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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EHdn calls in HuRef were validated at 77% against long-read data.
“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]
Genome STRiP combined read-pair and read-depth features, implying that using different evidence types can improve structural-variant discovery.
“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]
Obtaining phase from sequence data alone is not trivial.
“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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Self-citation
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The regulated retrotransposon transcriptome of mammalian cells
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“Sanger sequencing was used to obtain the first consensus sequence of the human genome in 2001 (Lander et al., 2001; Venter et al., 2001) and the first individual human diploid sequence (J. Craig Venter) in 2007 (Levy et al., 2007).”
MethodNatural mutagenesis of human genomes by endogenous retrotransposons
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Variation in Transcription Factor Binding Among Humans
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Self-citationDe novo assembly of haplotype-resolved genomes with trio binning
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Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm
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Complete Khoisan and Bantu genomes from southern Africa
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Annotating non-coding regions of the genome.
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Self-citationHuman Genome Sequencing in Health and Disease
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“Of the 22 loci discordant with HapMap, the errors fell into three classes: (1) nine are homozygous reference genotypes with a HapMap homozygous alternate, (2) five are heterozygous genotypes with a HapMap homozygous reference and (3) eight are homozygous reference with a HapMap heterozygous genotype (Supplementary Tab…”
Statistical analysis strategies for association studies involving rare variants
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Self-citationWhatsHap: fast and accurate read-based phasingPreprint
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Single-molecule sequencing of an individual human genome
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Copy number variants, diseases and gene expression
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Satellite DNA: An Evolving Topic
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Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications
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Massively Parallel Sequencing: The Next Big Thing in Genetic Medicine
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- 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
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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