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Haplotype-resolved diverse human genomes and integrated analysis of structural variation
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Abstract
Resolving genomic structural variation: Many human genomes have been reported using short-read technology, but it is difficult to resolve structural variants (SVs) using these data. These genomes thus lack comprehensive comparisons among individuals and populations. Ebert et al. used long-read structural variation calling across 64 human genomes representing diverse populations and developed new methods for variant discovery. This approach allowed the authors to increase the number of confirmed SVs and to describe the patterns of variation across populations. From this dataset, they identified quantitative trait loci affected by these SVs and determined how they may affect gene expression and potentially explain genome-wide association study hits. This information provides insights into patterns of normal human genetic variation and generates reference genomes that better represent the diversity of our species. Science , this issue p. eabf7117
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“Either the graphs needed to be constructed from variant calls against a reference 3,6,32 and, therefore, unable to properly represent nested variation while still suffering from some reference bias, or they were limited to only SVs 16 and unable to effectively be used for short-read mapping with current tools 6 .”
From Pangenome graph construction from genome alignments with Minigraph-Cactus (2024) · cites this paper as [32]
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“Previous studies have identified tens of megabases of sequence contained within structural variants (SVs) that are polymorphic within the population5.”
From A draft human pangenome reference. (2023) · cites this paper as [5]
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“This provides a large set of fully phased human genome assemblies and outperforms earlier efforts on many levels of assembly quality5,16,60.”
From A draft human pangenome reference. (2023) · cites this paper as [5]
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“In line with previous results5,54, we obtained high genotype concordance across all variant types and genomic contexts (Extended Data Fig. 9).”
From A draft human pangenome reference. (2023) · cites this paper as [5]
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“Ebert et al.5 showed that using PanGenie, a pangenomic approach, with 32 samples, a subset of these variants could be genotyped in short-read genomes (about 13,000 genotyped on average, ranging from 12,000 to 15,000 per sample).”
From A draft human pangenome reference. (2023) · cites this paper as [5]
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“The HGSVC and HPRC call sets are based on variant calls produced from haplotype-resolved assemblies of 32 and 44 samples, respectively5.”
From A draft human pangenome reference. (2023) · cites this paper as [5]
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“For example, compared with Ebert et al.5, the average median base level accuracy is nearly an order of magnitude higher, the N50 contiguity is nearly double and the structural accuracy is higher33.”
From A draft human pangenome reference. (2023) · cites this paper as [5]
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“This result confirms that short-read-based SV discovery relative to a linear reference genome misses a large proportion of SVs5,6,8.”
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“This result confirms that SV callers based on short reads alone miss a large proportion of SVs located in regions inaccessible by short-read alignments, which has been previously reposed by several studies5,8.”
From A draft human pangenome reference. (2023) · cites this paper as [5]
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Self-citationTransposable element-mediated rearrangements are prevalent in human genomes
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Self-citationHaplotype-aware pantranscriptome analyses using spliced pangenome graphs
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Genome structural variation in human evolution
Hollox, E. J., Zuccherato, L. W., & Tucci, S. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.06.015 · Cited by 93
Genetic mosaicism in the human brain: from lineage tracing to neuropsychiatric disorders
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A multi‐omics framework reveals strawberry flavor genes and their regulatory elements
Fan, Z., Tieman, D. M., Knapp, S. J., Zerbe, P., Famula, R. A., Barbey, C. R., Folta, K. M., Amadeu, R. R., Lee, M., Oh, Y., et al. (2022) · New Phytologist · doi:10.1111/nph.18416 · Cited by 80
The Somatic Mosaicism across Human Tissues Network
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Self-citationThe complete and fully-phased diploid genome of a male Han Chinese
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Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak
Chen, Y., Wang, A. Y., Barkley, C. A., Zhang, Y., Zhao, X., Gao, M., Edmonds, M. D., & Chong, Z. (2023) · Nature Communications · doi:10.1038/s41467-023-35996-1 · Cited by 78
Self-citationThe EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
Rozowsky, J. S., Gao, J., Borsari, B., Yang, Y., Galeev, T. R., Gürsoy, G., Epstein, C. B., Xiong, K., Xu, J., Li, T., et al. (2023) · Cell · doi:10.1016/j.cell.2023.02.018 · Cited by 79
Self-citationComplex genomic rearrangements: an underestimated cause of rare diseases
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Common Variable Immunodeficiency: More Pathways than Roads to Rome
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Ferraj, A., Audano, P. A., Balachandran, P., Czechanski, A., Flores, J. I., Radecki, A. A., Mosur, V., Gordon, D., Walawalkar, I. A., Eichler, E. E., et al. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100291 · Cited by 80
Self-citationHow Important Are Structural Variants for Speciation?
Zhang, L., Reifová, R., Halenková, Z., & Gompert, Z. (2021) · Genes · doi:10.3390/genes12071084 · Cited by 78
Structurally divergent and recurrently mutated regions of primate genomes
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Self-citationDysgu: efficient structural variant calling using short or long reads
Cleal, K., & Baird, D. M. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac039 · Cited by 75
Familial long-read sequencing increases yield of de novo mutations
Noyes, M. D., Harvey, W. T., Porubskỳ, D., Sulovari, A., Li, R., Rose, N. R., Audano, P. A., Munson, K. M., Lewis, A. P., Hoekzema, K., et al. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.02.014 · Cited by 68
Self-citationWidespread somatic L1 retrotransposition in normal colorectal epithelium
Nam, C. H., Youk, J., Kim, J. Y., Lim, J., Park, J. W., Oh, S. A., Lee, H. J., Won, H., Won, H., Lee, D.-S., et al. (2023) · Nature · doi:10.1038/s41586-023-06046-z · Cited by 71
Self-citationAnalysis and benchmarking of small and large genomic variants across tandem repeats
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Beyond assembly: the increasing flexibility of single-molecule sequencing technology
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Self-citationLong read sequencing on its way to the routine diagnostics of genetic diseases
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Diversity and consequences of structural variation in the human genome
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Self-citation3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database
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Cas9 targeted enrichment of mobile elements using nanopore sequencing
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“These results are consistent with the greater African genetic diversity, with recent evidence of “ African ” genomes demonstrating unexplored structural variation 23 and more variability in copy numbers of SMN1 , SMN2 and CYP2D6 14,15 .”
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REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats
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Cue: a deep-learning framework for structural variant discovery and genotyping
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Gaps and complex structurally variant loci in phased genome assemblies
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Self-citationLong-read whole-genome analysis of human single cells
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A framework to score the effects of structural variants in health and diseasePreprint
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Metadata
- Authors
- Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., Yilmaz, F., Zhao, X., Hsieh, P., Lee, J., Kumar, S., Lin, J., Rausch, T., Chen, Y., Ren, J., Santamarina, M., Höps, W., Ashraf, H., Chuang, N. T., Yang, X., Munson, K. M., Lewis, A. P., Fairley, S., Tallon, L. J., Clarke, W. E., Basile, A. O., Byrska-Bishop, M., Corvelo, A., Evani, U. S., Lu, T.-Y., Chaisson, M. J. P., Chen, J., Li, C., Brand, H., Wenger, A. M., Ghareghani, M., Harvey, W. T., Raeder, B., Hasenfeld, P., Regier, A. A., Abel, H. J., Hall, I. M., Flicek, P., Stegle, O., Gerstein, M. B., Tubio, J. M. C., Mu, Z., Li, Y. I., Shi, X., Hastie, A. R., Ye, K., Chong, Z., Sanders, A. D., Zody, M. C., Talkowski, M. E., Mills, R. E., Devine, S. E., Lee, C., Korbel, J. O., Marschall, T., & Eichler, E. E.
- Affiliations
- Heinrich Heine University Düsseldorf (DE)
- University of Washington (US)
- The Jackson Laboratory for Genomic Medicine (US)
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
- German Cancer Research Center (DE)
- University of Michigan (US)
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.
- Broad Institute (US)
- BioNano Genomics (United States) (US)
- Yale University (US)
- Xi'an Jiaotong University (CN)
- European Molecular Biology Laboratory (DE)
- University of Alabama at Birmingham (US)
- University of Southern California (US)
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- University of Maryland, Baltimore (US)
- European Bioinformatics Institute (GB)
- New York Genome Center (US)
- New York Genome Center, New York, NY 10013, USA.
- Temple University (US)
- Pacific Biosciences (United States) (US)
- Max Planck Institute for Informatics (DE)
- Washington University in St. Louis (US)
- University of Chicago (US)
- Ewha Womans University (KR)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Lee, Charles
- Korbel, Jan O.
- Marschall, Tobias
- Eichler, Evan E.
- ORCID
- Ebert, Peter
- Audano, Peter A.
- Zhu, Qihui
- Rodriguez-Martin, Bernardo
- Porubsky, David
- Bonder, Marc Jan
- Sulovari, Arvis
- Ebler, Jana
- Zhou, Weichen
- Serra Mari, Rebecca
- Yilmaz, Feyza
- Zhao, Xuefang
- Hsieh, PingHsun
- Lee, Joyce
- Kumar, Sushant
- Lin, Jiadong
- Rausch, Tobias
- Chen, Yu
- Ren, Jingwen
- Höps, Wolfram
- Ashraf, Hufsah
- Chuang, Nelson T.
- Yang, Xiaofei
- Munson, Katherine M.
- Lewis, Alexandra P.
- Fairley, Susan
- Tallon, Luke J.
- Clarke, Wayne E.
- Basile, Anna O.
- Byrska-Bishop, Marta
- Corvelo, André
- Evani, Uday S.
- Lu, Tsung-Yu
- Chaisson, Mark J. P.
- Chen, Junjie
- Li, Chong
- Brand, Harrison
- Wenger, Aaron M.
- Ghareghani, Maryam
- Harvey, William T.
- Raeder, Benjamin
- Hasenfeld, Patrick
- Regier, Allison A.
- Abel, Haley J.
- Hall, Ira M.
- Flicek, Paul
- Stegle, Oliver
- Gerstein, Mark B.
- Tubio, Jose M. C.
- Mu, Zepeng
- Li, Yang I.
- Shi, Xinghua
- Hastie, Alex R.
- Ye, Kai
- Chong, Zechen
- Sanders, Ashley D.
- Zody, Michael C.
- Talkowski, Michael E.
- Mills, Ryan E.
- Devine, Scott E.
- Lee, Charles
- Korbel, Jan O.
- Marschall, Tobias
- Eichler, Evan E.
- Venue
- Science
- Published
- 2021-04-02
- Volume
- 372
- Issue
- 6537
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC8026704
- OpenAlex
- W3130788486
- Cited by
- 702
- References
- 212
- Citations by year
- 2026: 97 · 2025: 143 · 2024: 135 · 2023: 128 · 2022: 134 · 2021: 62
- FWCI
- 66.01
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nd
- Locations
- Science (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- Funders
- National Institutes of Health (U24HG007497, R01HG002898, R01HD081256, 1U01HG010973, R01HG002385, R15HG009565, 1R35GM138212, 1OT3HL147154, 1R01HG007068-01A1, R01MH115957, R01GM130738)
- National Human Genome Research Institute (3UM1HG008901-03S1, 3UM1HG008901-04S2, K99HG011041, UM1HG008901)
- National Science Foundation of China (32070663)
- Wellcome (WT104947/Z/14/Z)
- Bundesministerium für Bildung und Forschung (031L0184, 031L0181A)
- Deutsche Forschungsgemeinschaft (391137747, 395192176)
- European Research Council (773026, 716290)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- haplotype-resolved genome, structural variants, de novo genome assembly, long-read sequencing, strand-specific sequencing, transposable elements, expression quantitative trait loci, positive selection, human genetic variation
- MeSH terms
- Whole Genome Sequencing, Female, Genotype, Haplotypes, Humans, Male, Genetic Variation, Genome, Human, Sequence Analysis, DNA, Retroelements, Interspersed Repetitive Sequences, Quantitative Trait Loci, Population Groups, INDEL Mutation, Sequence Inversion, High-Throughput Nucleotide Sequencing
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.
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