Characterizing the Major Structural Variant Alleles of the Human Genome

The Sequence Alignment/Map format and SAMtools

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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

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Initial sequencing and analysis of the human genome

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A global reference for human genetic variation

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Analysis of protein-coding genetic variation in 60,706 humans

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

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Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing

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Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue

Bhati, M., Mapel, X. M., Lloret‐Villas, A., & Pausch, H. (2023) · Genetics · doi:10.1093/genetics/iyad161 · Cited by 21

Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications

Prodanov, T., & Bansal, V. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa829 · Cited by 20

Advanced techniques for gene heterogeneity research: Single‐cell sequencing and on‐chip gene analysis systems

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Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing

Soto, D. C., Shew, C. J., Mastoras, M., Schmidt, J. M., Sahasrabudhe, R. M., Kaya, G., Andrés, A. M., & Dennis, M. Y. (2020) · Genes · doi:10.3390/genes11030276 · Cited by 18

Major impacts of widespread structural variation on sorghumPreprint

Zhang, Z., Viana, J. P. G., Zhang, B., Walden, K. K. O., Paul, H. M., Moose, S. P., Morris, G. P., Daum, C. G., Barry, K., Shakoor, N., et al. (2024) · Genome Research · doi:10.1101/gr.278396.123 · Cited by 19

Methods and Developments in Graphical Pangenomics

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The TALE never ends: A comprehensive overview of the role of PBX1, a TALE transcription factor, in human developmental defects

Mary, L., Leclerc, D., Gilot, D., Belaud‐Rotureau, M., & Jaillard, S. (2022) · Human Mutation · doi:10.1002/humu.24388 · Cited by 21

Pan‐genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees

Yancan, L., Yao, J., Sang, H., Wang, Q., Su, L., Zhao, X., Xia, Z., Wang, F., Wang, K., Lou, D., et al. (2023) · Molecular Ecology Resources · doi:10.1111/1755-0998.13905 · Cited by 21

PhenoSV: interpretable phenotype-aware model for the prioritization of genes affected by structural variants

Xu, Z., Li, Q., Marchionni, L., & Wang, K. (2023) · Nature Communications · doi:10.1038/s41467-023-43651-y · Cited by 22

Long-read sequencing of 945 Han individuals identifies structural variants associated with phenotypic diversity and disease susceptibility

Gong, J., Sun, H., Wang, K., Yanhui, Z., Huang, Y., Chen, Q., Qiao, H., Gao, Y., Zhao, J., Ling, Y., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56661-9 · Cited by 20

Genome-driven Chinese precision medicine: Biobank-scale genomic research as a new paradigm

Wang, M., Duan, S., Li, X., Yang, J., Yuan, H., Liu, C., & He, G. (2025) · The Innovation Life · doi:10.59717/j.xinn-life.2025.100131 · Cited by 24

A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans

Zhao, Y., Long, L., Wan, J., Biliya, S., Brady, S. C., Lee, D., Ojemakinde, A. A., Andersen, E. C., Vannberg, F. O., Lu, H., et al. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008606 · Cited by 17

Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads

Zhou, X., Zhang, L., Weng, Z., Dill, D., & Sidow, A. (2021) · Nature Communications · doi:10.1038/s41467-021-21395-x · Cited by 16

Thyroid cancer under the scope of emerging technologies

Tarabichi, M., Demetter, P., Craciun, L., Maenhaut, C., & Detours, V. (2021) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2021.111491 · Cited by 18

Population Genomic Approaches for Weed Science

Martin, S. L., Parent, J., Laforest, M. F., Page, E. R., Kreiner, J. M., & James, T. (2019) · Plants · doi:10.3390/plants8090354 · Cited by 18

SVJedi: genotyping structural variations with long reads

Lecompte, L., Peterlongo, P., Lavenier, D. D., & Lemaitre, C. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa527 · Cited by 21

Structural Variants: Mechanisms, Mapping, and Interpretation in Human Genetics

Pande, S., Dawood, M., & Grochowski, C. M. (2025) · Genes · doi:10.3390/genes16080905 · Cited by 22

Generation and Application of Inducible Chimeric RNA ASTN2-PAPPAas Knockin Mouse Model

Luo, Y., Du, L., Yao, Z., Fan, L., Li, K., Li, F., Zhu, J., Coppes, R. P., Zhang, D., Pan, Y., et al. (2022) · Cells · doi:10.3390/cells11020277 · Cited by 16

Comparison and benchmark of structural variants detected from long read and long-read assembly

Lin, J., Jia, P., Wang, S., Kosters, W. A., & Ye, K. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad188 · Cited by 21

A High-Continuity Genome Assembly of Chinese Flowering Cabbage (Brassica rapa var. parachinensis) Provides New Insights into Brassica Genome Structure Evolution

Li, G., Wang, J., Liao, Y., Jiang, D., Zhang, T., Dai, X., 任海龙, Lei, J., Chen, C., 曹必好, et al. (2023) · Plants · doi:10.3390/plants12132498 · Cited by 16

Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration

Smeds, L., Huson, L. S. A., & Ellegren, H. (2024) · Evolutionary Applications · doi:10.1111/eva.13652 · Cited by 20

Discovery of genomic variation across a generation

Trost, B., Loureiro, L. O., & Scherer, S. W. (2021) · Human Molecular Genetics · doi:10.1093/hmg/ddab209 · Cited by 20

Integration of transcriptomics and long-read genomics prioritizes structural variants in rare diseasePreprint

Jensen, T. D., Ni, B., Reuter, C. M., Gorzynski, J. E., Fazal, S., Bonner, D. E., Ungar, R. A., Goddard, P. C., Raja, A. N., Ashley, E. A., et al. (2025) · Genome Research · doi:10.1101/gr.279323.124 · Cited by 16

A landscape of complex tandem repeats within individual human genomes

Ichikawa, K., Kawahara, R., Asano, T., & Morishita, S. (2023) · Nature Communications · doi:10.1038/s41467-023-41262-1 · Cited by 14

Genomic insights into demographic history, structural variation landscape, and complex traits from 514 Hu sheep genomes

Chen, K., Zhang, Y., Pan, Y., Xiang, X., Peng, C., He, J., Huang, G., Wang, Z., & Zhao, P. (2024) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2024.11.015 · Cited by 15

Leveraging long-read sequencing technologies for pharmacogenomic testing: applications, analytical strategies, challenges, and future perspectives

Tafazoli, A., Hemmati, M., Rafigh, M., Alimardani, M., Khaghani, F., Korostyński, M., & Karnes, J. H. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1435416 · Cited by 18

Exome-wide analysis of copy number variation shows association of the human leukocyte antigen region with asthma in UK Biobank

Fawcett, K. A., Demidov, G. M., Shrine, N. R. G., Paynton, M. L., Ossowski, S., Sayers, I., Wain, L. V., & Hollox, E. J. (2022) · BMC Medical Genomics · doi:10.1186/s12920-022-01268-y · Cited by 16

Fully-sensitive seed finding in sequence graphs using a hybrid index

Ghaffaari, A., & Marschall, T. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz341 · Cited by 14

Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence

Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · BMC Genomics · doi:10.1186/s12864-021-07776-y · Cited by 15

HDAC9structural variants disruptingTWIST1transcriptional regulation lead to craniofacial and limb malformationsPreprint

Hirsch, N., Dahan, I., D’haene, E., Avni, M., Vergult, S., Vidal‐García, M., Magini, P., Graziano, C., Severi, G., Bonora, E., et al. (2022) · Genome Research · doi:10.1101/gr.276196.121 · Cited by 16

Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis

Gilbertson, S. E., & Weinmann, A. S. (2021) · Trends in Immunology · doi:10.1016/j.it.2021.10.007 · Cited by 12

Population-scale genotyping of structural variation in the era of long-read sequencing

Quan, C., Lu, H. X., Lu, Y., & Zhou, G. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.05.047 · Cited by 14

The fragility of a structurally diverse duplication block triggers recurrent genomic amplification

Suzuki, R., Murata, M. M., Manguso, N., Watanabe, T., Mouakkad, L., Igari, F., Rahman, M. M., Qu, Y., Cui, X., Giuliano, A. E., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1136 · Cited by 13

Robust Benchmark Structural Variant Calls of an Asian Using State-of-the-Art Long-Read Sequencing Technologies

Du, X., Li, L., Liang, F., Liu, S., Zhang, W., Sun, S., Sun, Y., Fan, F., Wang, L., Liang, X., et al. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2020.10.006 · Cited by 13

GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing

Valls-Margarit, J., Galván‐Femenía, I., Matías-Sánchez, D., Blay, N., Puiggròs, M., Carreras, A., Salvoro, C., Cortés, B., Amela, R., Farré, X., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac076 · Cited by 13

SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencingPreprint

Heller, D., Vingron, M., Church, G. M., Li, H., & Garg, S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.25.964445 · Cited by 14

Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology

Otsuki, A., Okamura, Y., Ishida, N., Tadaka, S., Takayama, J., Kumada, K., Kawashima, J., Taguchi, K., Minegishi, N., Kuriyama, S., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03953-1 · Cited by 12

Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption

Li, X., Liu, Q., Fu, C., Li, M., Li, C., Li, X., Zhao, S., & Zheng, Z. (2023) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2023.11.005 · Cited by 13

Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles

Wu, Z., Li, T., Jiang, Z., Zheng, J., Gu, Y., Liu, Y., Liu, Y., & Xie, Z. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae086 · Cited by 14

Clinical Massively Parallel Sequencing

Gao, G., & Smith, D. I. (2019) · Clinical Chemistry · doi:10.1373/clinchem.2019.303305 · Cited by 14

A strategy for building and using a human reference pangenome

Llamas, B., Narzisi, G., Schneider, V. A., Audano, P., Biederstedt, E., Blauvelt, L. J., Bradbury, P., Chang, X., Chin, C., Fungtammasan, A., et al. (2019) · F1000Research · doi:10.12688/f1000research.19630.1 · Cited by 16

Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study

Arthur, C., Rezayee, F., Mogensen, N., Saft, L., Rosenquist, R., Nordenskjöld, M., Harila‐Saari, A. H., Tham, E., & Barbany, G. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.899325 · Cited by 13

Closing Human Reference Genome Gaps: Identifying and Characterizing Gap-Closing Sequences

Zhao, T., Duan, Z., Genchev, G. Z., & Lu, H. J. (2020) · G3 Genes Genomes Genetics · doi:10.1534/g3.120.401280 · Cited by 13

A novel variant in DYNC1H1 could contribute to human amyotrophic lateral sclerosis-frontotemporal dementia spectrum.Preprint

Mentis, A. A., Vlachakis, D., Papakonstantinou, E., Zaganas, I. V., Patrinos, G. P., Chrousos, G. P., & Dardiotis, E. (2021) · Molecular Case Studies · doi:10.1101/mcs.a006096 · Cited by 13

Transcriptomics and chromatin accessibility in multiple African population samplesPreprint

DeGorter, M. K., Goddard, P. C., Karakoç, E., Kundu, S., Yan, S. M., Nachun, D. C., Abell, N. S., Aguirre, M., Carstensen, T., Chen, Z., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.04.564839 · Cited by 18

Structural variation in humans and our primate kin in the era of telomere-to-telomere genomes and pangenomics

Rocha, J. L., Lou, R. N., & Sudmant, P. H. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102233 · Cited by 11

Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders

Zhou, B., Arthur, J. G., Guo, H., Kim, T., Huang, Y., Pattni, R., Wang, T., Kundu, S., Luo, J. X. J., Lee, H., et al. (2024) · Cell · doi:10.1016/j.cell.2024.09.014 · Cited by 11

Decomposing mosaic tandem repeats accurately from long reads

Masutani, B., Kawahara, R., & Morishita, S. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad185 · Cited by 12

Genome-wide associations of structural variants with human traits through imputation from long-read assemblies

Bai, W.-Y., Liu, S., Duan, Z., Yang, J.-J., Chen, J., Hou, J., Wu, L., Li, N., Qi, T., & Yang, J. (2026) · Nature Genetics · doi:10.1038/s41588-026-02612-z · Cited by 12

A variant selection framework for genome graphs

Jain, C., Tavakoli, N., & Aluru, S. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab302 · Cited by 11

The design and construction of reference pangenome graphsPreprint

Li, H., Feng, X., & Chu, C. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2003.06079 · Cited by 16

Small polymorphisms are a source of ancestral bias in structural variant breakpoint placementPreprint

Audano, P. A., & Beck, C. R. (2024) · Genome Research · doi:10.1101/gr.278203.123 · Cited by 13

Structural variants and tandem repeats in the founder individuals of four F2 pig crosses and implications to F2 GWAS results

Blaj, I., Tetens, J., Bennewitz, J., Thaller, G. E., & Falker‐Gieske, C. (2022) · BMC Genomics · doi:10.1186/s12864-022-08716-0 · Cited by 10

Uncovering structural variants in Creole cattle from Guadeloupe and their impact on environmental adaptation through whole genome sequencing

Jemaa, S. B., Boussaha, M., Mandonnet, N., Bardou, P., & Navès, M. (2024) · PLoS ONE · doi:10.1371/journal.pone.0309411 · Cited by 12

Young KRAB-zinc finger gene clusters are highly dynamic incubators of ERV-driven genetic heterogeneity in mice

Bruno, M., Farhana, S. M., Mitra, A., Costello, K. R., Watkins‐Chow, D. E., Logsdon, G. A., Gambogi, C. W., Dumont, B. L., Black, B. E., Keane, T., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-64609-2 · Cited by 8

Multiplatform discovery and regulatory function analysis of structural variations in non-small cell lung carcinoma

Lin, X., Wang, Z., Wu, X., Zeng, T., Luo, W., Hu, X., Ni, Y., Che, G., Liu, L., Zhang, W., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109660 · Cited by 10

PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform

Wang, Y., Ling, Y., Gong, J., Zhao, X., Zhou, H., Xie, B., Lou, H., Zhuang, X., Li, J., Initiative, T. H., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac905 · Cited by 10

Resolving the Insertion Sites of Polymorphic Duplications Reveals a HERC2 Haplotype under Selection

Saitou, M., & Gökçümen, Ö. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz107 · Cited by 10

Personalized genome structure via single gamete sequencing

Lyu, R., Tsui, V., McCarthy, D. J., & Crismani, W. (2021) · Genome biology · doi:10.1186/s13059-021-02327-w · Cited by 12

NIPT-PG: empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach

Xue, Z., Zhou, A., Zhu, X., Li, L., Zhu, H., Jin, X., & Wang, J. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae266 · Cited by 10

Genome-wide investigation of VNTR motif polymorphisms in 8,222 genomes: Implications for biological regulation and human traits

Zhang, S., Song, Q., Zhang, P., Wang, X., Guo, R., Li, Y., Liu, S., Yan, X., Zhang, J., Niu, Y., et al. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100699 · Cited by 9

K-mer analysis of long-read alignment pileups for structural variant genotyping

English, A. C., Cunial, F., Metcalf, G., Gibbs, R. A., & Sedlazeck, F. J. (2025) · Nature Communications · doi:10.1038/s41467-025-58577-w · Cited by 10

Compacta: a fast contig clustering tool for de novo assembled transcriptomes

Razo-Mendivil, F. G., Martínez, O., & Hayano‐Kanashiro, C. (2020) · BMC Genomics · doi:10.1186/s12864-020-6528-x · Cited by 9

Comprehensive assessments of germline deletion structural variants reveal the association between prognostic MUC4 and CEP72 deletions and immune response gene expression in colorectal cancer patients

Lin, P., Chen, H.-O., Lee, C.-J., Yeh, Y., Shen, M., & Chiang, J.-H. (2021) · Human Genomics · doi:10.1186/s40246-020-00302-3 · Cited by 9

Intronic Breakpoint Signatures Enhance Detection and Characterization of Clinically Relevant Germline Structural Variants

van den Akker, J., Hon, L., Ondov, A., Mahkovec, Z., O'Connor, R., Chan, R. C., Lock, J., Zimmer, A. D., Rostamianfar, A., Ginsberg, J., et al. (2021) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2021.01.015 · Cited by 9

Comparison of Structural and Short Variants Detected by Linked-Read and Whole-Exome Sequencing in Multiple Myeloma

Kumar, A., Adhikari, S., Kankainen, M., & Heckman, C. A. (2021) · Cancers · doi:10.3390/cancers13061212 · Cited by 10

Multi-tissue integrative analysis of personal epigenomes

Rozowsky, J. S., Drenkow, J., Yang, Y., Gürsoy, G., Galeev, T. R., Borsari, B., Epstein, C. B., Xiong, K., Xu, J., Gao, J., et al. (2021) · CaltechAUTHORS (California Institute of Technology) · Cited by 9

Targeted long-read sequencing resolves complex structural variants and identifies missing disease-causing variantsPreprint

Miller, D. E., Sulovari, A., Wang, T., Loucks, H., Hoekzema, K., Munson, K. M., Lewis, A. P., Fuerte, E. P. A., Paschal, C. R., Thies, J. M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.03.365395 · Cited by 9

Genomics and Inflammation in Cardiovascular Disease

Dhande, I. S., & Doris, P. A. (2021) · Comprehensive physiology · doi:10.1002/cphy.c200032 · Cited by 14

Structural Variants Contribute to Phenotypic Variation in Maize

Catlin, N. S., Agha, H. I., Platts, A. E., Munasinghe, M., Hirsch, C. N., & Josephs, E. B. (2025) · Molecular Ecology · doi:10.1111/mec.17662 · Cited by 8

High-quality assembly of the T2T genome for Isodon rubescens f. lushanensis reveals genomic structure variations between 2 typical forms of Isodon rubescens

Yang, H., Lian, C., Liu, J., Yu, H., Zhao, L., He, N., Liu, X., Xue, S., Sun, X., Zhang, L., et al. (2024) · GigaScience · doi:10.1093/gigascience/giae075 · Cited by 8

Recovery of non-reference sequences missing from the human reference genome

Li, R., Tian, X., Yang, P., Fan, Y., Li, M., Zheng, H., Wang, X., & Jiang, Y. (2019) · BMC Genomics · doi:10.1186/s12864-019-6107-1 · Cited by 8

Critical length in long-read resequencing

Coster, W. D., Stražišar, M., & Rijk, P. D. (2020) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqz027 · Cited by 8

A strategy for building and using a human reference pangenome

Llamas, B., Narzisi, G., Schneider, V., Audano, P. A., Biederstedt, E., Blauvelt, L., Bradbury, P. J., Chang, X. H., Chin, C.-S., Fungtammasan, A., et al. (2019) · F1000Research · doi:10.12688/f1000research.19630.2 · Cited by 17

Insertion variants missing in the human reference genome are widespread among human populations

Lee, Y., Lee, J.-Y., Kim, J., & Kim, Y.-J. (2020) · BMC Biology · doi:10.1186/s12915-020-00894-1 · Cited by 8

Recombination of repeat elements generates somatic complexity in human genomesPreprint

Pascarella, G., Hashimoto, K., Busch, A., Luginbühl, J., Parr, C., Hon, C.-C., Yip, W. H., Abe, K., Kratz, A., Bonetti, A., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.02.163816 · Cited by 8

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact modelsPreprint

Rozowsky, J. S., Drenkow, J., Yang, Y. T., Gürsoy, G., Galeev, T. R., Borsari, B., Epstein, C. B., Xiong, K., Xu, J., Gao, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.26.441442 · Cited by 8

A high-resolution map of small-scale inversions in the gibbon genomePreprint

Mercuri, L., Palmisano, D., L’Abbate, A., D’Addabbo, P., Montinaro, F., Catacchio, C. R., Hasenfeld, P., Ventura, M., Korbel, J. O., Sanders, A. D., et al. (2022) · Genome Research · doi:10.1101/gr.276960.122 · Cited by 7

Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integrationPreprint

Miao, Z., & Yue, J. (2025) · Genome Research · doi:10.1101/gr.279461.124 · Cited by 8

Deciphering IGH rearrangement complexity and detection strategies in acute lymphoblastic leukaemia

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Haplotype‐resolved genome and pan‐genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens

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