This web page was created programmatically, to learn the article in its authentic location you may go to the hyperlink bellow:
https://www.nature.com/articles/s41596-025-01270-5
and if you wish to take away this text from our website please contact us
Nesta, A. V., Tafur, D. & Beck, C. R. Hotspots of human mutation. Trends Genet. 37, 717–729 (2021).
Eichler, E. E. Genetic variation, comparative genomics, and the analysis of illness. N. Engl. J. Med. 381, 64–74 (2019).
Pang, A. W. et al. Towards a complete structural variation map of a person human genome. Genome Biol. 11, R52 (2010).
Gilissen, C., Hoischen, A., Brunner, H. G. & Veltman, J. A. Unlocking Mendelian illness utilizing exome sequencing. Genome Biol. 12, 228 (2011).
Logsdon, G. A., Vollger, M. R. & Eichler, E. E. Long-read human genome sequencing and its purposes. Nat. Rev. Genet. 21, 597–614 (2020).
Mantere, T., Kersten, S. & Hoischen, A. Long-read sequencing rising in medical genetics. Front. Genet. 10, 426 (2019).
Merker, J. D. et al. Long-read genome sequencing identifies causal structural variation in a Mendelian illness. Genet. Med. 20, 159–163 (2018).
Miao, H. et al. Long-read sequencing recognized a causal structural variant in an exome-negative case and enabled preimplantation genetic analysis. Hereditas 155, 32 (2018).
Loomis, E. W. et al. Sequencing the unsequenceable: expanded CGG-repeat alleles of the delicate X gene. Genome Res. 23, 121–128 (2013).
Schüle, B. et al. Parkinson’s illness related to pure ATXN10 repeat growth. NPJ Parkinson’s Dis. 3, 27 (2017).
Höijer, I. et al. Detailed evaluation of HTT repeat components in human blood utilizing focused amplification-free long-read sequencing. Hum. Mutat. 39, 1262–1272 (2018).
Cumming, S. A. et al. De novo repeat interruptions are related to diminished somatic instability and gentle or absent scientific options in myotonic dystrophy kind 1. Eur. J. Hum. Genet. 26, 1635–1647 (2018).
Wang, Y., Zhao, Y., Bollas, A., Wang, Y. & Au, Ok. F. Nanopore sequencing know-how, bioinformatics and purposes. Nat. Biotechnol. 39, 1348–1365 (2021).
Nurk, S. et al. The full sequence of a human genome. Science 376, 44–53 (2022).
Lander, E. S. et al. Initial sequencing and evaluation of the human genome. Nature 409, 860–921 (2001).
Hoyt, S. J. et al. From telomere to telomere: the transcriptional and epigenetic state of human repeat components. Science 376, eabk3112 (2022).
Ayarpadikannan, S. & Kim, H.-S. The impression of transposable components in genome evolution and genetic instability and their implications in numerous ailments. Genomics Inform. 12, 98–104 (2014).
Hancks, D. C. & Kazazian, H. H. Roles for retrotransposon insertions in human illness. Mob. DNA 7, 9 (2016).
Gardner, E. J. et al. The Mobile Element Locator Tool (MELT): population-scale cellular aspect discovery and biology. Genome Res. 27, 1916–1929 (2017).
Thung, D. T. et al. Mobster: correct detection of cellular aspect insertions in subsequent era sequencing knowledge. Genome Biol. 15, 488 (2014).
Tubio, J. M. C. et al. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in most cancers genomes. Science 345, 1251343 (2014).
Torene, R. I. et al. Mobile aspect insertion detection in 89,874 scientific exomes. Genet. Med. 22, 974–978 (2020).
Shiraishi, Y. et al. Precise characterization of somatic advanced structural variations from tumor/management paired long-read sequencing knowledge with nanomonsv. Nucleic Acids Res. 51, e74 (2023).
Lei, Y. et al. Overview of structural variation calling: simulation, identification, and visualization. Comput. Biol. Med. 145, 105534 (2022).
De Coster, W. et al. Structural variants recognized by Oxford Nanopore PromethION sequencing of the human genome. Genome Res. 29, 1178–1187 (2019).
Yang, L. A sensible information for structural variation detection in human genome. Curr. Protoc. Hum. Genet. 107, e103 (2020).
Tham, C. Y. et al. NanoVar: correct characterization of sufferers’ genomic structural variants utilizing low-depth nanopore sequencing. Genome Biol. 21, 56 (2020).
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
Katoh, Ok., Misawa, Ok., Kuma, Ok. & Miyata, T. MAFFT: a novel technique for fast a number of sequence alignment based mostly on quick Fourier remodel. Nucleic Acids Res. 30, 3059–3066 (2002).
Smit, AFA, Hubley, R. & Green, P. RepeatMasker Open-4.0 (2013–2015).
Cretu Stancu, M. et al. Mapping and phasing of structural variation in affected person genomes utilizing nanopore sequencing. Nat. Commun. 8, 1326 (2017).
Gong, L. et al. Picky comprehensively detects high-resolution structural variants in nanopore lengthy reads. Nat. Methods 15, 455–460 (2018).
Sedlazeck, F. J. et al. Accurate detection of advanced structural variations utilizing single molecule sequencing. Nat. Methods 15, 461–468 (2018).
Smolka, M. et al. Detection of mosaic and population-level structural variants with Sniffles2. Nat. Biotechnol. 42, 1571–1580 (2024).
Jiang, T. et al. Long-read-based human genomic structural variation detection with cuteSV. Genome Biol. 21, 189 (2020).
Jiang, T. et al. cuteFC: regenotyping structural variants by means of an correct and environment friendly force-calling technique. Genome Biol. 26, 166 (2025).
Jiang, T. et al. Long-read sequencing settings for environment friendly structural variation detection based mostly on complete analysis. BMC Bioinforma. 22, 552 (2021).
Heller, D. & Vingron, M. SVIM: structural variant identification utilizing mapped lengthy reads. Bioinformatics 35, 2907–2915 (2019).
Tham, C. Y. & Benoukraf, T. Correspondence on NanoVar’s efficiency outlined by Jiang T. et al. in “Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation”. BMC Bioinformatics 24, 350 (2023).
Dierckxsens, N., Li, T., Vermeesch, J. R. & Xie, Z. A benchmark of structural variation detection by lengthy reads by means of a practical simulated mannequin. Genome Biol. 22, 342 (2021).
Wu, Z. et al. Structural variants within the Chinese inhabitants and their impression on phenotypes, ailments and inhabitants adaptation. Nat. Commun. 12, 6501 (2021).
Liu, Y. H., Luo, C., Golding, S. G., Ioffe, J. B. & Zhou, X. M. Tradeoffs in alignment and assembly-based strategies for structural variant detection with long-read sequencing knowledge. Nat. Commun. 15, 2447 (2024).
Liu, Y. et al. Comparison of structural variants detected by PacBio-CLR and ONT sequencing in pear. BMC Genomics 23, 830 (2022).
Fiol, A., Jurado-Ruiz, F., López-Girona, E. & Aranzana, M. J. An environment friendly CRISPR-Cas9 enrichment sequencing technique for characterizing advanced and extremely duplicated genomic areas. A case research within the Prunus salicina LG3-MYB10 genes cluster. Plant Methods 18, 105 (2022).
De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M. & Van Broeckhoven, C. NanoPack: visualizing and processing long-read sequencing knowledge. Bioinformatics 34, 2666–2669 (2018).
De Coster, W. & Rademakers, R. NanoPack2: population-scale analysis of long-read sequencing knowledge. Bioinformatics 39, btad311 (2023).
Asmaa, S., Tham, C. Y., Dyer, M. & Benoukraf, T. Dataset for ‘NanoVar: a Comprehensive Workflow for Structural Variant Detection to uncover the Genome’s Hidden Patterns’. Zenodo (2025).
Kiełbasa, S. M., Wan, R., Sato, Ok., Horton, P. & Frith, M. C. Adaptive seeds tame genomic sequence comparability. Genome Res. 21, 487–493 (2011).
Sović, I. et al. Fast and delicate mapping of nanopore sequencing reads with GraphMap. Nat. Commun. 7, 11307 (2016).
Zhou, A., Lin, T. & Xing, J. Evaluating nanopore sequencing knowledge processing pipelines for structural variation identification. Genome Biol. 20, 237 (2019).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
Jeffares, D. C. et al. Transient structural variations have sturdy results on quantitative traits and reproductive isolation in fission yeast. Nat. Commun. 8, 14061 (2017).
English, A. C., Menon, V. Ok., Gibbs, R. A., Metcalf, G. A. & Sedlazeck, F. J. Truvari: refined structural variant comparability preserves allelic range. Genome Biol. 23, 271 (2022).
Kirsche, M. et al. Jasmine and Iris: population-scale structural variant comparability and evaluation. Nat. Methods 20, 408–417 (2023).
Zheng, Z. et al. A sequence-aware merger of genomic structural variations at inhabitants scale. Nat. Commun. 15, 960 (2024).
McLaren, W. et al. The Ensembl Variant Effect Predictor. Genome Biol. 17, 122 (2016).
Yates, A. et al. The Ensembl REST API: Ensembl knowledge for any language. Bioinformatics 31, 143–145 (2015).
Geoffroy, V. et al. AnnotSV: an built-in device for structural variations annotation. Bioinformatics 34, 3572–3574 (2018).
Cunningham, F., Moore, B., Ruiz-Schultz, N., Ritchie, G. R. & Eilbeck, Ok. Improving the Sequence Ontology terminology for genomic variant annotation. J. Biomed. Semant. 6, 32 (2015).
Cingolani, P. et al. A program for annotating and predicting the consequences of single nucleotide polymorphisms, SnpEff: SNPs within the genome of Drosophila melanogaster pressure w1118; iso-2; iso-3. Fly 6, 80–92 (2012).
Zwaig, M. et al. Linked-read based mostly evaluation of the medulloblastoma genome. Front. Oncol. 13, 1221611 (2023).
Klever, M.-Ok. et al. AML with advanced karyotype: excessive genomic complexity revealed by mixed long-read sequencing and Hi-C know-how. Blood Adv. 7, 6520–6531 (2023).
Greer, S. U. et al. Implementation of Nanopore sequencing as a realistic workflow for copy quantity variant affirmation within the clinic. J. Transl. Med. 21, 378 (2023).
Gladysheva-Azgari, M. et al. A de novo genome meeting of cultivated Prunus persica cv. ‘Sovetskiy’. PLoS ONE 17, e0269284 (2022).
Ji, C.-M., Feng, X.-Y., Huang, Y.-W. & Chen, R.-A. The purposes of nanopore sequencing know-how in animal and human virus analysis. Viruses 16, 798 (2024).
Elrick, H. et al. SAVANA: dependable evaluation of somatic structural variants and duplicate quantity aberrations utilizing long-read sequencing. Nat. Methods 22, 1436–1446 (2025).
Keskus, A. G. et al. Severus detects somatic structural variation and complicated rearrangements in most cancers genomes utilizing long-read sequencing. Nat. Biotechnol. (2025).
Liu, L. et al. Performance of somatic structural variant calling in lung most cancers utilizing Oxford Nanopore sequencing know-how. BMC Genomics 25, 898 (2024).
Cameron, D. L., Di Stefano, L. & Papenfuss, A. T. Comprehensive analysis and characterisation of quick learn general-purpose structural variant calling software program. Nat. Commun. 10, 3240 (2019).
Kosugi, S. et al. Comprehensive analysis of structural variation detection algorithms for complete genome sequencing. Genome Biol. 20, 117 (2019).
Alioto, T. S. et al. A complete evaluation of somatic mutation detection in most cancers utilizing whole-genome sequencing. Nat. Commun. 6, 10001 (2015).
Ewing, A. D. et al. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nat. Methods 12, 623–630 (2015).
Cuenca-Guardiola, J. et al. Detection and annotation of transposable aspect insertions and deletions on the human genome utilizing nanopore sequencing. iScience 26, 108214 (2023).
Xu, L. et al. Long-read sequencing identifies novel structural variations in colorectal most cancers. PLoS Genet. 19, e1010514 (2023).
Liu, Z., Xie, Z. & Li, M. Comprehensive and deep analysis of structural variation detection pipelines with third-generation sequencing knowledge. Genome Biol. 25, 188 (2024).
Quan, C., Lu, H., Lu, Y. & Zhou, G. Population-scale genotyping of structural variation within the period of long-read sequencing. Comput. Struct. Biotechnol. J. 20, 2639–2647 (2022).
Aganezov, S. et al. An entire reference genome improves evaluation of human genetic variation. Science 376, eabl3533 (2022).
Landrum, M. J. et al. ClinVar: public archive of relationships amongst sequence variation and human phenotype. Nucleic Acids Res. 42, D980–D985 (2014).
Karczewski, Ok. J. et al. The mutational constraint spectrum quantified from variation in 141,456 people. Nature 581, 434–443 (2020).
Zhao, P., Li, L., Jiang, X. & Li, Q. Mismatch restore deficiency/microsatellite instability-high as a predictor for anti-PD-1/PD-L1 immunotherapy efficacy. J. Hematol. Oncol. 12, 54 (2019).
Cornish, A. J. et al. The genomic panorama of two,023 colorectal cancers. Nature 633, 127–136 (2024).
This web page was created programmatically, to learn the article in its authentic location you may go to the hyperlink bellow:
https://www.nature.com/articles/s41596-025-01270-5
and if you wish to take away this text from our website please contact us
