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The sequence of the human genome

Science, 291(5507): 1304--1351, 2001.
Authors: J. Craig Venter and Mark D. Adams and Eugene W. Myers and Peter W. Li and Richard J. Mural and Granger G. Sutton and Hamilton O. Smith and Mark Yandell and Cheryl A. Evans and Robert A. Holt and Jeannine D. Gocayne and Peter Amanatides and Richard M. Ballew and Daniel H. Huson and Jennifer Russo Wortman and Qing Zhang and Chinnappa D. Kodira and Xiangqun H. Zheng and Lin Chen and Marian Skupski and Gangadharan Subramanian and Paul D. Thomas and Jinghui Zhang and George L. Gabor Miklos and Catherine Nelson and Samuel Broder and Andrew G. Clark and Joe Nadeau and Victor A. McKusick and Norton Zinder and Arnold J. Levine and Richard J. Roberts and Mel Simon and Carolyn Slayman and Michael Hunkapiller and Randall Bolanos and Arthur Delcher and Ian Dew and Daniel Fasulo and Michael Flanigan and Liliana Florea and Aaron Halpern and Sridhar Hannenhalli and Saul Kravitz and Samuel Levy and Clark Mobarry and Knut Reinert and Karin Remington and Jane Abu-Threideh and Ellen Beasley and Kendra Biddick and Vivien Bonazzi and Rhonda Brandon and Michele Cargill and Ishwar Chandramouliswaran and Rosane Charlab and Kabir Chaturvedi and Zuoming Deng and Valentina Di Francesco and Patrick Dunn and Karen Eilbeck and Carlos Evangelista and Andrei E. Gabrielian and Weiniu Gan and Wangmao Ge and Fangcheng Gong and Zhiping Gu and Ping Guan and Thomas J. Heiman and Maureen E. Higgins and Rui-Ru Ji and Zhaoxi Ke and Karen A. Ketchum and Zhongwu Lai and Yiding Lei and Zhenya Li and Jiayin Li and Yong Liang and Xiaoying Lin and Fu Lu and Gennady V. Merkulov and Natalia Milshina and Helen M. Moore and Ashwinikumar K Naik and Vaibhav A. Narayan and Beena Neelam and Deborah Nusskern and Douglas B. Rusch and Steven Salzberg and Wei Shao and Bixiong Shue and Jingtao Sun and Zhen Yuan Wang and Aihui Wang and Xin Wang and Jian Wang and Ming-Hui Wei and Ron Wides and Chunlin Xiao and Chunhua Yan and Alison Yao and Jane Ye and Ming Zhan and Weiqing Zhang and Hongyu Zhang and Qi Zhao and Liansheng Zheng and Fei Zhong and Wenyan Zhong and Shiaoping C. Zhu and Shaying Zhao and Dennis Gilbert and Suzanna Baumhueter and Gene Spier and Christine Carter and Anibal Cravchik and Trevor Woodage and Feroze Ali and Huijin An and Aderonke Awe and Danita Baldwin and Holly Baden and Mary Barnstead and Ian Barrow and Karen Beeson and Dana Busam and Amy Carver and Angela Center and Ming Lai Cheng and Liz Curry and Steve Danaher and Lionel Davenport and Raymond Desilets and Susanne Dietz and Kristina Dodson and Lisa Doup and Steven Ferriera and Neha Garg and Andres Gluecksmann and Brit Hart and Jason Haynes and Charles Haynes and Cheryl Heiner and Suzanne Hladun and Damon Hostin and Jarrett Houck and Timothy Howland and Chinyere Ibegwam and Jeffery Johnson and Francis Kalush and Lesley Kline and Shashi Koduru and Amy Love and Felecia Mann and David May and Steven McCawley and Tina McIntosh and Ivy McMullen and Mee Moy and Linda Moy and Brian Murphy and Keith Nelson and Cynthia Pfannkoch and Eric Pratts and Vinita Puri and Hina Qureshi and Matthew Reardon and Robert Rodriguez and Yu-Hui Rogers and Deanna Romblad and Bob Ruhfel and Richard Scott and Cynthia Sitter and Michelle Smallwood and Erin Stewart and Renee Strong and Ellen Suh and Reginald Thomas and Ni Ni Tint and Sukyee Tse and Claire Vech and Gary Wang and Jeremy Wetter and Sherita Williams and Monica Williams and Sandra Windsor and Emily Winn-Deen and Keriellen Wolfe and Jayshree Zaveri and Karena Zaveri and Josep F. Abril and Roderic Guigo and Michael J. Campbell and Kimmen V. Sjolande and Brian Karlak and Anish Kejariwal and Huaiyu Mi and Betty Lazareva and Thomas Hatton and Apurva Narechania and Karen Diemer and Anushya Muruganujan and Nan Guo and Shinji Sato and Vineet Bafna and Sorin Istrail and Ross Lippert and Russell Schwartz and Brian Walenz and Shibu Yooseph and David Allen and Anand Basu and James Baxendale and Louis Blick and Marcelo Caminha and John Carnes-Stine and Parris Caulk and Yen-Hui Chiang and My Coyne and Carl Dahlke and Anne Deslattes Mays and Maria Dombroski and Michael Donnelly and Dale Ely and Shiva Esparham and Carl Fosler and Harold Gire and Stephen Glanowski and Kenneth Glasser and Anna Glodek and Mark Gorokhov and Ken Graham and Barry Gropman and Michael Harris and Jeremy Heil and Scott Henderson and Jeffrey Hoover and Donald Jennings and Catherine Jordan and James Jordan and John Kasha and Leonid Kagan and Cheryl Kraft and Alexander Levitsky and Mark Lewis and Xiangjun Liu and John Lopez and Daniel Ma and William Majoros and Joe McDaniel and Sean Murphy and Matthew Newman and Trung Nguyen and Ngoc Nguyen and Marc Nodell and Sue Pan and Jim Peck and Marshall Peterson and William Rowe and Robert Sanders and John Scott and Michael Simpson and Thomas Smith and Arlan Sprague and Timothy Stockwell and Russell Turner and Eli Venter and Mei Wang and Meiyuan Wen and David Wu and Mitchell Wu and Ashley Xia and Ali Zandieh and Xiaohong Zhu
URL: http://www.sciencemag.org/cgi/content/abstract/291/5507/1304?ijkey=I/Cyc3kWkJJbA
Tags: imported
Abstract: 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.
| URL | BibTeX  
@article{Venter:2001:full,
title = {{The sequence of the human genome}},
author = {J. Craig Venter and Mark D. Adams and Eugene W. Myers and Peter W. Li and Richard J. Mural and Granger G. Sutton and Hamilton O. Smith and Mark Yandell and Cheryl A. Evans and Robert A. Holt and Jeannine D. Gocayne and Peter Amanatides and Richard M. Ballew and Daniel H. Huson and Jennifer Russo Wortman and Qing Zhang and Chinnappa D. Kodira and Xiangqun H. Zheng and Lin Chen and Marian Skupski and Gangadharan Subramanian and Paul D. Thomas and Jinghui Zhang and George L. Gabor Miklos and Catherine Nelson and Samuel Broder and Andrew G. Clark and Joe Nadeau and Victor A. McKusick and Norton Zinder and Arnold J. Levine and Richard J. Roberts and Mel Simon and Carolyn Slayman and Michael Hunkapiller and Randall Bolanos and Arthur Delcher and Ian Dew and Daniel Fasulo and Michael Flanigan and Liliana Florea and Aaron Halpern and Sridhar Hannenhalli and Saul Kravitz and Samuel Levy and Clark Mobarry and Knut Reinert and Karin Remington and Jane Abu-Threideh and Ellen Beasley and Kendra Biddick and Vivien Bonazzi and Rhonda Brandon and Michele Cargill and Ishwar Chandramouliswaran and Rosane Charlab and Kabir Chaturvedi and Zuoming Deng and Valentina Di Francesco and Patrick Dunn and Karen Eilbeck and Carlos Evangelista and Andrei E. Gabrielian and Weiniu Gan and Wangmao Ge and Fangcheng Gong and Zhiping Gu and Ping Guan and Thomas J. Heiman and Maureen E. Higgins and Rui-Ru Ji and Zhaoxi Ke and Karen A. Ketchum and Zhongwu Lai and Yiding Lei and Zhenya Li and Jiayin Li and Yong Liang and Xiaoying Lin and Fu Lu and Gennady V. Merkulov and Natalia Milshina and Helen M. Moore and Ashwinikumar K Naik and Vaibhav A. Narayan and Beena Neelam and Deborah Nusskern and Douglas B. Rusch and Steven Salzberg and Wei Shao and Bixiong Shue and Jingtao Sun and Zhen Yuan Wang and Aihui Wang and Xin Wang and Jian Wang and Ming-Hui Wei and Ron Wides and Chunlin Xiao and Chunhua Yan and Alison Yao and Jane Ye and Ming Zhan and Weiqing Zhang and Hongyu Zhang and Qi Zhao and Liansheng Zheng and Fei Zhong and Wenyan Zhong and Shiaoping C. Zhu and Shaying Zhao and Dennis Gilbert and Suzanna Baumhueter and Gene Spier and Christine Carter and Anibal Cravchik and Trevor Woodage and Feroze Ali and Huijin An and Aderonke Awe and Danita Baldwin and Holly Baden and Mary Barnstead and Ian Barrow and Karen Beeson and Dana Busam and Amy Carver and Angela Center and Ming Lai Cheng and Liz Curry and Steve Danaher and Lionel Davenport and Raymond Desilets and Susanne Dietz and Kristina Dodson and Lisa Doup and Steven Ferriera and Neha Garg and Andres Gluecksmann and Brit Hart and Jason Haynes and Charles Haynes and Cheryl Heiner and Suzanne Hladun and Damon Hostin and Jarrett Houck and Timothy Howland and Chinyere Ibegwam and Jeffery Johnson and Francis Kalush and Lesley Kline and Shashi Koduru and Amy Love and Felecia Mann and David May and Steven McCawley and Tina McIntosh and Ivy McMullen and Mee Moy and Linda Moy and Brian Murphy and Keith Nelson and Cynthia Pfannkoch and Eric Pratts and Vinita Puri and Hina Qureshi and Matthew Reardon and Robert Rodriguez and Yu-Hui Rogers and Deanna Romblad and Bob Ruhfel and Richard Scott and Cynthia Sitter and Michelle Smallwood and Erin Stewart and Renee Strong and Ellen Suh and Reginald Thomas and Ni Ni Tint and Sukyee Tse and Claire Vech and Gary Wang and Jeremy Wetter and Sherita Williams and Monica Williams and Sandra Windsor and Emily Winn-Deen and Keriellen Wolfe and Jayshree Zaveri and Karena Zaveri and Josep F. Abril and Roderic Guigo and Michael J. Campbell and Kimmen V. Sjolande and Brian Karlak and Anish Kejariwal and Huaiyu Mi and Betty Lazareva and Thomas Hatton and Apurva Narechania and Karen Diemer and Anushya Muruganujan and Nan Guo and Shinji Sato and Vineet Bafna and Sorin Istrail and Ross Lippert and Russell Schwartz and Brian Walenz and Shibu Yooseph and David Allen and Anand Basu and James Baxendale and Louis Blick and Marcelo Caminha and John Carnes-Stine and Parris Caulk and Yen-Hui Chiang and My Coyne and Carl Dahlke and Anne Deslattes Mays and Maria Dombroski and Michael Donnelly and Dale Ely and Shiva Esparham and Carl Fosler and Harold Gire and Stephen Glanowski and Kenneth Glasser and Anna Glodek and Mark Gorokhov and Ken Graham and Barry Gropman and Michael Harris and Jeremy Heil and Scott Henderson and Jeffrey Hoover and Donald Jennings and Catherine Jordan and James Jordan and John Kasha and Leonid Kagan and Cheryl Kraft and Alexander Levitsky and Mark Lewis and Xiangjun Liu and John Lopez and Daniel Ma and William Majoros and Joe McDaniel and Sean Murphy and Matthew Newman and Trung Nguyen and Ngoc Nguyen and Marc Nodell and Sue Pan and Jim Peck and Marshall Peterson and William Rowe and Robert Sanders and John Scott and Michael Simpson and Thomas Smith and Arlan Sprague and Timothy Stockwell and Russell Turner and Eli Venter and Mei Wang and Meiyuan Wen and David Wu and Mitchell Wu and Ashley Xia and Ali Zandieh and Xiaohong Zhu},
journal = {Science},
number = {5507},
pages = {1304--1351},
url = {http://www.sciencemag.org/cgi/content/abstract/291/5507/1304?ijkey=I/Cyc3kWkJJbA},
volume = {291},
year = {2001},
abstract = {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.},
owner = {tkirsten}, __markedentry = {0},
keywords = {imported }
}