Characterizing the Major Structural Variant Alleles of the Human Genome

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An integrated map of genetic variation from 1,092 human genomes

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Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing

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The role of clustered protocadherins in neurodevelopment and neuropsychiatric diseases

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A benchmark of structural variation detection by long reads through a realistic simulated model

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Mitochondrial Damage-Associated Molecular Patterns Content in Extracellular Vesicles Promotes Early Inflammation in Neurodegenerative Disorders

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Characterization of genome-wide STR variation in 6487 human genomes

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Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

Quan, C., Li, Y., Liu, X., Wang, Y., Ping, J., Lu, Y., & Zhou, G. (2021) · Genome biology · doi:10.1186/s13059-021-02382-3 · Cited by 71

Diversity and consequences of structural variation in the human genome

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Cas9 targeted enrichment of mobile elements using nanopore sequencing

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The missing heritability of familial colorectal cancer

Schubert, S. A., Morreau, H. M., de Miranda, N. F. C. C., & van Wezel, T. (2019) · Mutagenesis · doi:10.1093/mutage/gez027 · Cited by 69

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

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Evolutionary origin of genomic structural variations in domestic yaks

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Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity

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A Practical Guide for Structural Variation Detection in the Human Genome

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Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism

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An open resource of structural variation for medical and population geneticsPreprint

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A robust benchmark for germline structural variant detectionPreprint

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Personalized and graph genomes reveal missing signal in epigenomic data

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Long-read whole-genome analysis of human single cells

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Towards a reference genome that captures global genetic diversity

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Structural Variation and Introgression from Wild Populations in East Asian Cattle Genomes Confer Adaptation to Local Environment

Xia, X., Zhang, F., Li, S., Luo, X., Peng, L., Dong, Z., Pausch, H., Leonard, A. S., Crysnanto, D., Wang, S., et al. (2023) · Genome biology · doi:10.1186/s13059-023-03052-2 · Cited by 53

The Telomere Paradox: Stable Genome Preservation with Rapidly Evolving Proteins

Saint‐Leandre, B., & Levine, M. T. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.01.007 · Cited by 51

Long-read trio sequencing of individuals with unsolved intellectual disability

Pauper, M., Küçük, E., Wenger, A. M., Chakraborty, S., Baybayan, P. A., Kwint, M. P., van der Sanden, B. P. G. H., Nelen, M. R., Derks, R. C., Brunner, H. G., et al. (2020) · European Journal of Human Genetics · doi:10.1038/s41431-020-00770-0 · Cited by 52

snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets

Tesi, N., van der Lee, S. J., Hulsman, M., Holstege, H. H., & Reinders, M. J. T. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab410 · Cited by 49

Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants

Zhang, P., Mbodj, A., Soundiramourtty, A., Llauro, C., Ghesquière, A., Ingouff, M., Slotkin, R. K., Pontvianne, F., Catoni, M., & Mirouze, M. (2023) · Nature Communications · doi:10.1038/s41467-023-41023-0 · Cited by 52

Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing

Pérez‐Rodríguez, D., Kalyva, M., Leija‐Salazar, M., Lashley, T., Tarabichi, M., Chelban, V., Gentleman, S., Schottlaender, L., Franklin, H., Vasmatzis, G., et al. (2019) · Acta Neuropathologica Communications · doi:10.1186/s40478-019-0873-5 · Cited by 51

Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning

Atak, Z. K., Taskiran, I. I., Demeulemeester, J., Flerin, C., Mauduit, D., Minnoye, L., Hulselmans, G., Christiaens, V., Ghanem, G.-E., Wouters, J., et al. (2021) · Genome Research · doi:10.1101/gr.260851.120 · Cited by 48

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Rice, E. S., Alberdi, A., Alfieri, J. M., Athrey, G., Balacco, J., Bardou, P., Blackmon, H., Charles, M., Cheng, H. H., Fedrigo, O. D., et al. (2023) · BMC Biology · doi:10.1186/s12915-023-01758-0 · Cited by 58

Challenges in quantifying genome erosion for conservation

Bosse, M., & van Loon, S. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.960958 · Cited by 50

Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs

Jiang, Y., Wang, S., Wang, C., Xu, R.-H., Wang, W., Jiang, Y., Wang, M., Jiang, L., Dai, L.-H., Wang, J., et al. (2023) · iScience · doi:10.1016/j.isci.2023.106119 · Cited by 43

A 25-year odyssey of genomic technology advances and structural variant discovery

Porubskỳ, D., & Eichler, E. E. (2024) · Cell · doi:10.1016/j.cell.2024.01.002 · Cited by 51

The landscape of genomic structural variation in Indigenous Australians

Reis, A. L. M., Rapadas, M., Hammond, J. W., Gamaarachchi, H., Stevanovski, I., Kumaheri, M. A., Chintalaphani, S. R., Dissanayake, D. S. B., Siggs, O. M., Hewitt, A. W., et al. (2023) · Nature · doi:10.1038/s41586-023-06842-7 · Cited by 51

Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits

Li, Q., Qiao, X., Li, L., Gu, C., Yin, H., Qi, K., Xie, Z., Yang, S. L., Zhao, Q., Wang, Z., et al. (2024) · Plant Communications · doi:10.1016/j.xplc.2024.101000 · Cited by 50

Functional and population genetic features of copy number variations in two dairy cattle populations

Lee, Y.-L., Bosse, M., Mullaart, E., Groenen, M. A. M., Veerkamp, R. F., & Bouwman, A. C. (2020) · BMC Genomics · doi:10.1186/s12864-020-6496-1 · Cited by 49

Structural variant landscapes reveal convergent signatures of evolution in sheep and goats

Yang, J. H., Wang, D.-F., Huang, J.-H., Zhu, Q., Luo, L.-Y., Lu, R., Xie, X.-L., Salehian-Dehkordi, H., Esmailizadeh, A., Liu, G. E., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03288-6 · Cited by 56

Local adaptation and archaic introgression shape global diversity at human structural variant loci

Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., & McCoy, R. C. (2021) · eLife · doi:10.7554/elife.67615 · Cited by 47

A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species

Dai, X., Bian, P., Hu, D., Luo, F., Huang, Y., Jiao, S., Wang, X., Gong, M., Li, R., Cai, Y., et al. (2023) · Genome Research · doi:10.1101/gr.277481.122 · Cited by 43

Characterizing mobile element insertions in 5675 genomes

Niu, Y., Teng, X., Zhou, H., Shi, Y., Li, Y., Tang, Y., Zhang, P., Luo, H., Kang, Q., Xu, T., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac128 · Cited by 46

Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recallPreprint

Harvey, W. T., Ebert, P., Ebler, J., Audano, P. A., Munson, K. M., Hoekzema, K., Porubskỳ, D., Beck, C. R., Marschall, T., Garimella, K. V., et al. (2023) · Genome Research · doi:10.1101/gr.278070.123 · Cited by 43

Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation

Jiang, T., Liu, S., Cao, S., Liu, Y., Cui, Z., Wang, Y., & Guo, H. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04422-y · Cited by 39

Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer

Ivancevic, A. M., Simpson, D. M., Joyner, O., Bagby, S. M., Nguyen, L. L., Bitler, B. G., Pitts, T. M., & Chuong, E. B. (2024) · Science Advances · doi:10.1126/sciadv.ado1218 · Cited by 42

Whole‐genome de novo assemblies reveal extensive structural variations and dynamic organelle‐to‐nucleus DNA transfers in African and Asian rice

Ma, X., Fan, J., Wu, Y., Zhao, S., Zheng, X., Sun, C., & Tan, L. (2020) · The Plant Journal · doi:10.1111/tpj.14946 · Cited by 40

Single individual structural variant detection uncovers widespread hemizygosity in molluscs

Calcino, A., Kenny, N. J., & Gerdol, M. (2021) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2020.0153 · Cited by 41

Genome‐Wide Analysis of Structural Variants in Parkinson Disease

Billingsley, K. J., Ding, J., Jerez, P. Á., Illarionova, A., Levine, K. S., Grenn, F. P., Makarious, M. B., Moore, A. K., Vitale, D., Reed, X., et al. (2023) · Annals of Neurology · doi:10.1002/ana.26608 · Cited by 41

Association of CNVs with methylation variation

Shi, X. M., Radhakrishnan, S., Wen, J., Chen, J. Y., Chen, J., Lam, B. A., Mills, R. E., Stranger, B. E., Lee, C., & Setlur, S. R. (2020) · npj Genomic Medicine · doi:10.1038/s41525-020-00145-w · Cited by 38

Chimeric RNAs Discovered by RNA Sequencing and Their Roles in Cancer and Rare Genetic Diseases

Sun, Y., & Li, H. (2022) · Genes · doi:10.3390/genes13050741 · Cited by 37

SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads

Denti, L., Khorsand, P., Bonizzoni, P., Hormozdiari, F., & Chikhi, R. (2022) · Nature Methods · doi:10.1038/s41592-022-01674-1 · Cited by 42

Ultrasensitive Detection of Organophosphorus Pesticides Using Single-Molecule Conductance Measurement

Dong, X., Tang, Z., Zhang, H., Hu, Y., Yao, Z., Huang, R., Bai, J., Yang, Y., & Hong, W. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c00691 · Cited by 36

Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats

Jakubosky, D. A., Smith, E. N., D’Antonio, M., Bonder, M. J., Greenwald, W. W. Y., D’Antonio‐Chronowska, A., Matsui, H., Bonder, M. J., Cai, N., Carcamo‐Orive, I., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16481-5 · Cited by 39

Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression

Garg, P., Martin-Trujillo, A., Rodriguez, O. L., Gies, S. J., Hadelia, E., Jadhav, B., Jain, M., Paten, B., & Sharp, A. J. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.03.016 · Cited by 37

The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi

Gorkovskiy, A., & Verstrepen, K. J. (2021) · Genes · doi:10.3390/genes12050699 · Cited by 44

Determining the impact of uncharacterized inversions in the human genome by droplet digital PCRPreprint

Puig, M., Lerga-Jaso, J., Giner-Delgado, C., Pacheco, S., Izquierdo, D., Delprat, A., Gayà‐Vidal, M., Regan, J. F., Karlin-Neumann, G. A., & Cáceres, M. (2020) · Genome Research · doi:10.1101/gr.255273.119 · Cited by 34

Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variationPreprint

Gustafson, J. A., Gibson, S. B., Damaraju, N., Zalusky, M. P., Hoekzema, K., Twesigomwe, D., Yang, L., Snead, A. A., Richmond, P. A., Coster, W. D., et al. (2024) · medRxiv · doi:10.1101/2024.03.05.24303792 · Cited by 34

Structural variants involved in high-altitude adaptation detected using single-molecule long-read sequencing

Shi, J., Jia, Z., Sun, J., Wang, X.-R., Zhao, X., Zhao, C., Liang, F., Song, X., Guan, J., Xue, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-44034-z · Cited by 37

MoMI-G: modular multi-scale integrated genome graph browser

Yokoyama, T., Sakamoto, Y., Seki, M., Suzuki, Y., & Kasahara, M. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3145-2 · Cited by 38

A pipeline for complete characterization of complex germline rearrangements from long DNA reads

Mitsuhashi, S., Ohori, S., Katoh, K., Frith, M. C., & Matsumoto, N. (2020) · Genome Medicine · doi:10.1186/s13073-020-00762-1 · Cited by 36

SVFX: a machine learning framework to quantify the pathogenicity of structural variants

Kumar, S., Harmanci, A. O., Vytheeswaran, J., & Gerstein, M. (2020) · Genome biology · doi:10.1186/s13059-020-02178-x · Cited by 36

Hidden biases in germline structural variant detection

Khayat, M. M., Sahraeian, S. M. E., Zarate, S., Carroll, A. W., Hong, H., Pan, B., Shi, L. M., Gibbs, R. A., Mohiyuddin, M., Zheng, Y., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02558-x · Cited by 33

Recent advances and current challenges in population genomics of structural variation in animals and plants

Pokrovac, I., & Pezer, Ž. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.1060898 · Cited by 34

Targeted Nanopore Sequencing with Cas9 for studies of methylation, structural variants, and mutationsPreprint

Gilpatrick, T., Lee, I., Graham, J. E., Raimondeau, E., Bowen, R., Heron, A., Sedlazeck, F. J., & Timp, W. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/604173 · Cited by 34

The landscape of human SVA retrotransposons

Chu, C., Lin, E. W., Tran, A. V., Jin, H., Ho, N. I., Veit, A. D., Cortés‐Ciriano, I., Burns, K. H., Ting, D. T., & Park, P. J. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad821 · Cited by 33

Structural variants in the 3D genome as drivers of disease

Sreenivasan, V. K. A., Yumiceba, V., & Spielmann, M. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-025-00862-x · Cited by 45

Long-read sequencing identifies novel structural variations in colorectal cancer

Xu, L., Wang, X., Lu, X., Liang, F., Liu, Z., Zhang, H., Li, X., Tian, S., Wang, L., & Wang, Z. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010514 · Cited by 35

Leveraging the power of long reads for targeted sequencingPreprint

Iyer, S. V., Goodwin, S., & McCombie, W. R. (2024) · Genome Research · doi:10.1101/gr.279168.124 · Cited by 36

Inversion polymorphism in a complete human genome assembly

Porubskỳ, D., Harvey, W. T., Rozanski, A. N., Ebler, J., Höps, W., Ashraf, H., Hasenfeld, P., Paten, B., Sanders, A. D., Marschall, T., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02919-8 · Cited by 34

An overview of recent technological developments in bovine genomics

Hossein‐Zadeh, N. G. (2024) · Veterinary and Animal Science · doi:10.1016/j.vas.2024.100382 · Cited by 36

Discovery of Novel Sequences in 1,000 Swedish Genomes

Eisfeldt, J., Mårtensson, G., Ameur, A., Nilsson, D., & Lindstrand, A. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz176 · Cited by 31

CRISPR–Cas9/long-read sequencing approach to identify cryptic mutations in BRCA1 and other tumour suppressor genes

Walsh, T., Casadei, S., Munson, K. M., Eng, M., Mandell, J. B., Gülsüner, S., & King, M. (2020) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2020-107320 · Cited by 31

Topologically associating domains are disrupted by evolutionary genome rearrangements forming species-specific enhancer connections in mice and humans

Gilbertson, S. E., Walter, H. C., Gardner, K., Wren, S. N., Vahedi, G., & Weinmann, A. S. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110769 · Cited by 31

Typical Enhancers, Super-Enhancers, and Cancers

Koutsi, M. A., Pouliou, M., Champezou, L., Vatsellas, G., Giannopoulou, A.-I., Piperi, C., & Agelopoulos, M. (2022) · Cancers · doi:10.3390/cancers14184375 · Cited by 28

Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance

Ren, L., Duan, X., Dong, L., Zhang, R., Yang, J., Gao, Y., Peng, R., Hou, W., Liu, Y., Li, J., et al. (2023) · Genome biology · doi:10.1186/s13059-023-03109-2 · Cited by 27

Structural variant identification and characterization

Balachandran, P., & Beck, C. R. (2020) · Chromosome Research · doi:10.1007/s10577-019-09623-z · Cited by 37

Implications of germline copy-number variations in psychiatric disorders: review of large-scale genetic studies

Nakatochi, M., Kushima, I., & Ozaki, N. (2020) · Journal of Human Genetics · doi:10.1038/s10038-020-00838-1 · Cited by 35

Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach

Dadshani, S., Mathew, B., Ballvora, A., Mason, A. S., & Léon, J. (2021) · Scientific Reports · doi:10.1038/s41598-021-85226-1 · Cited by 30

A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk lociPreprint

van Bree, E. J., Guimarães, R. L. F. P., Lundberg, M., Blujdea, E. R., Rosenkrantz, J. L., White, F. T. G., Poppinga, J., Ferrer‐Raventós, P., Schneider, A.-F. E., Clayton, I., et al. (2022) · Genome Research · doi:10.1101/gr.275515.121 · Cited by 30

cuteFC: regenotyping structural variants through an accurate and efficient force-calling method

Jiang, T., Cao, S., Liu, Y., Zhang, Z., Liu, B., Luo, R., Wang, G., & Wang, Y. (2025) · Genome biology · doi:10.1186/s13059-025-03642-2 · Cited by 30

The Platinum Pedigree: a long-read benchmark for genetic variants

Kronenberg, Z. N., Nolan, C., Porubskỳ, D., Mokveld, T., Rowell, W. J., Lee, S. Y., Dolzhenko, E., Chang, P.-C., Holt, J., Saunders, C. T., et al. (2025) · Nature Methods · doi:10.1038/s41592-025-02750-y · Cited by 34

CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing

Wallace, A. D., Sasani, T. A., Swanier, J., Gates, B. L., Greenland, J., Pedersen, B. S., Varley, K. E., & Quinlan, A. R. (2021) · PLoS ONE · doi:10.1371/journal.pone.0241253 · Cited by 29

A survey of current methods to detect and genotype inversions

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Genetic diagnosis of autoinflammatory disease patients using clinical exome sequencing

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