Segmental duplications and their variation in a complete human genome-Reference-Cited by-同舟云学术

Segmental duplications and their variation in a complete human genome

Published:2022-04 Issue:6588 Volume:376 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Vollger Mitchell R.¹^ORCID,Guitart Xavi¹^ORCID,Dishuck Philip C.¹^ORCID,Mercuri Ludovica²^ORCID,Harvey William T.¹^ORCID,Gershman Ariel³^ORCID,Diekhans Mark⁴^ORCID,Sulovari Arvis¹^ORCID,Munson Katherine M.¹^ORCID,Lewis Alexandra P.¹^ORCID,Hoekzema Kendra¹^ORCID,Porubsky David¹^ORCID,Li Ruiyang¹^ORCID,Nurk Sergey⁵^ORCID,Koren Sergey⁵^ORCID,Miga Karen H.⁴^ORCID,Phillippy Adam M.⁵^ORCID,Timp Winston³^ORCID,Ventura Mario²^ORCID,Eichler Evan E.¹⁶^ORCID

Affiliation:

1. Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.

2. Department of Biology, University of Bari, Aldo Moro, Bari 70125, Italy.

3. Department of Molecular Biology and Genetics, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.

4. UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.

5. Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.

6. Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.

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.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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