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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Previous studies have identified tens of megabases of sequence contained within structural variants that are polymorphic within the population.
“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]
The Results sections on structural variant distribution and complex structural variation document SVs and distinct structural haplotypes in human populations. But the reported ~279 Mbp is the genomic span of SV hotspots, not the amount of sequence contained within polymorphic SVs; the passages do not establish the claimed tens-of-megabases total. (LLM, conf=0.82)
Experimental — accuracy not yet measuredThe released assemblies provide a large set of fully phased human genome assemblies and outperform earlier efforts on many levels of assembly quality.
“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]
The Results section (“Sequencing and phased assembly of human genomes”; page unavailable) reports 70 phased human haplotypes and gives measures of their accuracy, contiguity, and phasing. The copy does not establish that these assemblies outperform earlier efforts across multiple measures of assembly quality; its comparison of assembly-quality measures is between HiFi and CLR assemblies in this study. (LLM, conf=0.85)
Experimental — accuracy not yet measuredPanGenie genotyping in a leave-one-out experiment obtained high genotype concordance across all variant types and genomic contexts.
“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]
The Results > Genotyping section (page unavailable) says PanGenie used concordance with assembly-based calls in a leave-out-one experiment to help filter SVs. It reports high allele-frequency correlations for SNVs, indels, and SVs, but those are not genotype-concordance results, and it does not report high genotype concordance across all variant types and genomic contexts. (LLM, conf=0.85)
Experimental — accuracy not yet measuredEbert et al. showed that using PanGenie with 32 samples, about 13,000 SVs on average (ranging from 12,000 to 15,000 per sample) could be genotyped in short-read genomes.
“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]
The Results (Genotyping) and Methods (short) support that the authors used PanGenie to genotype a subset of SVs in short-read genomes. The Discussion identifies 32 genomes as the long-read assembly panel, while the Methods say PanGenie was applied to 3,202 short-read genomes. The copy reports 24,107 strict or 50,340 lenient genotypable SVs, but does not substantiate an average of 13,000 or a range of 12,000–15,000 per sample. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe HGSVC and HPRC call sets are based on variant calls produced from haplotype-resolved assemblies of 32 and 44 samples, respectively.
“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]
The Methods (short; page unavailable) describe 32 samples, and the Results (‘Phased variant discovery’; page unavailable) say variants were called by comparing haplotype-resolved assemblies with the reference genome. The cited paper does not establish the claim about an HPRC call set based on 44 samples. (LLM, conf=0.87)
Experimental — accuracy not yet measured
Compared with Ebert et al., the average median base level accuracy is nearly an order of magnitude higher, the N50 contiguity is nearly double and the structural accuracy is higher.
“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]
Short-read-based SV discovery relative to a linear reference genome misses a large proportion of SVs.
“This result confirms that short-read-based SV discovery relative to a linear reference genome misses a large proportion of SVs5,6,8.”
From A draft human pangenome reference. (2023) · cites this paper as [5]
SV callers based on short reads alone miss a large proportion of SVs located in regions inaccessible by short-read alignments.
“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-citationGenome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication
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Self-citationEvolutionary changes in the genetic code
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Self-citationHuman Genome Assembly in 100 MinutesPreprint
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A draft human pangenome reference.
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Self-citationChromosomal inversion polymorphisms shape the genomic landscape of deer mice
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Genomics in the long-read sequencing era
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Self-citationCharacterization and visualization of tandem repeats at genome scale
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Self-citationChasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
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Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire
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A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypesPreprint
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Beyond the exome: What’s next in diagnostic testing for Mendelian conditions
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Self-citationAssembly of 43 human Y chromosomes reveals extensive complexity and variation
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Self-citationThe complete sequence and comparative analysis of ape sex chromosomes
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Self-citationThe Need for a Human Pangenome Reference Sequence
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Structural variation in 1,019 diverse humans based on long-read sequencing
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Self-citationGATK-gCNV enables the discovery of rare copy number variants from exome sequencing data
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Self-citationUtility of long-read sequencing for All of Us
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Self-citationHuman de novo mutation rates from a four-generation pedigree reference
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Self-citationBuilding consensus around the assessment and interpretation of Symbiodiniaceae diversity
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lra: A long read aligner for sequences and contigs
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Self-citationIncreased mutation and gene conversion within human segmental duplications
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Self-citationSVision: a deep learning approach to resolve complex structural variants
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Self-citationGenomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes
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Self-citationStructural Variation in Cancer: Role, Prevalence, and Mechanisms
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Applications of long-read sequencing to Mendelian genetics
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LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants
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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
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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
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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
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Self-citationThe EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
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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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Self-citationHow Important Are Structural Variants for Speciation?
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Structurally divergent and recurrently mutated regions of primate genomes
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Self-citationAnalysis and benchmarking of small and large genomic variants across tandem repeats
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Self-citationDysgu: efficient structural variant calling using short or long reads
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Familial long-read sequencing increases yield of de novo mutations
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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 68 · see citing works
Self-citationVialle, R. A., Lopes, K. D. P., Bennett, D. A., Crary, J. F., & Raj, T. (2022) · Nature Neuroscience · doi:10.1038/s41593-022-01031-7 · Cited by 64 · see citing works
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
Olivucci, G., Iovino, E., Innella, G., Turchetti, D., Pippucci, T., & Magini, P. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1374860 · Cited by 66 · see citing works
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
Quan, C., Ping, J., Lu, H. X., Zhou, G., & Lu, Y. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1008 · Cited by 65 · see citing works
Cas9 targeted enrichment of mobile elements using nanopore sequencing
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Self-citationMatalon, D. R., Zepeda‐Mendoza, C. J., Aarabi, M., Brown, K. M., Fullerton, S. M., Kaur, S., Quintero‐Rivera, F., & Vatta, M. (2023) · Genetics in Medicine · doi:10.1016/j.gim.2023.100812 · Cited by 63 · see citing works
Toffoli, M., Chen, X., Sedlazeck, F. J., Lee, C.-Y., Mullin, S., Higgins, A., Koletsi, S., Garcia-Segura, M. E., Sammler, E., Scholz, S. W., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03610-7 · Cited by 59 · see citing works
“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 .”
Self-citationRabanal, F. A., Gräff, M., Lanz, C., Fritschi, K., Llaca, V., Lang, M. G., Carbonell‐Bejerano, P., Henderson, I. R., & Weigel, D. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1115 · Cited by 62 · see citing works
REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats
Dolzhenko, E., Weisburd, B., Ibáñez, K., Rajan‐Babu, I., Anyansi, C., Bennett, M. F., Billingsley, K. J., Carroll, A., Clamons, S. E., Danzi, M. C., et al. (2022) · Genome Medicine · doi:10.1186/s13073-022-01085-z · Cited by 60 · see citing works
Cue: a deep-learning framework for structural variant discovery and genotyping
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Smith, T. P. L., Bickhart, D. M., Boichard, D., Chamberlain, A. J., Djikeng, A., Jiang, Y., Low, W. Y., Pausch, H., Demyda-Peyrás, S., Prendergast, J., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02975-0 · Cited by 57 · see citing works
Liu, Y. H., Luo, C., Golding, S. G. H., Ioffe, J. B., & Zhou, X. (2024) · Nature Communications · doi:10.1038/s41467-024-46614-z · Cited by 56 · see citing works
Kosugi, S., & Terao, C. C. (2024) · Human Genome Variation · doi:10.1038/s41439-024-00276-x · Cited by 60 · see citing works
Gaps and complex structurally variant loci in phased genome assemblies
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Self-citationLong-read whole-genome analysis of human single cells
Hård, J., Mold, J. E., Eisfeldt, J., Tellgren‐Roth, C., Häggqvist, S., Bunikis, I., Contreras‐López, O., Chin, C.-S., Nordlund, J., Rubin, C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-40898-3 · Cited by 54 · see citing works
A framework to score the effects of structural variants in health and diseasePreprint
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- 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 · 2020: 2 · 2017: 1
- 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.
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 ›
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