Cited by 513Genomic variations and chromosomal abnormalitiesGenome Rearrangement AlgorithmsGenomics and Phylogenetic Studies

The DOI matches its Crossref record; 73 of the 73 references it cites were found in a registry or an index.

Characterizing the Major Structural Variant Alleles of the Human Genome

Open access

Audano, Peter A., Sulovari, Arvis, Graves-Lindsay, Tina A., Cantsilieris, Stuart, Sorensen, Melanie, Welch, AnneMarie E., Dougherty, Max L., Nelson, Bradley J., Shah, Ankeeta, Dutcher, Susan K., Warren, Wesley C., Magrini, Vincent, McGrath, Sean D., Li, Yang I., Wilson, Richard K., Eichler, Evan E.·2019·Cell

DOI 10.1016/j.cell.2018.12.019PMC PMC6438697

Open this paper in CoChat — free account Open PDF

Abstract

In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1.6 Mbp) that are shared among all discovery genomes with an additional 13,053 (6.9 Mbp) present in the majority, indicating minor alleles or errors in the reference. Genotyping in 440 additional genomes confirms the most common SVs in unique euchromatin are now sequence resolved. We report a ninefold SV bias toward the last 5 Mbp of human chromosomes with nearly 55% of all VNTRs (variable number of tandem repeats) mapping to this portion of the genome. We identify SVs affecting coding and noncoding regulatory loci improving annotation and interpretation of functional variation. These data provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1016/j.cell.2018.12.019

Cites

73 of 73 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
Self-citation
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247
Self-citation
Analysis of protein-coding genetic variation in 60,706 humans
Exome Aggregation Consortium, Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O’Donnell-Luria, A. H., Ware, J. S., Hill, A. J., et al. (2016) · Nature · doi:10.1038/nature19057 · Cited by 9,587
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
Self-citation
dbSNP: the NCBI database of genetic variation
Sherry, S. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.308 · Cited by 7,502

Flagged first, then by citations

Show all 73 references

Sorted by citations

Items 301–400 of 513

Association of human-specific expanded short tandem repeats with neuron-specific regulatory features
Liu, Q., & Tian, W. (2025) · Science Advances · doi:10.1126/sciadv.adp9707 · Cited by 5
Interpreting the effect of mutations to protein binding sites from large-scale genomic screens
Parvar, S. J., Hall, B. A., & Shorthouse, D. (2024) · Methods · doi:10.1016/j.ymeth.2023.12.008 · Cited by 5
Jumping in the human brain: A review on somatic transposition
Zhang, Y., Guo, Y., Jia, H., Ma, H., Tan, S., & Zhang, Y. E. (2025) · Fundamental Research · doi:10.1016/j.fmre.2025.03.001 · Cited by 5
Flow Sorting Enrichment and Nanopore Sequencing of Chromosome 1 From a Chinese Individual
Kuderna, L. F. K., Solís-Moruno, M., Batlle-Masó, L., Julià, E., Lizano, E., Anglada, R., Ramírez, E., Bote, A., Tormo, M., Marquès‐Bonet, T., et al. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2019.01315 · Cited by 5
Comprehensive analysis of microsatellite polymorphisms in human populations
Gochi, L., Kawai, Y., & Fujimoto, A. (2022) · Human Genetics · doi:10.1007/s00439-022-02484-3 · Cited by 5
Assembly-free discovery of human novel sequences using long reads
Li, Q., Yan, B., Lam, T., & Luo, R. (2022) · DNA Research · doi:10.1093/dnares/dsac039 · Cited by 5
Illegitimate Recombination between Duplicated Genes Generated from Recursive Polyploidizations Accelerated the Divergence of the Genus Arachis
Shen, S., Li, Y., Wang, J., Wei, C., Wang, Z., Ge, W., Yuan, M., Zhang, L., Zhang, L., Sun, S., et al. (2021) · Genes · doi:10.3390/genes12121944 · Cited by 5
Self-citation
stLFRsv: A Germline Structural Variant Analysis Pipeline Using Co-barcoded Reads
Guo, J., Chang, S., Chen, X., Wang, O., Liu, P., Yang, H., Xu, X., Zhang, W., & Zhu, H. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.636239 · Cited by 4
NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data
Linderman, M. D., Paudyal, C., Shakeel, M., Kelley, W., Bashir, A., & Gelb, B. D. (2021) · GigaScience · doi:10.1093/gigascience/giab046 · Cited by 4
Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem RepeatsPreprint
Jakubosky, D. A., Smith, E. N., D’Antonio, M., Bonder, M. J., Greenwald, W. W. Y., D’Antonio‐Chronowska, A., Matsui, H., Stegle, O., Montgomery, S. B., DeBoever, C., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/713198 · Cited by 5
Microbial contaminants cataloged as novel human sequences in recent human pan-genomesPreprint
Manni, M., & Zdobnov, E. M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.16.994376 · Cited by 5
A powerful HUPAN on a pan-genome study: significance and perspectives
Yu, Y., & Wei, C. (2020) · Cancer Biology and Medicine · doi:10.20892/j.issn.2095-3941.2019.0317 · Cited by 5
Expectations and blind spots for structural variation detection from short-read alignment and long-read assemblyPreprint
Zhao, X., Collins, R. L., Lee, W.-P., Weber, A. M., Jun, Y., Zhu, Q., Weisburd, B., Huang, Y., Audano, P. A., Wang, H., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.03.168831 · Cited by 5
Self-citation
The genomics of linkage drag in sunflowerPreprint
Huang, K., Jahani, M., Gouzy, J., Legendre, A., Carrère, S., Lázaro-Guevara, J. M., Segovia, E. G. G., Todesco, M., Mayjonade, B., Rodde, N., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.07.495047 · Cited by 5
Approaches to Studying Viral Pangenome Variation Graphs
Downing, T. (2026) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzag003 · Cited by 6
Structuring Race into the Machine: The Spoiled Promise of Postgenomic Sequencing Technologies
Kowal, E. (2022) · Springer eBooks · doi:10.1007/978-981-16-7084-8_8 · Cited by 4
Systematic assessment of structural variant annotation tools for genomic interpretation
Liu, X., Gu, L., Hao, C., Xu, W., Leng, F., Zhang, P., & Li, W. (2024) · Life Science Alliance · doi:10.26508/lsa.202402949 · Cited by 4
Structure of a polymorphic repeat at the CACNA1C schizophrenia locus
Moya, R., Wang, X., Tsien, R. W., & Maurano, M. T. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2415650122 · Cited by 6
Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants
Fukasawa, Y. (2026) · BMC Genomics · doi:10.1186/s12864-025-12259-5 · Cited by 6
Probability, Populations, Phylogenetics, and Hominin Speciation
Caldararo (2018) · Human Biology · doi:10.13110/humanbiology.90.2.04 · Cited by 7
Rediscovering tandem repeat variation in schizophrenia: challenges and opportunities
Birnbaum, R. (2023) · Translational Psychiatry · doi:10.1038/s41398-023-02689-8 · Cited by 4
Perspectives and opportunities in forensic human, animal, and plant integrative genomics in the Pangenome era
He, G., Liu, C., & Wang, M. (2025) · Forensic Science International · doi:10.1016/j.forsciint.2025.112370 · Cited by 4
Prioritizing long range interactions in noncoding regions using GWAS and deletions perturbed TADs
Liu, X., Xu, W., Leng, F., Hao, C., Kolora, S. R. R., & Li, W. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.10.014 · Cited by 4
Novel sequencing technologies and bioinformatic tools for deciphering the non-coding genome
Schwarz, J. M., Lüpken, R., Seelow, D., & Kehr, B. (2021) · Medizinische Genetik · doi:10.1515/medgen-2021-2072 · Cited by 5
Genome-wide analysis of mobile element insertions in human genomesPreprint
Niu, Y., Teng, X., Shi, Y., Li, Y., Tang, Y., Zhang, P., Luo, H., Kang, Q., Initiative, T. H., Xu, T., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.22.427873 · Cited by 4
Self-citation
Characterizing the genetic polymorphisms in 370 challenging medically relevant genes using long-read sequencing data from 41 human individuals among 19 global populationsPreprint
Ji, Y., Gong, J., Sedlazeck, F. J., & Fan, S. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.03.502734 · Cited by 5
A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variantsPreprint
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) · Research Square · doi:10.21203/rs.3.rs-3086064/v1 · Cited by 4
Self-citation
Genome Assembly and Structural Variation Analysis of Luffa acutangula Provide Insights on Flowering Time and Ridge Development
Huang, A., Feng, S., Ye, Z., Zhang, T., Chen, S., Chen, C., & Chen, S. (2024) · Plants · doi:10.3390/plants13131828 · Cited by 3
Flexible and rapid validation of structural variation using adaptive sampling
Paivandy, A., Lenner, F., Eisfeldt, J., Jonson, T., Ehrencrona, H., Lindstrand, A., Scherer, S. W., & Feuk, L. (2026) · European Journal of Human Genetics · doi:10.1038/s41431-026-02039-4 · Cited by 3
GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations
Chirmade, S., Wang, Z., Mastromatteo, S., Sanders, E., Thiruvahindrapuram, B., Nalpathamkalam, T., Pellecchia, G., Fan, L., Keenan, K., Patel, R. V., et al. (2025) · Heredity · doi:10.1038/s41437-025-00809-2 · Cited by 4
Population history modulates the fitness effects of Copy Number Variation in the Roma
Antinucci, M., Comas, D., & Calafell, F. (2023) · Human Genetics · doi:10.1007/s00439-023-02579-5 · Cited by 3
GGTyper: genotyping complex structural variants using short-read sequencing data
Mirus, T., Lohmayer, R., Döhring, C., Halldórsson, B. V., & Kehr, B. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae391 · Cited by 4
Performance evaluation of structural variation detection using DNBSEQ whole-genome sequencing
Rao, J., Luo, H., An, D., Liang, X., Peng, L., & Chen, F. (2025) · BMC Genomics · doi:10.1186/s12864-025-11494-0 · Cited by 4
The genomic basis of medicine
Stankiewicz, P., & Lupski, J. R. (2020) · doi:10.1093/med/9780198746690.003.0030 · Cited by 3
Unveiling novel genetic variants in 370 challenging medically relevant genes using the long read sequencing data of 41 samples from 19 global populations
Ji, Y., Zhao, J., Gong, J., Sedlazeck, F. J., & Fan, S. (2024) · Molecular Genetics and Genomics · doi:10.1007/s00438-024-02158-x · Cited by 8
A Strategy of Assessing Gene Copy Number Differentiation Between Populations Using Ultra‐Fast De Novo Assembly of Next‐Generation Sequencing Data
Shi, T., Gao, Z., Zhang, Y., Rausher, M. D., & Chen, J. (2025) · Molecular Ecology Resources · doi:10.1111/1755-0998.14080 · Cited by 2
Enhanced detection and characterization of germline structural variants in cancer predisposition genes via genome sequencing
Kargaran, P. K., Ding, Q., Choate, L. A., Sellers, H. L., Stein, M. I., Moyers, B. A., Basu, S., Tandale, P. P., Setlem, R., Bishop, M. F., et al. (2025) · Genetics in Medicine Open · doi:10.1016/j.gimo.2025.103459 · Cited by 2
Identification of Chimeric RNAs Using RNA-Seq Reads and Protein–Protein Interactions of Translated Chimeras
Frenkel‐Morgenstern, M. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9904-0_3 · Cited by 2
Genetic changes in F1 hybrids of the genetically divergent Solanum L., Solanum melongena L. × Solanum aethiopicum L.
Ning, Y., Gan, G., Li, D., Li, W., Jiang, Y., Yang, Q., Wang, P., Li, W., & Wang, Y. (2022) · Plant Growth Regulation · doi:10.1007/s10725-022-00926-6 · Cited by 3
[Retracted] Correlation Analysis of Cytochrome P450 SNPs in Hepatitis B‐Caused Cirrhosis Patients
Li, Q., Yang, X.-N., & Guo, Z.-Z. (2022) · BioMed Research International · doi:10.1155/2022/9891184 · Cited by 2
Retracted
Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach
Yang, X., Zheng, G., Jia, P., Wang, S., & Ye, K. (2024) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzae008 · Cited by 2
Analysis of Preimplantation and Clinical Outcomes of Two Cases by Oxford Nanopore Sequencing
Ou, J., Wang, J., Sun, J., Ni, M., Meng, Q., Ding, J., Fan, H., Feng, S., Huang, Y., Li, H., et al. (2024) · Reproductive Sciences · doi:10.1007/s43032-024-01470-6 · Cited by 2
The prevalence of copy number increase at multiallelic copy number variants associated with cave colonization
Pokrovac, I., Rohner, N., & Pezer, Ž. (2024) · Molecular Ecology · doi:10.1111/mec.17339 · Cited by 2
Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia
Sun, W., Xiong, D., Ouyang, J., Xiao, X., Jiang, Y., Wang, Y., Li, S., Xie, Z., Wang, J., Tang, Z., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49376-w · Cited by 2
Characterizing p53 structural insights of variants in vertebrates that interfere its regulatory interaction with Mdm2
Kalathiya, U., Marek-Trzonkowska, N. M., & Padariya, M. (2026) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2026.105554 · Cited by 2
The Landscape of Micro-Inversions Provide Clues for Population Genetic Analysis of Humans
Li, Q., Wang, L., He, F., Han, Y., Yang, L., Wang, M. D., & Zhu, H. (2020) · Interdisciplinary Sciences Computational Life Sciences · doi:10.1007/s12539-020-00392-6 · Cited by 2
ChArmTelo Enables Large‐Scale Chromosome Arm‐Level Telomere Analysis across Human Populations and in Cancer Patients
Guo, M., Songyang, Z., & Xiong, Y. (2023) · Small Methods · doi:10.1002/smtd.202300385 · Cited by 1
Fully-sensitive Seed Finding in Sequence Graphs Using a Hybrid IndexPreprint
Ghaffaari, A., & Marschall, T. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/587717 · Cited by 2
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. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/766915 · Cited by 2
Structural variant selection for high-altitude adaptation using single-molecule long-read sequencingPreprint
Shi, J., Jia, Z., Zhao, X., Sun, J., Liang, F., Park, M., Zhao, C., Wang, X.-R., Chen, Q., Song, X., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.27.436702 · Cited by 2
VRPG: an interactive visualization framework for reference-projected pangenome graphPreprint
Miao, Z., & Yue, J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.20.524991 · Cited by 2
Small allelic variants are a source of ancestral bias in structural variant breakpoint placementPreprint
Audano, P. A., & Beck, C. R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.25.546295 · Cited by 3
Self-citation
Applications of Long-Read Sequencing Technology in Clinical Genomics
Sathyanarayana, S. H., Deharvengt, S. J., Huang, G., Barney, R. E., Shah, P. S., & Lefferts, J. A. (2022) · Advances in Molecular Pathology · doi:10.1016/j.yamp.2022.07.004 · Cited by 1
ASVBM: Structural variant benchmarking with local joint analysis for multiple callsets
Mu, P., Feng, X., Tong, L., Huang, J., Zhu, C., Wang, F., Quan, W., Ma, Y., Dong, Y., & Zhu, X. M. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.06.045 · Cited by 1
BVSim: A benchmarking variation simulator mimicking human variation spectrum
Luo, Y., Zhang, Z., Wang, S., Shi, J., Hao, J., Lian, S., Hu, T., Ishibashi, T., Wang, D., Yu, W., et al. (2025) · GigaScience · doi:10.1093/gigascience/giaf095 · Cited by 1
Tissue-specific gene dosage disruption is a key feature and pathogenic mechanism of structural variants in the human genome
Liu, X., Chen, Z., Jiang, Q., Shen, H., Liu, H., Wang, Z., Li, Z., Wu, J., Jiang, H., & Li, X. (2026) · Genome Medicine · doi:10.1186/s13073-026-01653-7 · Cited by 1
THE HUMAN PANGENOME AND THE END OF THE SINGLE- REFERENCE PARADIGM: T2T-CHM13, HPRC, AND THE PARTI FRAMEWORK FOR ADOPTION-READINESS EVALUATION
Markovski, T. (2024) · Cosmological and Astrobiological Review Journal for the Study of the Universe Life and the Natural Sciences · doi:10.65932/car-2024-1-4 · Cited by 1
Centromeric tandem repeats expansions in plateau zokor enhance chromosome stability for high-altitude adaptation
Wang, Z.-L., Shi, L., Liu, X., Yao, X.-Q., Li, M.-Y., Wang, Q.-H., Wu, H., Gong, H.-S., Liu-yang, F., Chang, G., et al. (2026) · Genome biology · doi:10.1186/s13059-026-04159-y · Cited by 1
High Rate of Mutation and Efficient Removal by Selection of Structural Variants From Natural Populations of Caenorhabditis Elegans
Saxena, A. S., & Baer, C. F. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag145 · Cited by 4
dicast: a machine learning method for accurate structural variant detection from short-read sequencing data
Alavi, N., Moeinzadeh, M.-H., Hertzberg, J., Melo, U. S., Raei, L. W. A., Infantino, P., Ghareghani, M., Savarese, M., Mundlos, S., & Vingron, M. (2026) · Genome biology · doi:10.1186/s13059-026-04280-y
The power of whole genomic sequencing in biomedical research and clinical applications
Sobhani, N., D’Angelo, A., Conter, F. U., Morris, R. M., & Li, Y. (2023) · Elsevier eBooks · doi:10.1016/b978-0-12-824010-6.00044-7 · Cited by 1
Self-citation
Effect of Carcinomas on Autosomal Trait Screening: A Review Article
Alhatim, H. A., Abdullah, M. N. H., Bakar, S. A., & Amer, S. A. M. (2023) · Current Issues in Molecular Biology · doi:10.3390/cimb45090460 · Cited by 1
Novel and Recurrent Copy Number Variants in ABCA4-Associated Retinopathy
Corradi, Z., Dhaenens, C., Grunewald, O., Kocabaş, I. S., Meunier, I., Banfi, S., Karali, M., Cremers, F. P. M., & Hitti‐Malin, R. J. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25115940 · Cited by 1
A note on optimal sampling strategy for structural variant detection using optical mapping
Li, W., Hannig, J., & Jones, C. D. (2020) · Communication in Statistics- Theory and Methods · doi:10.1080/03610926.2020.1723638 · Cited by 1
Population Structure, Stratification and Introgression of Human Structural VariationPreprint
Almarri, M. A., Bergström, A., Prado-Martinez, J., Yang, F., Fu, B., Dunham, A. S., Chen, Y., Hurles, M. E., Tyler-Smith, C., & Xue, Y. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/746172 · Cited by 1
VNTR prediction on sequence characteristics using long-read annotation and validation by short-read pileupPreprint
van Batenburg, D. C., Linthorst, J., Holstege, H. H., & Reinders, M. J. T. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.17.185983 · Cited by 1
Repetitive DNA Sequences
Clark, A. G., Barbash, D. A., Lower, S. E., & Dion-Coté, A.-M. (2020) · MDPI eBooks · doi:10.3390/books978-3-03928-367-5 · Cited by 1
Perspective and Opportunity for forensic integrative genomics in the Human Pangenome Reference sequence eraPreprint
He, G., Huang, Y., Chen, J., Wang, Z., Li, X., Duan, S., Sun, Q., Yan, J., Liu, C., & Wang, M. (2023) · doi:10.22541/au.168933511.19000548/v1
A note on optimal sampling strategy for structural variant detection using optical mapping
Jones, C. D., Li, W., & Hannig, J. (2021) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/ab4j-wh50
A High Quality Asian Genome Assembly Identifies Features of Common Missing Regions
Kim, J., Sung, J., Han, K., Lee, W., Mun, S., Lee, J., Bahk, K., Yang, I., Bae, Y.-K., Kim, C., et al. (2020) · Genes · doi:10.3390/genes11111350
HUMAN GENETIC VARIANTS AND THEIR ANALYSIS: CURRENT STATE AND FUTURE PERSPECTIVES
Slavec, L., Geršak, K., Kuželički, N. K., & Podkrajšek, K. T. (2020) · Slovenska pediatrija revija pediatrov Slovenije in specialistov šolske ter visokošolske medicine Slovenije · doi:10.38031/slovpediatr-2020-4-01en
ClipSV: improving structural variation detection by read extension, spliced alignment and tree-based decision rules
Xu, P., Chen, Y., Gao, M., & Chong, Z. (2021) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqab003
SVhound: Detection of future Structural Variation hotspotsPreprint
Paulin, L. F., Raveendran, M., Harris, R. A., Rogers, J., von Haeseler, A., & Sedlazeck, F. J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.09.439237
Leveraging technological opportunities in cancer genomics
Valle-Inclán, J. E. (2021) · Utrecht University Repository (Utrecht University) · doi:10.33540/480
Structural variation in genomes and its role in disease
Vlaar, J. M. (2021) · Utrecht University Repository (Utrecht University) · doi:10.33540/902
Structural Variants Are a Major Component of the Missing Heritability of Autism Spectrum DisorderPreprint
Kainer, D., Templeton, A. R., Prates, E. T., Allan, E. R. O., Climer, S., Jacobson, D., & Garvin, M. R. (2021) · medRxiv · doi:10.1101/2021.10.10.21264819
Documentation of units of inheritance and their contribution to phenotype
Smith, M. (2021) · Elsevier eBooks · doi:10.1016/b978-0-323-91547-2.00011-7
NPGREAT: Assembly of the human subtelomere regions with the use of ultralong Nanopore reads and Linked-ReadsPreprint
Adam, E., Ranjan, D., & Riethman, H. C. (2021) · Research Square · doi:10.21203/rs.3.rs-1080088/v1
Faculty Opinions recommendation of Pan-genomics in the human genome era.
Mulder, N. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.737328554.793579953
Faculty Opinions recommendation of Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Tang, F. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.739619698.793585652
Genetic changes in F1 hybrids of the genetically divergent Solanum L., Solanum melongena L. and Solanum aethiopicum L.Preprint
Yu, N., Gan, G., Li, D., Li, W., Jiang, Y., Yang, Q., Wang, P., Li, W., & Wang, Y. (2022) · Research Square · doi:10.21203/rs.3.rs-1893350/v1
Assessment of accuracy in identifying structural variants using third-generation sequencing for breast cancer in the absence of gold standardPreprint
Song, Q., Hu, T., Liang, B., Zhang, Z., Yang, L., Wu, J., Zhao, J. X., Long, M., Lian, S., Fan, X., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-1970335/v1
Application of genomics technology in biodiversity conservation research
Liu, S., Qiu, N., Zhang, S., Zhao, Z., & Zhou, X. (2022) · Biodiversity Science · doi:10.17520/biods.2022441
SVhound: detection of regions that harbor yet undetected structural variation
Paulin, L. F., Raveendran, M., Harris, R. A., Rogers, J., von Haeseler, A., & Sedlazeck, F. J. (2023) · BMC Bioinformatics · doi:10.1186/s12859-022-05046-6
Smaller, denser, smarter: improved Strand-seq library preparation, inversion genotyping, and phasing
Hanlon, V. C. T. (2023) · University of Groningen research database (University of Groningen / Centre for Information Technology) · doi:10.33612/diss.570000248
Introduction to Genomics and Genetics
Fatima, M., Zia, S. K., Murtaza, M., Shafique, A., Muneer, A., Sattar, J., Nabeel, M. A., & Aqib, A. I. (2023) · doi:10.1002/9781394213726.ch1
Human pangenome: far-reaching implications in precision medicine
Yu, Y., & Chen, H. (2023) · Frontiers of Medicine · doi:10.1007/s11684-023-1039-1
Structural characterization of a polymorphic repeat at the CACNA1C schizophrenia locusPreprint
Moya, R., Wang, X., Tsien, R. W., & Maurano, M. T. (2024) · medRxiv · doi:10.1101/2024.03.05.24303780
Deciphering the role of germline complex de novo structural variations in rare disordersPreprint
Jung, H., Yang, T.-P., Walker, S., Danecek, P., Salinas, I. G., Neville, M. D. C., Firth, H. V., Scally, A., Hurles, M. E., Campbell, P. J., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.03.587925
Additional file 10 of 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) · Figshare · doi:10.6084/m9.figshare.14677091
Self-citation
Additional file 6 of 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) · Figshare · doi:10.6084/m9.figshare.14812540
Self-citation
Additional file 8 of 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) · Figshare · doi:10.6084/m9.figshare.14677127
Self-citation
Additional file 3 of 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) · Figshare · doi:10.6084/m9.figshare.14812531
Self-citation
Additional file 5 of 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) · Figshare · doi:10.6084/m9.figshare.14677118
Self-citation
Additional file 12 of 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) · Figshare · doi:10.6084/m9.figshare.14677097
Self-citation
Additional file 7 of 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) · Figshare · doi:10.6084/m9.figshare.14677124
Self-citation
Additional file 3 of 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) · Figshare · doi:10.6084/m9.figshare.14677112
Self-citation
Additional file 4 of 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) · Figshare · doi:10.6084/m9.figshare.14677115
Self-citation
Additional file 14 of 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) · Figshare · doi:10.6084/m9.figshare.14812471
Self-citation
Additional file 9 of 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) · Figshare · doi:10.6084/m9.figshare.14677130
Self-citation

Authors: Audano, P. A., Sulovari, A., Graves-Lindsay, T. A., Cantsilieris, S., Sorensen, M., Welch, A. E., Dougherty, M. L., Nelson, B. J., Shah, A., Dutcher, S. K., Warren, W. C., Magrini, V., McGrath, S. D., Li, Y. I., Wilson, R. K., & Eichler, E. E.
Affiliations: University of Washington (US)
Washington University in St. Louis (US)
University of Chicago (US)
Nationwide Children's Hospital (US)
Howard Hughes Medical Institute (US)
Corresponding author: Eichler, Evan E.
ORCID: Audano, Peter A.
Sulovari, Arvis
Graves-Lindsay, Tina A.
Sorensen, Melanie
Welch, AnneMarie E.
Dougherty, Max L.
Nelson, Bradley J.
Shah, Ankeeta
Dutcher, Susan K.
Warren, Wesley C.
Magrini, Vincent
McGrath, Sean D.
Li, Yang I.
Wilson, Richard K.
Eichler, Evan E.
Venue: Cell
Publisher: Elsevier BV
Published: 2019-01
Volume: 176
Issue: 3
Pages: 663-675.e19
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2018.12.019
PMC: PMC6438697
OpenAlex: W2908721251
Cited by: 492
References: 73
Citations by year: 2026: 31 · 2025: 37 · 2024: 49 · 2023: 68 · 2022: 60 · 2021: 121 · 2020: 84 · 2019: 41
FWCI: 48.23
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 389 d)
Locations: Cell (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: U.S. National Institutes of Health (HG002385, HG007635, HG009081, HG003079, HG009478, T32 HG000035-23)
National Health and Medical Research Council
NHMRC (1073726)
Howard Hughes Medical Institute
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: structural variants, human genome, insertion, deletion, inversion, long-read sequencing, variable number tandem repeats, euchromatin, regulatory loci, allelic diversity
MeSH terms: Alleles, Gene Frequency, Humans, Genome, Human, Sequence Analysis, DNA, Minisatellite Repeats, Euchromatin, Genomics, Genomic Structural Variation

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Characterizing the Major Structural Variant Alleles of the Human Genome

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks