Initial sequencing and analysis of the human genome
Open accessAbstract
The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
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Together, LINEs and SINEs account for 40-50% of human DNA.
“Together, LINEs and SINEs account for 40–50% of human DNA (85).”
From The Discovery of Reverse Transcriptase (2016) · cites this paper as [85]
In “Transposon-derived repeats” (page not provided), the paper reports that SINEs comprise 13% and LINEs 20% of the sequence—a combined 33%, not 40–50%. Its approximately 45% figure refers to all recognized transposable-element classes, including LTR retrotransposons and DNA transposons. (LLM, conf=0.91)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredApproximately 8% of the human genome is made up of endogenous retroviral DNA, more than the DNA that encodes proteins.
“For instance, ∼8% of the human genome is made up of endogenous retroviral DNA—more than the DNA that encodes proteins (85).”
From The Discovery of Reverse Transcriptase (2016) · cites this paper as [85]
In “Transposon-derived repeats” (page unavailable), the paper estimates that LTR retroposon copies comprise 8% of the genome and discusses endogenous retroviruses within that category. It does not explicitly assign the entire 8% to endogenous retroviral DNA. “Protein-coding genes” (page unavailable) estimates that coding sequence comprises about 1.5%, supporting the comparison. (LLM, conf=0.84)
Experimental — accuracy not yet measuredRetrotransposons comprise at least 60% of the human genome.
“For example, retrotransposons comprise at least 60% of the human genome [3] and results presented here and elsewhere [34] suggest that the number of endogenous retroviruses in chimpanzees may be higher than in humans.”
From Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses (2006) · cites this paper as [3]
In “Transposon-derived repeats” (page unavailable), the paper reports that recognized SINEs, LINEs, and LTR retroposons occupy 13%, 20%, and 8% of the draft genome sequence, respectively. It says additional ancient transposon-derived sequence may be unrecognized, but does not establish that retrotransposons comprise at least 60% of the human genome. (LLM, conf=0.89)
Experimental — accuracy not yet measuredThe human reference genome has formed the backbone of human genomics since its initial draft release more than 20 years ago.
“The human reference genome has formed the backbone of human genomics since its initial draft release more than 20 years ago2.”
From A draft human pangenome reference. (2023) · cites this paper as [2]
The Abstract reports the initial, freely available draft human genome sequence, and the Background to the Human Genome Project says it would let researchers begin extracting information from the genome (page numbers unavailable in our copy). The 2001 paper cannot establish the retrospective claim that the reference genome remained the backbone of human genomics for more than 20 years. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThe human genome includes genes for 57 cytochrome P450 enzymes.
“The human genome includes genes for 57 cytochrome P450 enzymes (47,48).”
From The Molecular Biology, Biochemistry, and Physiology of Human Steroidogenesis and Its Disorders (2011) · cites this paper as [48]
The Comparative proteome analysis identifies cytochrome P450 enzymes as a protein family in the human-genome analysis. The passages found do not give a count of 57 genes, so the numerical part of the claim is unsupported by our copy. (LLM, conf=0.79)
Experimental — accuracy not yet measured
Completion of the draft human genome sequence reduced obstacles to disease-gene mapping and propelled a fourfold increase in genes implicated as causal for rare single-gene disorders.
“Completion of the draft human genome sequence1 reduced many of the obstacles to disease-gene mapping and propelled a fourfold increase in the genes implicated as causal for rare, single-gene disorders (Fig. 1).”
From A brief history of human disease genetics (2020) · cites this paper as [1]
Culture-independent molecular methods based on DNA sequence similarities allowed identification and characterization of microbial communities and improved the ability to culture previously unculturable bacteria.
“gave way to culture-independent molecular approaches allowing us to not only identify and characterize microbial communities based on similarities in DNA sequences, but also provide knowledge that has significantly improved our ability culture bacteria that were previously considered unculturable6.”
From The gut Microbiome in adult and pediatric functional gastrointestinal disorders (2019) · cites this paper as [4]
Nearly 99% of the human genome does not encode proteins and the approximately 21,000 human protein-coding genes are generally surprisingly similar across placental mammals.
“Indeed, the human genome project has made it clear that nearly 99% of the human genome does not encode proteins and that the approximately 21,000 human protein-coding genes are in general surprisingly similar across placental mammals (Lander, 2011; Lander et al., 2001; Venter et al., 2001).”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Lander et al., 2001
Resveratrol inhibits retrotransposition of Long Interspersed Nuclear Element-1 (LINE-1), comprising cca 17% of the human genome, which is related to SIRT6 and SIRT7.
“Resveratrol has been found to inhibit retrotransposition of Long Interspersed Nuclear Element-1 (LINE-1), comprising cca 17% of the human genome (Lander et al. 2001), which in turn is related to SIRT6 and SIRT7.”
From Reactive Oxygen Species, Toxicity, Oxidative Stress, and Antioxidants: Chronic Diseases and Aging (2023) · cites this paper as Lander et al. 2001
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The Human Genome Browser at UCSC
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Self-citationThe protein kinase complement of the human genome
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“About 8% of the human genome is of retroviral origin (27); however due to their ancient origins most human ERV loci have accumulated nonsense mutations and can no longer encode”
DNA methylation patterns and epigenetic memory
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The International HapMap Project
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The complete sequence of a human genome
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Highly accurate protein structure prediction for the human proteome
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De novo assembly of human genomes with massively parallel short read sequencing
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Integrating common and rare genetic variation in diverse human populations
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A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
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Self-citationReactive Oxygen Species, Toxicity, Oxidative Stress, and Antioxidants: Chronic Diseases and Aging
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DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources
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Interactome Networks and Human Disease
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The Diploid Genome Sequence of an Individual Human
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Self-citationUltraconserved Elements in the Human Genome
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Self-citationHigh-resolution haplotype structure in the human genome
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Self-citationExploring tissue architecture using spatial transcriptomics
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A N <scp>EW</scp> A <scp>PPROACH TO</scp> D <scp>ECODING</scp> L <scp>IFE</scp> : Systems Biology
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Self-citationEngineered CRISPR-Cas9 nucleases with altered PAM specificities
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Humans Have Evolved Specialized Skills of Social Cognition: The Cultural Intelligence Hypothesis
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A census of human transcription factors: function, expression and evolution
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Serine/threonine phosphatases: mechanism through structure
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Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate
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Protein Analysis by Shotgun/Bottom-up Proteomics
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Evolutionary and biomedical insights from the rhesus macaque genome.
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Self-citationA reference map of the human binary protein interactome
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The human ATP-binding cassette (ABC) transporter superfamily
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Single-cell sequencing-based technologies will revolutionize whole-organism science
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A draft human pangenome reference.
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A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome
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Positive Natural Selection in the Human Lineage
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- Authors
- International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J. P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., The Sanger Centre:, Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J. C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Washington University Genome Sequencing Center, Waterston, R. H., Wilson, R. K., Hillier, L. W., McPherson, J. D., Marra, M. A., Mardis, E. R., Fulton, L. A., Chinwalla, A. T., Pepin, K. H., Gish, W. R., Chissoe, S. L., Wendl, M. C., Delehaunty, K. D., Miner, T. L., Delehaunty, A., Kramer, J. B., Cook, L. L., Fulton, R. S., Johnson, D. L., Minx, P. J., Clifton, S. W., US DOE Joint Genome Institute:, Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J.-F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E., Frazier, M., Baylor College of Medicine Human Genome Sequencing Center:, Gibbs, R. A., Muzny, D. M., Scherer, S. E., Bouck, J. B., Sodergren, E. J., Worley, K. C., Rives, C. M., Gorrell, J. H., Metzker, M. L., Naylor, S. L., Kucherlapati, R. S., Nelson, D. L., Weinstock, G. M., RIKEN Genomic Sciences Center:, Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., UMR-8030:, G. A. C., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Department of Genome Analysis, I. O. M. B., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., GTC Sequencing Center:, Smith, D. R., Doucette-Stamm, L., Rubenfield, M., Weinstock, K., Lee, H. M., Dubois, J., Beijing Genomics Institute/Human Genome Center:, Yang, H., Yu, J., Wang, J., Huang, G., Gu, J., Multimegabase Sequencing Center, T. I. F. S. B., Hood, L., Rowen, L., Madan, A., Qin, S., Stanford Genome Technology Center:, Davis, R. W., Federspiel, N. A., Abola, A. P., Proctor, M. J., University of Oklahoma's Advanced Center for Genome Technology:, Roe, B. A., Chen, F., Pan, H., Max Planck Institute for Molecular Genetics:, Ramser, J., Lehrach, H., Reinhardt, R., Cold Spring Harbor Laboratory, L. A. H. G. C., McCombie, W. R., de la Bastide, M., Dedhia, N., GBF—German Research Centre for Biotechnology:, Blöcker, H., Hornischer, K., Nordsiek, G., *Genome Analysis Group (listed in alphabetical order, A. I. I. L. U. O. H., Agarwala, R., Aravind, L., Bailey, J. A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D. G., Burge, C. B., Cerutti, L., Chen, H.-C., Church, D., Clamp, M., Copley, R. R., Doerks, T., Eddy, S. R., Eichler, E. E., Furey, T. S., Galagan, J., Gilbert, J. G. R., Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W., Johnson, L. S., Jones, T. A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W. J., Kitts, P., Koonin, E. V., Korf, I., Kulp, D., Lancet, D., Lowe, T. M., McLysaght, A., Mikkelsen, T., Moran, J. V., Mulder, N., Pollara, V. J., Ponting, C. P., Schuler, G., Schultz, J., Slater, G., Smit, A. F. A., Stupka, E., Szustakowki, J., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y. I., Wolfe, K. H., Yang, S.-P., Yeh, R.-F., Scientific management: National Human Genome Research Institute, U. N. I. O. H., Collins, F., Guyer, M. S., Peterson, J., Felsenfeld, A., Wetterstrand, K. A., Stanford Human Genome Center:, Myers, R. M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D. R., University of Washington Genome Center:, Olson, M. V., Kaul, R., Raymond, C., Department of Molecular Biology, K. U. S. O. M., Shimizu, N., Kawasaki, K., Minoshima, S., University of Texas Southwestern Medical Center at Dallas:, Evans, G. A., Athanasiou, M., Schultz, R., Office of Science, U. D. O. E., Patrinos, A., The Wellcome Trust:, & Morgan, M. J.
- Affiliations
- Whitehead Institute for Biomedical Research (US)
- University of Washington (US)
- Wellcome Sanger Institute (GB)
- Washington University in St. Louis (US)
- Joint Genome Institute (US)
- Baylor College of Medicine (US)
- The University of Texas at San Antonio Health Science Center (US)
- Albert Einstein College of Medicine (US)
- RIKEN (JP)
- Centre National de la Recherche Scientifique (FR)
- Chinese Academy of Sciences (CN)
- Institute for Systems Biology (US)
- Stanford University (US)
- University of Oklahoma (US)
- Max Planck Institute for Molecular Genetics (DE)
- Cold Spring Harbor Laboratory (US)
- Helmholtz Centre for Infection Research (DE)
- National Institutes of Health (US)
- University Hospitals of Cleveland (US)
- European Bioinformatics Institute (GB)
- Max Delbrück Center (DE)
- Howard Hughes Medical Institute (US)
- University of California, Santa Cruz (US)
- Stanford Medicine (US)
- Trinity College Dublin (IE)
- University of Michigan (US)
- University of Oxford (GB)
- Keio University (JP)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- United States Department of Energy (US)
- The University of Texas Southwestern Medical Center (US)
- Wellcome Trust (GB)
- Corresponding author
- Lander, Eric S.
- Sulston, John
- Waterston, Robert H.
- Collins, Francis
- ORCID
- Lander, Eric S.
- Birren, Bruce
- Nusbaum, Chad
- Zody, Michael C.
- Dewar, Ken
- Howland, John
- Kann, Lisa
- Lehoczky, Jessica
- McKernan, Kevin
- Meldrim, James
- Mesirov, Jill P.
- Subramanian, Aravind
- Beck, Stephan
- Deloukas, Panos
- Dunham, Ian
- Durbin, Richard
- French, Lisa
- Gregory, Simon
- Hubbard, Tim
- Humphray, Sean
- Hunt, Adrienne
- Jones, Matthew
- McMurray, Amanda
- Milne, Sarah
- Mullikin, James C.
- Mungall, Andrew
- Ross, Mark
- Sims, Sarah
- Waterston, Robert H.
- McPherson, John D.
- Marra, Marco A.
- Mardis, Elaine R.
- Chinwalla, Asif T.
- Pepin, Kymberlie H.
- Wendl, Michael C.
- Kramer, Jason B.
- Cook, Lisa L.
- Fulton, Robert S.
- Minx, Patrick J.
- Branscomb, Elbert
- Doggett, Norman
- Cheng, Jan-Fang
- Olsen, Anne
- Lucas, Susan
- Gibbs, Richard A.
- Muzny, Donna M.
- Scherer, Steven E.
- Sodergren, Erica J.
- Worley, Kim C.
- Kucherlapati, Raju S.
- Nelson, David L.
- Weinstock, George M.
- Hattori, Masahira
- Yada, Tetsushi
- Toyoda, Atsushi
- Itoh, Takehiko
- Totoki, Yasushi
- Taylor, Todd
- Weissenbach, Jean
- Wincker, Patrick
- Platzer, Matthias
- Rump, Andreas
- Yang, Huanming
- Wang, Jian
- Hood, Leroy
- Madan, Anup
- Davis, Ronald W.
- Chen, Feng
- Pan, Huaqin
- Reinhardt, Richard
- McCombie, W. Richard
- Agarwala, Richa
- Aravind, L.
- Bailey, Jeffrey A.
- Bateman, Alex
- Batzoglou, Serafim
- Birney, Ewan
- Brown, Daniel G.
- Burge, Christopher B.
- Cerutti, Lorenzo
- Church, Deanna
- Copley, Richard R.
- Eddy, Sean R.
- Eichler, Evan E.
- Furey, Terrence S.
- Galagan, James
- Gilbert, James G. R.
- Harmon, Cyrus
- Hayashizaki, Yoshihide
- Haussler, David
- Hermjakob, Henning
- Hokamp, Karsten
- Jang, Wonhee
- Kasif, Simon
- Koonin, Eugene V.
- Korf, Ian
- Kulp, David
- Lancet, Doron
- Lowe, Todd M.
- McLysaght, Aoife
- Mikkelsen, Tarjei
- Moran, John V.
- Mulder, Nicola
- Ponting, Chris P.
- Schultz, Jörg
- Slater, Guy
- Smit, Arian F. A.
- Stupka, Elia
- Wheeler, Raymond
- Wolf, Yuri I.
- Wolfe, Kenneth H.
- Collins, Francis
- Wetterstrand, Kris A.
- Myers, Richard M.
- Schmutz, Jeremy
- Grimwood, Jane
- Cox, David R.
- Olson, Maynard V.
- Kaul, Rajinder
- Raymond, Christopher
- Kawasaki, Kazuhiko
- Venue
- Nature
- Published
- 2001-02-01
- Volume
- 409
- Issue
- 6822
- Pages
- 860-921
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2168909179
- Semantic Scholar
- 040e3692c4855e5d2e41cacf7aeaa36c00c11570
- Cited by
- 24,216
- References
- 458
- Citations by year
- 2026: 390 · 2025: 694 · 2024: 771 · 2023: 760 · 2022: 759 · 2021: 977 · 2020: 848 · 2019: 768 · 2018: 818 · 2017: 834 · 2016: 832 · 2015: 838 · 2014: 879 · 2013: 1002 · 2012: 1000
- FWCI
- 569.69
- Type
- journal article
- Language
- en
- Update notices
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, public-domain)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Deep Blue (University of Michigan) (submittedVersion, public-domain)
- HAL (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Research Explorer (The University of Manchester) (submittedVersion)
- Tokyo Tech Research Repository (Tokyo Institute of Technology) (submittedVersion)
- Funders
- National Science Foundation
- U.S. Department of Energy
- University of Pennsylvania
- Achievement Rewards for College Scientists Foundation
- Wellcome Trust
- European Commission
- Deutsche Forschungsgemeinschaft
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- National Natural Science Foundation of China
- Bundesministerium für Bildung und Forschung
- Chinese Academy of Sciences
- National Yang-Ming University
- National Institutes of Health
- Medical Research Council
- Institute of Medical Science, University of Tokyo
- National Human Genome Research Institute
- Biological and Environmental Research
- Institute of Genetics
- Office of Experimental Program to Stimulate Competitive Research
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- human genome, genome sequencing, draft genome sequence, genome annotation, human evolution, human development, human physiology, human medicine
- MeSH terms
- Animals, Chromosome Mapping, DNA Transposable Elements, Drug Industry, Forecasting, Genes, Genetics, Medical, Humans, Mutation, Proteins, Repetitive Sequences, Nucleic Acid, RNA, Species Specificity, Genome, Human, Human Genome Project, Databases, Factual, Conserved Sequence, Private Sector, Public Sector, Sequence Analysis, DNA, CpG Islands, Evolution, Molecular, Gene Duplication, Proteome, GC Rich Sequence, Genetic Diseases, Inborn
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