabilistic model that combines parallel analyses of DP and SR such that both contribute independently to the detection of breakpoints35. Alignment of paired-end sequencing reads to a reference genome is used to infer sites of discontinuity or breakpoints. As an alternative to ad-hoc filtering of SV callsets, Varlociraptor and Lancet, respectively, compare breakpoints and aberrant reads between tumor-normal samples at an earlier stage of the analysis (Fig. A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies. Commun. Genome Res. Nat. However, error-correction strategies come with trade-offs for SV detection. Laver, T. et al. Hnisz, D. et al. The chromatin remodeler ALC1 underlies resistance to PARP inhibitor treatment. & Misteli, T. Conservation of relative chromosome positioning in normal and cancer cells. https://doi.org/10.1146/annurev-cancerbio-070620-094029 (2022). The genomic landscape of schwannoma. 27, 25132530 (2013). Genet. Spies, N. et al. addresses different ensemble integration approaches currently in use in germline SV research4. Trends Genet. The phenotypic effect of CNVs is often better understood than for SVs and established technologies have had more opportunity to collect samples, including rare cancer types. A sufficiently large panel-of-normals can provide more statistical power for filtering recurrent germline variants, but is less effective than a patient-derived normal sample when filtering rare or private germline variants4. 41, 849853 (2009). Discovery of new fusion transcripts in a cohort of pediatric solid cancers at relapse and relevance for personalized medicine. Immunity 35, 501513 (2011). Long-read sequencing for non-small-cell lung cancer genomes. Specialized gene fusion algorithms predict gene fusions from chimeric transcripts by using read-alignment patterns such as SR crossing exonic junctions and DP mapping to both gene partners71. Limitations in both short-read and long-read WGS can potentially be overcome by using a multi-platform approach and as such improve the identification of TSSVs.