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The Diploid Genome Sequence of an Individual Human
Open accessAbstract
Presented here is a genome sequence of an individual human. It was produced from approximately 32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2-206 bp), 292,102 heterozygous insertion/deletion events (indels)(1-571 bp), 559,473 homozygous indels (1-82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information.
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“We could validate 77% of the tandem repeats detected by EHdn in the HuRef genome31 by comparing to tandem repeats detected by an orthogonal strategy involving long-read sequencing data”
From Genome-wide detection of tandem DNA repeats that are expanded in autism (2020) · cites this paper as [31]
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“This method, Genome STRiP (to be described elsewhere36), integrated both RP and RD features (PD), implying that considering different evidence types can improve SV discovery.”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [36]
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“Thus, leveraging phase information in an association study of rare variants may be crucial, but obtaining phase from sequence data alone is not trivial.24, 91–93”
From Statistical analysis strategies for association studies involving rare variants (2010) · cites this paper as [93]
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Metadata
- Authors
- Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P., Axelrod, N., Huang, J., Kirkness, E. F., Denisov, G., Lin, Y., MacDonald, J. R., Pang, A. W. C., Shago, M., Stockwell, T. B., Tsiamouri, A., Bafna, V., Bansal, V., Kravitz, S. A., Busam, D. A., Beeson, K. Y., McIntosh, T. C., Remington, K. A., Abril, J. F., Gill, J., Borman, J., Rogers, Y.-H., Frazier, M. E., Scherer, S. W., Strausberg, R. L., & Venter, J. C.
- Affiliations
- J. Craig Venter Institute (US)
- University of Toronto (CA)
- University of California San Diego (US)
- Universitat de Barcelona (ES)
- Corresponding author
- Levy, Samuel
- ORCID
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2007-09-04
- Volume
- 5
- Issue
- 10
- Pages
- e254
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- PMC
- PMC1964779
- OpenAlex
- W2142642738
- Cited by
- 1,778
- References
- 112
- Citations by year
- 2026: 14 · 2025: 25 · 2024: 24 · 2023: 21 · 2022: 40 · 2021: 36 · 2020: 81 · 2019: 52 · 2018: 69 · 2017: 74 · 2016: 80 · 2015: 97 · 2014: 95 · 2013: 152 · 2012: 153
- FWCI
- 79.94
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (publishedVersion, other-oa)
- National University of Singapore (submittedVersion, cc-by)
- Dipòsit Digital de la Universitat de Barcelona (Universitat de Barcelona) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Canadian Institute for Advanced Research
- Genome Canada
- Ontario Genomics
- Ontario Genomics Institute
- Sick Kids Foundation
- Hospital for Sick Children
- Canadian Institutes of Health Research
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- single nucleotide polymorphisms, structural variants, indels, copy number variation, segmental duplication, inversion, haplotype assembly, genome assembly
- MeSH terms
- Base Sequence, Chromosome Mapping, Chromosomes, Human, Diploidy, Genotype, Haplotypes, Humans, Male, Middle Aged, Molecular Sequence Data, Pedigree, Phenotype, Reproducibility of Results, Genome, Human, Human Genome Project, In Situ Hybridization, Fluorescence, Sequence Analysis, DNA, Gene Dosage, Polymorphism, Single Nucleotide, Chromosomes, Human, Y, Microarray Analysis, INDEL Mutation
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