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Science 16 February 2001:
Vol. 291. no. 5507, pp. 1304 - 1351
DOI: 10.1126/science.1058040
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Review

The Sequence of the Human Genome

J. Craig Venter,1* Mark D. Adams,1 Eugene W. Myers,1 Peter W. Li,1 Richard J. Mural,1 Granger G. Sutton,1 Hamilton O. Smith,1 Mark Yandell,1 Cheryl A. Evans,1 Robert A. Holt,1 Jeannine D. Gocayne,1 Peter Amanatides,1 Richard M. Ballew,1 Daniel H. Huson,1 Jennifer Russo Wortman,1 Qing Zhang,1 Chinnappa D. Kodira,1 Xiangqun H. Zheng,1 Lin Chen,1 Marian Skupski,1 Gangadharan Subramanian,1 Paul D. Thomas,1 Jinghui Zhang,1 George L. Gabor Miklos,2 Catherine Nelson,3 Samuel Broder,1 Andrew G. Clark,4 Joe Nadeau,5 Victor A. McKusick,6 Norton Zinder,7 Arnold J. Levine,7 Richard J. Roberts,8 Mel Simon,9 Carolyn Slayman,10 Michael Hunkapiller,11 Randall Bolanos,1 Arthur Delcher,1 Ian Dew,1 Daniel Fasulo,1 Michael Flanigan,1 Liliana Florea,1 Aaron Halpern,1 Sridhar Hannenhalli,1 Saul Kravitz,1 Samuel Levy,1 Clark Mobarry,1 Knut Reinert,1 Karin Remington,1 Jane Abu-Threideh,1 Ellen Beasley,1 Kendra Biddick,1 Vivien Bonazzi,1 Rhonda Brandon,1 Michele Cargill,1 Ishwar Chandramouliswaran,1 Rosane Charlab,1 Kabir Chaturvedi,1 Zuoming Deng,1 Valentina Di Francesco,1 Patrick Dunn,1 Karen Eilbeck,1 Carlos Evangelista,1 Andrei E. Gabrielian,1 Weiniu Gan,1 Wangmao Ge,1 Fangcheng Gong,1 Zhiping Gu,1 Ping Guan,1 Thomas J. Heiman,1 Maureen E. Higgins,1 Rui-Ru Ji,1 Zhaoxi Ke,1 Karen A. Ketchum,1 Zhongwu Lai,1 Yiding Lei,1 Zhenya Li,1 Jiayin Li,1 Yong Liang,1 Xiaoying Lin,1 Fu Lu,1 Gennady V. Merkulov,1 Natalia Milshina,1 Helen M. Moore,1 Ashwinikumar K Naik,1 Vaibhav A. Narayan,1 Beena Neelam,1 Deborah Nusskern,1 Douglas B. Rusch,1 Steven Salzberg,12 Wei Shao,1 Bixiong Shue,1 Jingtao Sun,1 Zhen Yuan Wang,1 Aihui Wang,1 Xin Wang,1 Jian Wang,1 Ming-Hui Wei,1 Ron Wides,13 Chunlin Xiao,1 Chunhua Yan,1 Alison Yao,1 Jane Ye,1 Ming Zhan,1 Weiqing Zhang,1 Hongyu Zhang,1 Qi Zhao,1 Liansheng Zheng,1 Fei Zhong,1 Wenyan Zhong,1 Shiaoping C. Zhu,1 Shaying Zhao,12 Dennis Gilbert,1 Suzanna Baumhueter,1 Gene Spier,1 Christine Carter,1 Anibal Cravchik,1 Trevor Woodage,1 Feroze Ali,1 Huijin An,1 Aderonke Awe,1 Danita Baldwin,1 Holly Baden,1 Mary Barnstead,1 Ian Barrow,1 Karen Beeson,1 Dana Busam,1 Amy Carver,1 Angela Center,1 Ming Lai Cheng,1 Liz Curry,1 Steve Danaher,1 Lionel Davenport,1 Raymond Desilets,1 Susanne Dietz,1 Kristina Dodson,1 Lisa Doup,1 Steven Ferriera,1 Neha Garg,1 Andres Gluecksmann,1 Brit Hart,1 Jason Haynes,1 Charles Haynes,1 Cheryl Heiner,1 Suzanne Hladun,1 Damon Hostin,1 Jarrett Houck,1 Timothy Howland,1 Chinyere Ibegwam,1 Jeffery Johnson,1 Francis Kalush,1 Lesley Kline,1 Shashi Koduru,1 Amy Love,1 Felecia Mann,1 David May,1 Steven McCawley,1 Tina McIntosh,1 Ivy McMullen,1 Mee Moy,1 Linda Moy,1 Brian Murphy,1 Keith Nelson,1 Cynthia Pfannkoch,1 Eric Pratts,1 Vinita Puri,1 Hina Qureshi,1 Matthew Reardon,1 Robert Rodriguez,1 Yu-Hui Rogers,1 Deanna Romblad,1 Bob Ruhfel,1 Richard Scott,1 Cynthia Sitter,1 Michelle Smallwood,1 Erin Stewart,1 Renee Strong,1 Ellen Suh,1 Reginald Thomas,1 Ni Ni Tint,1 Sukyee Tse,1 Claire Vech,1 Gary Wang,1 Jeremy Wetter,1 Sherita Williams,1 Monica Williams,1 Sandra Windsor,1 Emily Winn-Deen,1 Keriellen Wolfe,1 Jayshree Zaveri,1 Karena Zaveri,1 Josep F. Abril,14 Roderic Guigó,14 Michael J. Campbell,1 Kimmen V. Sjolander,1 Brian Karlak,1 Anish Kejariwal,1 Huaiyu Mi,1 Betty Lazareva,1 Thomas Hatton,1 Apurva Narechania,1 Karen Diemer,1 Anushya Muruganujan,1 Nan Guo,1 Shinji Sato,1 Vineet Bafna,1 Sorin Istrail,1 Ross Lippert,1 Russell Schwartz,1 Brian Walenz,1 Shibu Yooseph,1 David Allen,1 Anand Basu,1 James Baxendale,1 Louis Blick,1 Marcelo Caminha,1 John Carnes-Stine,1 Parris Caulk,1 Yen-Hui Chiang,1 My Coyne,1 Carl Dahlke,1 Anne Deslattes Mays,1 Maria Dombroski,1 Michael Donnelly,1 Dale Ely,1 Shiva Esparham,1 Carl Fosler,1 Harold Gire,1 Stephen Glanowski,1 Kenneth Glasser,1 Anna Glodek,1 Mark Gorokhov,1 Ken Graham,1 Barry Gropman,1 Michael Harris,1 Jeremy Heil,1 Scott Henderson,1 Jeffrey Hoover,1 Donald Jennings,1 Catherine Jordan,1 James Jordan,1 John Kasha,1 Leonid Kagan,1 Cheryl Kraft,1 Alexander Levitsky,1 Mark Lewis,1 Xiangjun Liu,1 John Lopez,1 Daniel Ma,1 William Majoros,1 Joe McDaniel,1 Sean Murphy,1 Matthew Newman,1 Trung Nguyen,1 Ngoc Nguyen,1 Marc Nodell,1 Sue Pan,1 Jim Peck,1 Marshall Peterson,1 William Rowe,1 Robert Sanders,1 John Scott,1 Michael Simpson,1 Thomas Smith,1 Arlan Sprague,1 Timothy Stockwell,1 Russell Turner,1 Eli Venter,1 Mei Wang,1 Meiyuan Wen,1 David Wu,1 Mitchell Wu,1 Ashley Xia,1 Ali Zandieh,1 Xiaohong Zhu1

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies--a whole-genome assembly and a regional chromosome assembly--were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional ~12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

1 Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.
2 GenetixXpress, 78 Pacific Road, Palm Beach, Sydney 2108, Australia.
3 Berkeley Drosophila Genome Project, University of California, Berkeley, CA 94720, USA.
4 Department of Biology, Penn State University, 208 Mueller Lab, University Park, PA 16802, USA.
5 Department of Genetics, Case Western Reserve University School of Medicine, BRB-630, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
6 Johns Hopkins University School of Medicine, Johns Hopkins Hospital, 600 North Wolfe Street, Blalock 1007, Baltimore, MD 21287-4922, USA.
7 Rockefeller University, 1230 York Avenue, New York, NY 10021-6399, USA.
8 New England BioLabs, 32 Tozer Road, Beverly, MA 01915, USA.
9 Division of Biology, 147-75, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
10 Yale University School of Medicine, 333 Cedar Street, P.O. Box 208000, New Haven, CT 06520-8000, USA.
11 Applied Biosystems, 850 Lincoln Centre Drive, Foster City, CA 94404, USA.
12 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
13 Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900 Israel.
14 Grup de Recerca en Informàtica Mèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, 08003-Barcelona, Catalonia, Spain.
*   To whom correspondence should be addressed. E-mail: humangenome{at}celera.com

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Low Exchangeability of Selenocysteine, the 21st Amino Acid, in Vertebrate Proteins.
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Mol. Biol. Evol. 26, 2031-2040
   Abstract »    Full Text »    PDF »
Harnessing nature's toolbox: regulatory elements for synthetic biology.
P. M. Boyle and P. A. Silver (2009)
J R Soc Interface 6, S535-S546
   Abstract »    Full Text »    PDF »
Systems Diagnostics: The Systems Approach to Molecular Imaging.
D. Y. Lee and K. C. P. Li (2009)
Am. J. Roentgenol. 193, 287-294
   Abstract »    Full Text »    PDF »
Intelligently deciphering unintelligible designs: algorithmic algebraic model checking in systems biology.
B. Mishra (2009)
J R Soc Interface 6, 575-597
   Abstract »    Full Text »    PDF »
FINDSITE: a combined evolution/structure-based approach to protein function prediction.
J. Skolnick and M. Brylinski (2009)
Brief Bioinform 10, 378-391
   Abstract »    Full Text »    PDF »
Genome assembly reborn: recent computational challenges.
M. Pop (2009)
Brief Bioinform 10, 354-366
   Abstract »    Full Text »    PDF »
Genomic regulatory blocks in vertebrates and implications in human disease.
P. Navratilova and T. S. Becker (2009)
Briefings in Functional Genomics 8, 333-342
   Abstract »    Full Text »    PDF »
Pan-vertebrate conserved non-coding sequences associated with developmental regulation.
G. Elgar (2009)
Briefings in Functional Genomics 8, 256-265
   Abstract »    Full Text »    PDF »
Reassessing the concept of a medialization of science: a story from the "book of life".
S. Rodder (2009)
Public Understanding of Science 18, 452-463
   Abstract »    PDF »
Introduction to the Special Issue: Psychological Aspects of Genomics and Child Health.
K. P. Tercyak (2009)
J. Pediatr. Psychol. 34, 589-595
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Pharmacogenomic variability and anaesthesia.
R. Searle and P. M. Hopkins (2009)
Br. J. Anaesth. 103, 14-25
   Abstract »    Full Text »    PDF »
Functional Analysis of Transcription Factors in Arabidopsis.
N. Mitsuda and M. Ohme-Takagi (2009)
Plant Cell Physiol. 50, 1232-1248
   Abstract »    Full Text »    PDF »
Human-Specific Modulation of Transcriptional Activity Provided by Endogenous Retroviral Insertions.
E. Gogvadze, E. Stukacheva, A. Buzdin, and E. Sverdlov (2009)
J. Virol. 83, 6098-6105
   Abstract »    Full Text »    PDF »
Towards a virtual fly brain.
J. D. Armstrong and J. I. van Hemert (2009)
Phil Trans R Soc A 367, 2387-2397
   Abstract »    Full Text »    PDF »
Rapid identification of multidrug-resistant Mycobacterium tuberculosis isolates by rpoB gene scanning using high-resolution melting curve PCR analysis.
A. T. Pietzka, A. Indra, A. Stoger, J. Zeinzinger, M. Konrad, P. Hasenberger, F. Allerberger, and W. Ruppitsch (2009)
J. Antimicrob. Chemother. 63, 1121-1127
   Abstract »    Full Text »    PDF »
Minireview: Evolution of NURSA, the Nuclear Receptor Signaling Atlas.
N. J. McKenna, A. J. Cooney, F. J. DeMayo, M. Downes, C. K. Glass, R. B. Lanz, M. A. Lazar, D. J. Mangelsdorf, D. D. Moore, J. Qin, et al. (2009)
Mol. Endocrinol. 23, 740-746
   Abstract »    Full Text »    PDF »
Finding the fifth base: Genome-wide sequencing of cytosine methylation.
R. Lister and J. R. Ecker (2009)
Genome Res. 19, 959-966
   Abstract »    Full Text »    PDF »
ABySS: A parallel assembler for short read sequence data.
J. T. Simpson, K. Wong, S. D. Jackman, J. E. Schein, S. J.M. Jones, and I. Birol (2009)
Genome Res. 19, 1117-1123
   Abstract »    Full Text »    PDF »
SNP detection for massively parallel whole-genome resequencing.
R. Li, Y. Li, X. Fang, H. Yang, J. Wang, K. Kristiansen, and J. Wang (2009)
Genome Res. 19, 1124-1132
   Abstract »    Full Text »    PDF »
CloudBurst: highly sensitive read mapping with MapReduce.
M. C. Schatz (2009)
Bioinformatics 25, 1363-1369
   Abstract »    Full Text »    PDF »


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