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Completing the human genome: the progress and challenge of satellite DNA assembly

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Abstract

Genomic studies rely on accurate chromosome assemblies to explore sequence-based models of cell biology, evolution and biomedical disease. However, even the extensively studied human genome has not yet reached a complete, ‘telomere-to-telomere’, chromosome assembly. The largest assembly gaps remain in centromeric regions and acrocentric short arms, sites known to contain megabase-sized arrays of tandem repeats, or satellite DNAs. This review aims to briefly address the progress and challenges of generating correct assemblies of satellite DNA arrays. Although the focus is placed on the human genome, many concepts presented here are applicable to other genomes.

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Abbreviations

HVGM:

Human Variation Genome Map

ONT:

Oxford Nanopore Technology

PacBio:

Pacific Biosciences

rDNA:

Ribosomal DNA

WGS:

Whole genome shotgun

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Authors and Affiliations

  1. Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA

    Karen H. Miga

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  1. Karen H. Miga
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Correspondence to Karen H. Miga.

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Responsible Editors: Maria Assunta Biscotti, Pat Heslop-Harrison and Ettore Olmo

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Miga, K.H. Completing the human genome: the progress and challenge of satellite DNA assembly. Chromosome Res 23, 421–426 (2015). https://doi.org/10.1007/s10577-015-9488-2

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  • DOI: https://doi.org/10.1007/s10577-015-9488-2

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