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Segmental duplications and their variation in a complete human genome
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Abstract
Despite their importance in disease and evolution, highly identical segmental duplications (SDs) are among the last regions of the human reference genome (GRCh38) to be fully sequenced. Using a complete telomere-to-telomere human genome (T2T-CHM13), we present a comprehensive view of human SD organization. SDs account for nearly one-third of the additional sequence, increasing the genome-wide estimate from 5.4 to 7.0% [218 million base pairs (Mbp)]. An analysis of 268 human genomes shows that 91% of the previously unresolved T2T-CHM13 SD sequence (68.3 Mbp) better represents human copy number variation. Comparing long-read assemblies from human ( n = 12) and nonhuman primate ( n = 5) genomes, we systematically reconstruct the evolution and structural haplotype diversity of biomedically relevant and duplicated genes. This analysis reveals patterns of structural heterozygosity and evolutionary differences in SD organization between humans and other primates.
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“Furthermore, collapsed segmental duplications in GRCh38 and GRCh37, such as the GPRIN2A/B region [28, 38], often result in erroneous variant calls.”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [28]
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Chromosome heteromorphisms: an impact on infertility
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Self-citationThe Evolution of Human Segmental Duplications and the Core Duplicon HypothesisPreprint
Marquès‐Bonet, T., & Eichler, E. E. (2009) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2009.74.011 · Cited by 77
Self-citationHuman Population Cytogenetics: A Review
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Recurrent inversion toggling and great ape genome evolution
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Self-citationBehaviour of human heterochromatic regions during the synapsis of homologous chromosomes
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Transcriptional fates of human-specific segmental duplications in brainPreprint
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Self-citationAre heterochromatin polymorphisms associated with recurrent miscarriage?
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Euchromatic heteromorphism or duplication without phenotypic effect?
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Flagged first, then by citations
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Cited by
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Self-citation
Metadata
- Authors
- Vollger, M. R., Guitart, X., Dishuck, P. C., Mercuri, L., Harvey, W. T., Gershman, A., Diekhans, M., Sulovari, A., Munson, K. M., Lewis, A. P., Hoekzema, K., Porubsky, D., Li, R., Nurk, S., Koren, S., Miga, K. H., Phillippy, A. M., Timp, W., Ventura, M., & Eichler, E. E.
- Affiliations
- University of Washington (US)
- University of Bari Aldo Moro (IT)
- Johns Hopkins University (US)
- University of California, Santa Cruz (US)
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- National Institutes of Health (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Eichler, Evan E.
- ORCID
- Vollger, Mitchell R.
- Guitart, Xavi
- Dishuck, Philip C.
- Mercuri, Ludovica
- Harvey, William T.
- Gershman, Ariel
- Diekhans, Mark
- Sulovari, Arvis
- Munson, Katherine M.
- Lewis, Alexandra P.
- Hoekzema, Kendra
- Porubsky, David
- Li, Ruiyang
- Nurk, Sergey
- Koren, Sergey
- Miga, Karen H.
- Phillippy, Adam M.
- Timp, Winston
- Ventura, Mario
- Eichler, Evan E.
- Venue
- Science
- Published
- 2022-04
- Volume
- 376
- Issue
- 6588
- Pages
- eabj6965-eabj6965
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC8979283
- OpenAlex
- W4225379371
- Cited by
- 350
- References
- 118
- Citations by year
- 2026: 51 · 2025: 81 · 2024: 98 · 2023: 73 · 2022: 41
- FWCI
- 47.03
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by
- Locations
- Science (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion, cc-by-nc-nd)
- Funders
- Howard Hughes Medical Institute
- Oxford Nanopore Technologies
- National Institutes of Health
- National Human Genome Research Institute (U01HG010973, U01HG010971, U41HG007234, R01HG009190, R01HG011274, R01HG002385, U24HG007234)
- National Institute of General Medical Sciences (T32GM007445)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- segmental duplication, human genome, telomere-to-telomere genome assembly, T2T-CHM13, copy number variation, structural heterozygosity, duplicate genes, long-read genome assembly, genome evolution
- MeSH terms
- Humans, Proto-Oncogene Proteins, Genome, Human, Evolution, Molecular, Gene Duplication, Polymorphism, Single Nucleotide, GTPase-Activating Proteins, DNA Copy Number Variations, Segmental Duplications, Genomic
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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