{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T16:29:32Z","timestamp":1792513772472,"version":"4.5.0"},"reference-count":162,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2025,7,29]],"date-time":"2025-07-29T00:00:00Z","timestamp":1753747200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Human Genome Sequencing Center, Baylor College of Medicine"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Structural variations (SVs) represent genomic variations that involve breakage and rejoining of DNA segments. SVs can alter normal gene dosage, lead to rearrangements of genes and regulatory elements within a topologically associated domain, and potentially contribute to physical traits, genomic disorders, or complex traits. Recent advances in sequencing technologies and bioinformatics have greatly improved SV detection and interpretation at unprecedented resolution and scale. Despite these advances, the functional impact of SVs, the underlying SV mechanism(s) contributing to complex traits, and the technical challenges associated with SV detection and annotation remain active areas of research. This review aims to provide an overview of structural variations, their mutagenesis mechanisms, and their detection in the genomics era, focusing on the biological significance, methodologies, and future directions in the field.<\/jats:p>","DOI":"10.3390\/genes16080905","type":"journal-article","created":{"date-parts":[[2025,7,29]],"date-time":"2025-07-29T12:39:29Z","timestamp":1753792769000},"page":"905","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Structural Variants: Mechanisms, Mapping, and Interpretation in Human Genetics"],"prefix":"10.3390","volume":"16","author":[{"given":"Shruti","family":"Pande","sequence":"first","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moez","family":"Dawood","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA"},{"name":"Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA"},{"name":"Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3884-7720","authenticated-orcid":false,"given":"Christopher M.","family":"Grochowski","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA"},{"name":"Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,7,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/s41586-020-2287-8","article-title":"A structural variation reference for medical and population genetics","volume":"581","author":"Collins","year":"2020","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1038\/s41586-024-07278-3","article-title":"The variation and evolution of complete human centromeres","volume":"629","author":"Logsdon","year":"2024","journal-title":"Nature"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1038\/nrg.2015.25","article-title":"Mechanisms underlying structural variant formation in genomic disorders","volume":"17","author":"Carvalho","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Lupski, J.R., and Stankiewicz, P. (2005). Genomic Disorders: Molecular Mechanisms for Rearrangements and Conveyed Phenotypes. PLoS Genet., 1.","DOI":"10.1371\/journal.pgen.0010049"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"100590","DOI":"10.1016\/j.xgen.2024.100590","article-title":"Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci","volume":"4","author":"CGrochowski","year":"2024","journal-title":"Cell Genom."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1038\/s41431-024-01680-1","article-title":"Genomic Balancing Act: Deciphering DNA rearrangements in the complex chromosomal aberration involving 5p15.2, 2q31.1, and 18q21.32","volume":"33","author":"Dardas","year":"2024","journal-title":"Eur. J. Hum. Genet."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1134","DOI":"10.1016\/j.tig.2022.06.003","article-title":"Complex genomic rearrangements: An underestimated cause of rare diseases","volume":"38","author":"Schuy","year":"2022","journal-title":"Trends Genet."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Grochowski, C.M., Krepischi, A.C., Eisfeldt, J., Du, H., Bertola, D.R., Oliveira, D., Costa, S.S., Lupski, J.R., Lindstrand, A., and Carvalho, C.M. (2021). Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin\u2013Siris Syndrome. Front. Genet., 12.","DOI":"10.3389\/fgene.2021.708348"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.1002\/humu.24106","article-title":"Cytogenetically visible inversions are formed by multiple molecular mechanisms","volume":"41","author":"Pettersson","year":"2020","journal-title":"Hum. Mutat."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.1101\/gr.6557307","article-title":"Gene copy number variation spanning 60 million years of human and primate evolution","volume":"17","author":"Dumas","year":"2007","journal-title":"Genome Res."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1755-8417-1-4","article-title":"Mechanisms for human genomic rearrangements","volume":"1","author":"Gu","year":"2008","journal-title":"Pathogenetics"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Lupski, J.R. (2015). Structural Variation Mutagenesis of the Human Genome: Impact on Disease and Evolution, John Wiley and Sons Inc.","DOI":"10.1002\/em.21943"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/S0168-9525(02)02592-1","article-title":"Genome architecture, rearrangements and genomic disorders","volume":"18","author":"Stankiewicz","year":"2002","journal-title":"Trends Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1086\/512864","article-title":"Characterization of Potocki-Lupski Syndrome (dup(17)(p11.2p11.2)) and Delineation of a Dosage-Sensitive Critical Interval That Can Convey an Autism Phenotype","volume":"80","author":"Potocki","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1002\/(SICI)1096-8628(19960329)62:3<247::AID-AJMG9>3.0.CO;2-Q","article-title":"Multi-disciplinary clinical study of Smith-Magenis syndrome (deletion 17p11.2)","volume":"62","author":"Greenberg","year":"1996","journal-title":"Am. J. Med. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1016\/j.cell.2007.11.037","article-title":"A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders","volume":"131","author":"Lee","year":"2007","journal-title":"Cell"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1146\/annurev.biochem.052308.093131","article-title":"The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway","volume":"79","author":"Lieber","year":"2010","journal-title":"Annu. Rev. Biochem."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Hastings, P.J., Ira, G., Lupski, J.R., and Matic, I. (2009). A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation. PLoS Genet., 5.","DOI":"10.1371\/journal.pgen.1000327"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1038\/nm.2988","article-title":"Chromoanagenesis and cancer: Mechanisms and consequences of localized, complex chromosomal rearrangements","volume":"18","author":"Holland","year":"2012","journal-title":"Nat. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1038\/ng.399","article-title":"The DNA replication FoSTeS\/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans","volume":"41","author":"Zhang","year":"2009","journal-title":"Nat. Genet."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/j.semcdb.2021.01.004","article-title":"Chromoanagenesis, the mechanisms of a genomic chaos","volume":"123","author":"Pellestor","year":"2022","journal-title":"Semin. Cell Dev. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/s41588-019-0576-7","article-title":"Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing","volume":"52","author":"Lee","year":"2020","journal-title":"Nat. Genet."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.semcdb.2021.02.001","article-title":"Chromothripsis, DNA repair and checkpoints defects","volume":"123","author":"Simovic","year":"2022","journal-title":"Semin. Cell Dev. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1016\/j.ccr.2013.04.025","article-title":"Chromoplexy: A New Category of Complex Rearrangements in the Cancer Genome","volume":"23","author":"Shen","year":"2013","journal-title":"Cancer Cell"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/j.ajhg.2019.02.024","article-title":"The Iceberg under Water: Unexplored Complexity of Chromoanagenesis in Congenital Disorders","volume":"104","author":"Morton","year":"2019","journal-title":"Am. J. Hum. Genet."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Cai, H., Kumar, N., Bagheri, H.C., von Mering, C., Robinson, M.D., and Baudis, M. (2014). Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. BMC Genom., 15.","DOI":"10.1186\/1471-2164-15-82"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Collins, R.L., Brand, H., Redin, C.E., Hanscom, C., Antolik, C., Stone, M.R., Glessner, J.T., Mason, T., Pregno, G., and Dorrani, N. (2017). Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome. Genome Biol., 18.","DOI":"10.1186\/s13059-017-1158-6"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1016\/j.ajhg.2015.02.005","article-title":"Chromothripsis in Healthy Individuals Affects Multiple Protein-Coding Genes and Can Result in Severe Congenital Abnormalities in Offspring","volume":"96","author":"Baas","year":"2015","journal-title":"Am. J. Hum. Genet."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.trecan.2015.10.007","article-title":"Deciphering the Code of the Cancer Genome: Mechanisms of Chromosome Rearrangement","volume":"1","author":"Willis","year":"2015","journal-title":"Trends Cancer"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1016\/j.ajhg.2011.09.009","article-title":"Frequency of Nonallelic Homol-ogous Recombination Is Correlated with Length of Homology: Evidence that Ectopic Synapsis Precedes Ec-topic Crossing-Over","volume":"89","author":"Liu","year":"2011","journal-title":"Am. J. Hum. Genet."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"D986","DOI":"10.1093\/nar\/gkt958","article-title":"The Database of Genomic Variants: A curated collection of structural variation in the human genome","volume":"42","author":"MacDonald","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"D936","DOI":"10.1093\/nar\/gks1213","article-title":"dbVar and DGVa: Public archives for genomic structural variation","volume":"41","author":"Lappalainen","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature09708","article-title":"Mapping copy number variation by population-scale genome sequencing","volume":"470","author":"Mills","year":"2011","journal-title":"Nature"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Nicholas, T.J., Cormier, M.J., and Quinlan, A.R. (2022). Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate. BMC Bioinform., 23.","DOI":"10.1186\/s12859-022-05008-y"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1038\/s41576-024-00808-9","article-title":"Diversity and consequences of structural variation in the human genome","volume":"26","author":"Collins","year":"2025","journal-title":"Nat. Rev. Genet."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/nrc2091","article-title":"The impact of translocations and gene fusions on cancer causation","volume":"7","author":"Mitelman","year":"2007","journal-title":"Nat. Rev. Cancer"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/modpathol.2008.184","article-title":"Secretory breast carcinomas with ETV6-NTRK3 fusion gene belong to the basal-like carcinoma spectrum","volume":"22","author":"Chouchane","year":"2009","journal-title":"Mod. Pathol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.1182\/blood-2008-03-144790","article-title":"Molecular biology of bcr-abl1\u2013positive chronic myeloid leukemia","volume":"113","author":"Cortes","year":"2009","journal-title":"Blood"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/j.gim.2021.10.025","article-title":"Consistent count region\u2013copy number variation (CCR-CNV): An expandable and robust tool for clinical diagnosis of copy number variation at the exon level using next-generation sequencing data","volume":"24","author":"Kim","year":"2022","journal-title":"Genet. Med."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1007\/s40142-017-0129-2","article-title":"Copy Number Variation Disorders","volume":"5","author":"Shaikh","year":"2017","journal-title":"Curr. Genet. Med. Rep."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1038\/s41436-020-0864-8","article-title":"CNVs cause autosomal recessive genetic diseases with or without involvement of SNV\/indels","volume":"22","author":"Yuan","year":"2020","journal-title":"Genet. Med."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"da Costa-Nunes, J.A., and Noordermeer, D. (2023). TADs: Dynamic structures to create stable regulatory functions. Curr. Opin. Struct. Biol., 81.","DOI":"10.1016\/j.sbi.2023.102622"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1016\/j.cell.2015.04.004","article-title":"Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions","volume":"161","author":"Kraft","year":"2015","journal-title":"Cell"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/nature19800","article-title":"Formation of new chromatin domains determines pathogenicity of genomic duplications","volume":"538","author":"Franke","year":"2016","journal-title":"Nature"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1186\/s13073-024-01378-5","article-title":"Chromatin conformation capture in the clinic: 4C-seq\/HiC distinguishes pathogenic from neutral duplications at the GPR101 locus","volume":"16","author":"Daly","year":"2024","journal-title":"Genome Med."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1475","DOI":"10.1038\/s41467-023-37057-z","article-title":"Combinatorial effects on gene expression at the Lbx1\/Fgf8 locus resolve split-hand\/foot malformation type 3","volume":"14","author":"Cova","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Salnikov, P., Korablev, A., Serova, I., Belokopytova, P., Yan, A., Stepanchuk, Y., Tikhomirov, S., and Fishman, V. (2024). Structural variants in the Epb41l4a locus: TAD disruption and Nrep gene misregulation as hypothetical drivers of neurodevelopmental outcomes. Sci. Rep., 14.","DOI":"10.1038\/s41598-024-52545-y"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/s41436-019-0686-8","article-title":"Technical standards for the interpretation and reporting of constitutional copy-number variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen)","volume":"22","author":"Riggs","year":"2020","journal-title":"Genet. Med."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1016\/j.ajhg.2009.03.010","article-title":"DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources","volume":"84","author":"Firth","year":"2009","journal-title":"Am. J. Hum. Genet."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"D1062","DOI":"10.1093\/nar\/gkx1153","article-title":"ClinVar: Improving access to variant interpretations and supporting evidence","volume":"46","author":"Landrum","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1601-5223.1956.tb03010.x","article-title":"The Chromosome Number Of Man","volume":"42","author":"Tjio","year":"2010","journal-title":"Hereditas"},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Harel, T., and Lupski, J. (2018). Genomic Disorders 20 Years on\u2014Mechanisms for Clinical Manifestations, Blackwell Publishing Ltd.","DOI":"10.1111\/cge.13146"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"2073","DOI":"10.1073\/pnas.68.9.2073","article-title":"Specific Banding Patterns of Human Chromosomes (heterochromatin\/Giemsa stain\/chromosome bands)","volume":"68","author":"Drets","year":"1971","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/s13039-015-0125-8","article-title":"History and evolution of cytogenetics","volume":"8","year":"2015","journal-title":"Mol. Cytogenet."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1590\/1806-9282.62.03.262","article-title":"Retrospective Karyotype Study in Mentally Retarded Patients","volume":"62","author":"Teixeira","year":"2016","journal-title":"Rev. Assoc. Med. Bras."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1002\/humu.23537","article-title":"Marker Chromosome Genomic Structure and Temporal Origin Implicate a Chro-moanasynthesis Event in a Family with Pleiotropic Psychiatric Phenotypes","volume":"39","author":"Grochowski","year":"2018","journal-title":"Hum. Mutat."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/gim.2016.132","article-title":"Clinical relevance of small copy-number variants in chromosomal microarray clinical testing","volume":"19","author":"Hollenbeck","year":"2017","journal-title":"Genet. Med."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1016\/j.ajhg.2010.04.006","article-title":"Consensus Statement: Chromosomal Microarray Is a First-Tier Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital Anomalies","volume":"86","author":"Miller","year":"2010","journal-title":"Am. J. Hum. Genet."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1097\/GIM.0b013e318177015c","article-title":"Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray","volume":"10","author":"Baldwin","year":"2008","journal-title":"Genet. Med."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1159\/000334066","article-title":"Interpretation of Array Comparative Genome Hybridization Data: A Major Challenge","volume":"135","author":"Gijsbers","year":"2011","journal-title":"Cytogenet. Genome Res."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Qian, G., Cai, L., Yao, H., and Dong, X. (2023). Chromosome microarray analysis combined with karyotype analysis is a powerful tool for the detection in pregnant women with high-risk indicators. BMC Pregnancy Childbirth, 23.","DOI":"10.1186\/s12884-023-06052-z"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1038\/ng0295-132","article-title":"The detection of subtelomeric chromosomal rearrangements in idiopathic mental retardation","volume":"9","author":"Flint","year":"1995","journal-title":"Nat. Genet."},{"key":"ref_63","unstructured":"Eijk-Van Os, P.G.C., and Schouten, J.P. (2011). Multiplex Ligation-Dependent Probe Amplification (MLPA\u00ae) for the Detection of Copy Number Variation in Genomic Sequences, Springer Nature."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"3245","DOI":"10.3390\/ijms13033245","article-title":"Use of the MLPA Assay in the Molecular Diagnosis of Gene Copy Number Alterations in Human Genetic Diseases","volume":"13","author":"Stuppia","year":"2012","journal-title":"Int. J. Mol. Sci."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1101\/gr.227975.117","article-title":"Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer","volume":"28","author":"Chan","year":"2018","journal-title":"Genome Res."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/s41597-022-01684-w","article-title":"Optical mapping compendium of structural variants across global cattle breeds","volume":"9","author":"Talenti","year":"2022","journal-title":"Sci. Data"},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Schrauwen, I., Rajendran, Y., Acharya, A., \u00d6hman, S., Arvio, M., Paetau, R., Siren, A., Avela, K., Granvik, J., and Leal, S.M. (2024). Optical genome mapping unveils hidden structural variants in neurodevelopmental disorders. Sci. Rep., 14.","DOI":"10.1038\/s41598-024-62009-y"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1186\/s13073-024-01411-7","article-title":"Structural variant allelic heterogeneity in MECP2 duplication syndrome provides insight into clinical severity and variability of disease expression","volume":"16","author":"Pehlivan","year":"2024","journal-title":"Genome Med."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Zhang, L., Bai, W., Yuan, N., Du, Z., and Ioshikhes, I. (2019). Comprehensively benchmarking applications for detecting copy number variation. PLoS Comput. Biol., 15.","DOI":"10.1371\/journal.pcbi.1007069"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1101\/gr.114876.110","article-title":"CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing","volume":"21","author":"Abyzov","year":"2011","journal-title":"Genome Res."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Schmidt, M., and Kutzner, A. (2023). MSV: A modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads. Genome Biol., 24.","DOI":"10.1186\/s13059-023-03009-5"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1093\/bioinformatics\/btv710","article-title":"Manta: Rapid detection of structural variants and indels for germline and cancer sequencing applications","volume":"32","author":"Chen","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"English, A.C., Salerno, W.J., A Hampton, O., Gonzaga-Jauregui, C., Ambreth, S., I Ritter, D., Beck, C.R., Davis, C.F., Dahdouli, M., and Ma, S. (2015). Assessing structural variation in a personal genome\u2014Towards a human reference diploid genome. BMC Genom., 16.","DOI":"10.1186\/s12864-015-1479-3"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1038\/s41592-018-0001-7","article-title":"Accurate detection of complex structural variations using single-molecule sequencing","volume":"15","author":"Sedlazeck","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Yi, D., Nam, J.-W., and Jeong, H. (2023). Toward the functional interpretation of somatic structural variations: Bulk-and single-cell approaches. Brief. Bioinform., 24.","DOI":"10.1093\/bib\/bbad297"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1865","DOI":"10.1093\/bioinformatics\/btp394","article-title":"Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads","volume":"25","author":"Ye","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Layer, R.M., Chiang, C., Quinlan, A.R., and Hall, I.M. (2014). LUMPY: A probabilistic framework for structural variant discovery. Genome Biol., 15.","DOI":"10.1186\/gb-2014-15-6-r84"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"i333","DOI":"10.1093\/bioinformatics\/bts378","article-title":"DELLY: Structural variant discovery by integrated paired-end and split-read analysis","volume":"28","author":"Rausch","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"e8214","DOI":"10.7717\/peerj.8214","article-title":"sv-callers: A highly portable parallel workflow for structural variant detection in whole-genome sequence data","volume":"8","author":"Kuzniar","year":"2020","journal-title":"PeerJ"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"2050","DOI":"10.1101\/gr.222109.117","article-title":"GRIDSS: Sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly","volume":"27","author":"Cameron","year":"2017","journal-title":"Genome Res."},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Dierckxsens, N., Li, T., Vermeesch, J.R., and Xie, Z. (2021). A benchmark of structural variation detection by long reads through a realistic simulated model. Genome Biol., 22.","DOI":"10.1186\/s13059-021-02551-4"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"gix091","DOI":"10.1093\/gigascience\/gix091","article-title":"Lightning-fast genome variant detection with GROM","volume":"6","author":"Smith","year":"2017","journal-title":"Gigascience"},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"English, A.C., Salerno, W.J., and Reid, J.G. (2014). PBHoney: Identifying Genomic Variants via Long-read Discord-ance and Interrupted mapping. BMC Bioinform., 15.","DOI":"10.1186\/1471-2105-15-180"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"1326","DOI":"10.1038\/s41467-017-01343-4","article-title":"Mapping and phasing of structural variation in patient genomes using nanopore sequencing","volume":"8","author":"Stancu","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Tham, C.Y., Tirado-Magallanes, R., Goh, Y., Fullwood, M.J., Koh, B.T., Wang, W., Ng, C.H., Chng, W.J., Thiery, A., and Tenen, D.G. (2020). NanoVar: Accurate characterization of patients\u2019 genomic structural variants using low-depth nanopore sequencing. Genome Biol., 21.","DOI":"10.1186\/s13059-020-01968-7"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"eaar6343","DOI":"10.1126\/science.aar6343","article-title":"High-resolution comparative analysis of great ape genomes","volume":"360","author":"Kronenberg","year":"2018","journal-title":"Science"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1038\/s41587-023-02024-y","article-title":"Detection of mosaic and population-level structural variants with Sniffles2","volume":"42","author":"Smolka","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"2907","DOI":"10.1093\/bioinformatics\/btz041","article-title":"SVIM: Structural variant identification using mapped long reads","volume":"35","author":"Heller","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"3647","DOI":"10.1093\/bioinformatics\/btab341","article-title":"SKSV: Ultrafast structural variation detection from circular consensus sequencing reads","volume":"37","author":"Liu","year":"2021","journal-title":"Bioinformatics"},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"Ding, H., and Luo, J. (2022). MAMnet: Detecting and genotyping deletions and insertions based on long reads and a deep learning approach. Brief. Bioinform., 23.","DOI":"10.1093\/bib\/bbac195"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/s41467-023-35996-1","article-title":"Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak","volume":"14","author":"Chen","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"2224","DOI":"10.1101\/gr.126599.111","article-title":"Assemblathon 1: A competitive assessment of de novo short read assembly methods","volume":"21","author":"Earl","year":"2011","journal-title":"Genome Res."},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Lee, H., Gurtowski, J., Yoo, S., Marcus, S., McCombie, W.R., and Schatz, M. (2014). Error correction and assembly complexity of single molecule sequencing reads. bioRxiv.","DOI":"10.1101\/006395"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1038\/nbt.1904","article-title":"Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly","volume":"29","author":"Li","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1038\/nmeth.4084","article-title":"novoBreak: Local assembly for breakpoint detection in cancer genomes","volume":"14","author":"Chong","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"3021","DOI":"10.1093\/bioinformatics\/btw369","article-title":"Assemblytics: A web analytics tool for the detection of variants from an assembly","volume":"32","author":"Nattestad","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Mar\u00e7ais, G., Delcher, A.L., Phillippy, A.M., Coston, R., Salzberg, S.L., Zimin, A., and Darling, A.E. (2018). MUMmer4: A fast and versatile genome alignment system. PLoS Comput. Biol., 14.","DOI":"10.1371\/journal.pcbi.1005944"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"3240","DOI":"10.1038\/s41467-019-11146-4","article-title":"Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software","volume":"10","author":"Cameron","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_99","doi-asserted-by":"crossref","unstructured":"Du, H., Lun, M.Y., Gagarina, L., Mehaffey, M.G., Hwang, J.P., Jhangiani, S.N., Bhamidipati, S.V., Muzny, D.M., Poli, M.C., and Ochoa, S. (2024). VizCNV: An integrated platform for concurrent phased BAF and CNV analysis with trio genome sequencing data. bioRxiv, preprint.","DOI":"10.1101\/2024.10.27.620363"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1101\/gr.221028.117","article-title":"SvABA: Genome-wide detection of structural variants and indels by local assembly","volume":"28","author":"Wala","year":"2018","journal-title":"Genome Res."},{"key":"ref_101","doi-asserted-by":"crossref","unstructured":"Chen, S., Krusche, P., Dolzhenko, E., Sherman, R.M., Petrovski, R., Schlesinger, F., Kirsche, M., Bentley, D.R., Schatz, M.C., and Sedlazeck, F.J. (2019). Paragraph: A graph-based structural variant genotyper for short-read sequence data. Genome Biol., 20.","DOI":"10.1186\/s13059-019-1909-7"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"2741","DOI":"10.1093\/bioinformatics\/btv204","article-title":"MetaSV: An accurate and integrative structural-variant caller for next generation sequencing","volume":"31","author":"Mohiyuddin","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"Roberts, R.J., Carneiro, M.O., and Schatz, M.C. (2013). The advantages of SMRT sequencing. Genome Biol., 14.","DOI":"10.1186\/gb-2013-14-7-405"},{"key":"ref_104","doi-asserted-by":"crossref","unstructured":"Jain, M., Olsen, H.E., Paten, B., and Akeson, M. (2016). The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community. Genome Biol., 17.","DOI":"10.1186\/s13059-016-1103-0"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1101\/gr.279975.124","article-title":"A Hitchhiker\u2019s Guide to long-read genomic analysis","volume":"35","author":"Mahmoud","year":"2025","journal-title":"Genome Res."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"eabf7117","DOI":"10.1126\/science.abf7117","article-title":"Haplotype-resolved diverse human genomes and integrated analysis of structural variation","volume":"372","author":"Ebert","year":"2021","journal-title":"Science"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/s41586-020-2371-0","article-title":"Mapping and characterization of structural variation in 17,795 human genomes","volume":"583","author":"Genomics","year":"2020","journal-title":"Nature"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"23243","DOI":"10.1073\/pnas.1912175116","article-title":"Human-specific tandem repeat expansion and differential gene expression during primate evolution","volume":"116","author":"Sulovari","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1038\/s41592-023-01932-w","article-title":"A survey of algorithms for the detection of genomic structural variants from long-read sequencing data","volume":"20","author":"Ahsan","year":"2023","journal-title":"Nat. Methods"},{"key":"ref_110","doi-asserted-by":"crossref","unstructured":"Aydin, S.K., Yilmaz, K.C., and Acar, A. (2025). Benchmarking long-read structural variant calling tools and combinations for detecting somatic variants in cancer genomes. Sci. Rep., 15.","DOI":"10.1038\/s41598-025-92750-x"},{"key":"ref_111","doi-asserted-by":"crossref","unstructured":"Helal, A.A., Saad, B.T., Saad, M.T., Mosaad, G.S., and Aboshanab, K.M. (2024). Benchmarking long-read aligners and SV callers for structural variation detection in Oxford nanopore sequencing data. Sci. Rep., 14.","DOI":"10.1038\/s41598-024-56604-2"},{"key":"ref_112","doi-asserted-by":"crossref","unstructured":"Jiang, T., Liu, Y., Jiang, Y., Li, J., Gao, Y., Cui, Z., Liu, Y., Liu, B., and Wang, Y. (2020). Long-read-based human genomic structural variation detection with cuteSV. Genome Biol., 21.","DOI":"10.1186\/s13059-020-02107-y"},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/s41592-022-01674-1","article-title":"SVDSS: Structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads","volume":"20","author":"Denti","year":"2023","journal-title":"Nat. Methods"},{"key":"ref_114","doi-asserted-by":"crossref","unstructured":"Zheng, Y., Shang, X., and Sung, W.-K. (2023). SVsearcher: A more accurate structural variation detection method in long read data. Comput. Biol. Med., 158.","DOI":"10.1016\/j.compbiomed.2023.106843"},{"key":"ref_115","doi-asserted-by":"crossref","unstructured":"Zheng, Y., and Shang, X. (2024). SVvalidation: A long-read-based validation method for genomic structural varia-tion. PLoS ONE, 19.","DOI":"10.1371\/journal.pone.0291741"},{"key":"ref_116","doi-asserted-by":"crossref","unstructured":"Zheng, Y., and Shang, X. (2023). SVcnn: An accurate deep learning-based method for detecting structural variation based on long-read data. BMC Bioinform., 24.","DOI":"10.1186\/s12859-023-05324-x"},{"key":"ref_117","doi-asserted-by":"crossref","unstructured":"Xia, Z., Xiang, W., Wang, Q., Li, X., Li, Y., Gao, J., Tang, T., Yang, C., Cui, Y., and Birol, I. (2024). CSV-Filter: A deep learning-based comprehensive structural variant filtering method for both short and long reads. Bioinformatics, 40.","DOI":"10.1093\/bioinformatics\/btae539"},{"key":"ref_118","doi-asserted-by":"crossref","unstructured":"Linderman, M.D., Wallace, J., van der Heyde, A., Wieman, E., Brey, D., Shi, Y., Hansen, P., Shamsi, Z., Liu, J., and Gelb, B.D. (2024). NPSV-deep: A deep learning method for genotyping structural variants in short read genome sequencing data. Bioinformatics, 40.","DOI":"10.1093\/bioinformatics\/btae129"},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"2406","DOI":"10.1038\/s41467-025-57756-z","article-title":"SVLearn: A dual-reference machine learning approach enables accurate cross-species genotyping of structural variants","volume":"16","author":"Yang","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/s41467-020-20850-5","article-title":"PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes","volume":"12","author":"Niehus","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"ii11","DOI":"10.1093\/bioinformatics\/btae391","article-title":"GGTyper: Genotyping complex structural variants using short-read sequencing data","volume":"40","author":"Mirus","year":"2024","journal-title":"Bioinformatics"},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1038\/s41592-021-01299-w","article-title":"Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads","volume":"18","author":"Shafin","year":"2021","journal-title":"Nat. Methods"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1038\/nmeth.2206","article-title":"DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution","volume":"9","author":"Falconer","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"e30560","DOI":"10.7554\/eLife.30560","article-title":"Genome-wide mapping of sister chromatid exchange events in single yeast cells using Strand-seq","volume":"6","author":"Claussin","year":"2017","journal-title":"Elife"},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1101\/gr.201160.115","article-title":"Characterizing polymorphic inversions in human genomes by single-cell sequencing","volume":"26","author":"Sanders","year":"2016","journal-title":"Genome Res."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/s41587-019-0366-x","article-title":"Single-cell analysis of structural variations and complex rearrangements with tri-channel processing","volume":"38","author":"Sanders","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_127","doi-asserted-by":"crossref","unstructured":"Weber, T., Cosenza, M.R., and Korbel, J. (2023). MosaiCatcher v2: A single-cell structural variations detection and analysis reference framework based on Strand-seq. Bioinformatics, 39.","DOI":"10.1093\/bioinformatics\/btad633"},{"key":"ref_128","doi-asserted-by":"crossref","unstructured":"Harewood, L., Kishore, K., Eldridge, M.D., Wingett, S., Pearson, D., Schoenfelder, S., Collins, V.P., and Fraser, P. (2017). Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours. Genome Biol., 18.","DOI":"10.1186\/s13059-017-1253-8"},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1007\/978-1-0716-1390-0_7","article-title":"Analysis of Hi-C Data for Discovery of Structural Variations in Cancer","volume":"2301","author":"Song","year":"2022","journal-title":"Methods Mol. Biol."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.ymeth.2012.05.001","article-title":"Hi\u2013C: A comprehensive technique to capture the conformation of genomes","volume":"58","author":"Belton","year":"2012","journal-title":"Methods"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1038\/s41588-018-0195-8","article-title":"Integrative detection and analysis of structural variation in cancer genomes","volume":"50","author":"Dixon","year":"2018","journal-title":"Nat. Genet."},{"key":"ref_132","doi-asserted-by":"crossref","unstructured":"Li, J., Gao, L., and Ye, Y. (2023). HiSV: A control-free method for structural variation detection from Hi-C data. PLoS Comput. Biol., 19.","DOI":"10.1371\/journal.pcbi.1010760"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1038\/nbt.3432","article-title":"Haplotyping germline and cancer genomes with high-throughput linked-read sequencing","volume":"34","author":"Zheng","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"4397","DOI":"10.1093\/bioinformatics\/btz239","article-title":"Structural variant analysis for linked-read sequencing data with gemtools","volume":"35","author":"Greer","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"5585","DOI":"10.1038\/s41467-019-13397-7","article-title":"LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data","volume":"10","author":"Fang","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_136","doi-asserted-by":"crossref","unstructured":"Gunturkun, M.H., Villani, F., Colonna, V., Ashbrook, D., Williams, R.W., and Chen, H. (2021). SVJAM: Joint Analysis of Structural Variants Using Linked Read Sequencing Data. bioRxiv, preprint.","DOI":"10.1101\/2021.11.02.467006"},{"key":"ref_137","doi-asserted-by":"crossref","unstructured":"Guichard, A., Legeai, F., Tagu, D., and Lemaitre, C. (2023). MTG-Link: Leveraging barcode information from linked-reads to assemble specific loci. BMC Bioinform., 24.","DOI":"10.1186\/s12859-023-05395-w"},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"1490","DOI":"10.12688\/f1000research.20233.1","article-title":"A Sequence Distance Graph framework for genome assembly and analysis","volume":"8","author":"Yanes","year":"2019","journal-title":"F1000Research"},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nrg2958","article-title":"Genome structural variation discovery and genotyping","volume":"12","author":"Alkan","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature15394","article-title":"An integrated map of structural variation in 2,504 human genomes","volume":"526","author":"Sudmant","year":"2015","journal-title":"Nature"},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"1784","DOI":"10.1038\/s41467-018-08148-z","article-title":"Multi-platform discovery of haplotype-resolved structural variation in human genomes","volume":"10","author":"Chaisson","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_142","doi-asserted-by":"crossref","unstructured":"Mahmoud, M., Gobet, N., Cruz-D\u00e1valos, D.I., Mounier, N., Dessimoz, C., and Sedlazeck, F.J. (2019). Structural Variant Calling: The Long and the Short of It, BioMed Central Ltd.","DOI":"10.1186\/s13059-019-1828-7"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/s41597-023-02076-4","article-title":"A collection of read depth profiles at structural variant breakpoints","volume":"10","author":"Bezdvornykh","year":"2023","journal-title":"Sci. Data"},{"key":"ref_144","doi-asserted-by":"crossref","unstructured":"Joe, S., Park, J.-L., Kim, J., Kim, S., Park, J.-H., Yeo, M.-K., Lee, D., Yang, J.O., and Kim, S.-Y. (2024). Comparison of structural variant callers for massive whole-genome sequence data. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10239-9"},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.1038\/s41587-020-0538-8","article-title":"A robust benchmark for detection of germline large deletions and insertions","volume":"38","author":"Zook","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1038\/nbt.4227","article-title":"Variation graph toolkit improves read mapping by representing genetic variation in the reference","volume":"36","author":"Garrison","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"ref_147","doi-asserted-by":"crossref","unstructured":"Rautiainen, M., and Marschall, T. (2020). GraphAligner: Rapid and versatile sequence-to-graph alignment. Genome Biol., 21.","DOI":"10.1186\/s13059-020-02157-2"},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"101928","DOI":"10.1016\/j.gimo.2024.101928","article-title":"11: To remap or not to remap: The relevance of the genome references to resolve rare inversions","volume":"3","author":"Carvalho","year":"2025","journal-title":"Genet. Med. Open"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1126\/science.abj6987","article-title":"The complete sequence of a human genome","volume":"376","author":"Nurk","year":"2022","journal-title":"Science"},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"eabl3533","DOI":"10.1126\/science.abl3533","article-title":"A complete reference genome improves analysis of human genetic variation","volume":"376","author":"Carvalho","year":"2022","journal-title":"Science"},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1038\/s41586-023-05896-x","article-title":"A draft human pangenome reference","volume":"617","author":"Liao","year":"2023","journal-title":"Nature"},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/j.cell.2018.12.019","article-title":"Characterizing the Major Structural Variant Alleles of the Human Genome","volume":"176","author":"Audano","year":"2019","journal-title":"Cell"},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"3426","DOI":"10.1016\/j.cell.2022.08.004","article-title":"High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios","volume":"185","author":"Evani","year":"2022","journal-title":"Cell"},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1101\/gr.214007.116","article-title":"Discovery and genotyping of structural variation from long-read haploid genome sequence data","volume":"27","author":"Huddleston","year":"2017","journal-title":"Genome Res."},{"key":"ref_155","doi-asserted-by":"crossref","unstructured":"Gupta, P., O\u2019nEill, H., Wolvetang, E.J., Chatterjee, A., and Gupta, I. (2024). Advances in single-cell long-read sequencing technologies. NAR Genom. Bioinform., 6.","DOI":"10.1093\/nargab\/lqae047"},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"giaa145","DOI":"10.1093\/gigascience\/giaa145","article-title":"Parliament2: Accurate structural variant calling at scale","volume":"9","author":"Zarate","year":"2020","journal-title":"Gigascience"},{"key":"ref_157","doi-asserted-by":"crossref","unstructured":"Dawood, M., Heavner, B., Wheeler, M.M., Ungar, R.A., LoTempio, J., Wiel, L., Berger, S., Bernstein, J.A., Chong, J.X., and D\u00e9lot, E.C. (2024). GREGoR: Accelerating Genomics for Rare Diseases. arXiv.","DOI":"10.1016\/j.gimo.2025.102104"},{"key":"ref_158","doi-asserted-by":"crossref","unstructured":"GTEx Consortium, Chiang, C., Scott, A.J., Davis, J.R., Tsang, E.K., Li, X., Kim, Y., Hadzic, T., Damani, F.N., and Ganel, L. (2017). The impact of structural variation on human gene expression. Nat. Genet., 49, 692\u2013699.","DOI":"10.1038\/ng.3834"},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"102240","DOI":"10.1016\/j.gde.2024.102240","article-title":"Deciphering the role of structural variation in human evolution: A functional perspective","volume":"88","author":"Karageorgiou","year":"2024","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"3572","DOI":"10.1093\/bioinformatics\/bty304","article-title":"AnnotSV: An integrated tool for structural variations annotation","volume":"34","author":"Geoffroy","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1093\/bioinformatics\/btw789","article-title":"SVScore: An impact prediction tool for structural variation","volume":"33","author":"Ganel","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1038\/nature08516","article-title":"Origins and functional impact of copy number variation in the human genome","volume":"464","author":"Conrad","year":"2010","journal-title":"Nature"}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/16\/8\/905\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:18:02Z","timestamp":1760033882000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/16\/8\/905"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,29]]},"references-count":162,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2025,8]]}},"alternative-id":["genes16080905"],"URL":"https:\/\/doi.org\/10.3390\/genes16080905","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,29]]}}}