Abstract
Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.
| Original language | English |
|---|---|
| Pages (from-to) | 724-731 |
| Number of pages | 8 |
| Journal | Nature |
| Volume | 434 |
| Issue number | 7034 |
| DOIs | |
| Publication status | Published - Apr 7 2005 |
| Externally published | Yes |
All Science Journal Classification (ASJC) codes
- General
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Generation and annotation of the DNA sequences of human chromosomes 2 and 4. / Hillier, La Deana W.; Graves, Tina A.; Fulton, Robert S.; Fulton, Lucinda A.; Pepin, Kymberlie H.; Minx, Patrick; Wagner-McPherson, Caryn; Layman, Dan; Wylie, Kristine; Sekhon, Mandeep; Becker, Michael C.; Fewell, Ginger A.; Delehaunty, Kimberly D.; Miner, Tracie L.; Nash, William E.; Kremitzki, Colin; Oddy, Lachlan; Du, Hui; Sun, Hui; Bradshaw-Cordum, Holland; Ali, Johar; Carter, Jason; Cordes, Matt; Harris, Anthony; Isak, Amber; Van Brunt, Andrew; Nguyen, Christine; Du, Feiyu; Courtney, Laura; Kalicki, Joelle; Ozersky, Philip; Abbott, Scott; Armstrong, Jon; Belter, Edward A.; Caruso, Lauren; Cedroni, Maria; Cotton, Marc; Davidson, Teresa; Desai, Anu; Elliott, Glendoria; Erb, Thomas; Fronick, Catrina; Gaige, Tony; Haakenson, William; Haglund, Krista; Holmes, Andrea; Harkins, Richard; Kim, Kyung; Kruchowski, Scott S.; Strong, Cynthia Madsen; Grewal, Neenu; Goyea, Ernest; Hou, Shunfang; Levy, Andrew; Martinka, Scott; Mead, Kelly; McLellan, Michael D.; Meyer, Rick; Randall-Maher, Jennifer; Tomlinson, Chad; Dauphin-Kohlberg, Sara; Kozlowicz-Reilly, Amy; Shah, Neha; Swearengen-Shahid, Sharhonda; Snider, Jacqueline; Strong, Joseph T.; Thompson, Johanna; Yoakum, Martin; Leonard, Shawn; Pearman, Charlene; Trani, Lee; Radionenko, Maxim; Waligorski, Jason E.; Wang, Chunyan; Rock, Susan M.; Tin-Wollam, Aye Mon; Maupin, Rachel; Latreille, Phil; Wendl, Michael C.; Yang, Shiaw Pyng; Pohl, Craig; Wallis, John W.; Spieth, John; Bieri, Tamberlyn A.; Berkowicz, Nicolas; Nelson, Joanne O.; Osborne, John; Ding, Li; Meyer, Rekha; Sabo, Aniko; Shotland, Yoram; Sinha, Prashant; Wohldmann, Patricia E.; Cook, Lisa L.; Hickenbotham, Matthew T.; Eldred, James; Williams, Donald; Jones, Thomas A.; She, Xinwei; Ciccarelli, Francesca D.; Izaurralde, Elisa; Taylor, James; Schmutz, Jeremy; Myers, Richard M.; Cox, David R.; Huang, Xiaoqiu; McPherson, John D.; Mardis, Elaine R.; Clifton, Sandra W.; Warren, Wesley C.; Chinwalla, Asif T.; Eddy, Sean R.; Marra, Marco A.; Ovcharenko, Ivan; Furey, Terrence S.; Miller, Webb; Eichler, Evan E.; Bork, Peer; Suyama, Mikita; Torrents, David; Waterston, Robert H.; Wilson, Richard K.
In: Nature, Vol. 434, No. 7034, 07.04.2005, p. 724-731.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Generation and annotation of the DNA sequences of human chromosomes 2 and 4
AU - Hillier, La Deana W.
AU - Graves, Tina A.
AU - Fulton, Robert S.
AU - Fulton, Lucinda A.
AU - Pepin, Kymberlie H.
AU - Minx, Patrick
AU - Wagner-McPherson, Caryn
AU - Layman, Dan
AU - Wylie, Kristine
AU - Sekhon, Mandeep
AU - Becker, Michael C.
AU - Fewell, Ginger A.
AU - Delehaunty, Kimberly D.
AU - Miner, Tracie L.
AU - Nash, William E.
AU - Kremitzki, Colin
AU - Oddy, Lachlan
AU - Du, Hui
AU - Sun, Hui
AU - Bradshaw-Cordum, Holland
AU - Ali, Johar
AU - Carter, Jason
AU - Cordes, Matt
AU - Harris, Anthony
AU - Isak, Amber
AU - Van Brunt, Andrew
AU - Nguyen, Christine
AU - Du, Feiyu
AU - Courtney, Laura
AU - Kalicki, Joelle
AU - Ozersky, Philip
AU - Abbott, Scott
AU - Armstrong, Jon
AU - Belter, Edward A.
AU - Caruso, Lauren
AU - Cedroni, Maria
AU - Cotton, Marc
AU - Davidson, Teresa
AU - Desai, Anu
AU - Elliott, Glendoria
AU - Erb, Thomas
AU - Fronick, Catrina
AU - Gaige, Tony
AU - Haakenson, William
AU - Haglund, Krista
AU - Holmes, Andrea
AU - Harkins, Richard
AU - Kim, Kyung
AU - Kruchowski, Scott S.
AU - Strong, Cynthia Madsen
AU - Grewal, Neenu
AU - Goyea, Ernest
AU - Hou, Shunfang
AU - Levy, Andrew
AU - Martinka, Scott
AU - Mead, Kelly
AU - McLellan, Michael D.
AU - Meyer, Rick
AU - Randall-Maher, Jennifer
AU - Tomlinson, Chad
AU - Dauphin-Kohlberg, Sara
AU - Kozlowicz-Reilly, Amy
AU - Shah, Neha
AU - Swearengen-Shahid, Sharhonda
AU - Snider, Jacqueline
AU - Strong, Joseph T.
AU - Thompson, Johanna
AU - Yoakum, Martin
AU - Leonard, Shawn
AU - Pearman, Charlene
AU - Trani, Lee
AU - Radionenko, Maxim
AU - Waligorski, Jason E.
AU - Wang, Chunyan
AU - Rock, Susan M.
AU - Tin-Wollam, Aye Mon
AU - Maupin, Rachel
AU - Latreille, Phil
AU - Wendl, Michael C.
AU - Yang, Shiaw Pyng
AU - Pohl, Craig
AU - Wallis, John W.
AU - Spieth, John
AU - Bieri, Tamberlyn A.
AU - Berkowicz, Nicolas
AU - Nelson, Joanne O.
AU - Osborne, John
AU - Ding, Li
AU - Meyer, Rekha
AU - Sabo, Aniko
AU - Shotland, Yoram
AU - Sinha, Prashant
AU - Wohldmann, Patricia E.
AU - Cook, Lisa L.
AU - Hickenbotham, Matthew T.
AU - Eldred, James
AU - Williams, Donald
AU - Jones, Thomas A.
AU - She, Xinwei
AU - Ciccarelli, Francesca D.
AU - Izaurralde, Elisa
AU - Taylor, James
AU - Schmutz, Jeremy
AU - Myers, Richard M.
AU - Cox, David R.
AU - Huang, Xiaoqiu
AU - McPherson, John D.
AU - Mardis, Elaine R.
AU - Clifton, Sandra W.
AU - Warren, Wesley C.
AU - Chinwalla, Asif T.
AU - Eddy, Sean R.
AU - Marra, Marco A.
AU - Ovcharenko, Ivan
AU - Furey, Terrence S.
AU - Miller, Webb
AU - Eichler, Evan E.
AU - Bork, Peer
AU - Suyama, Mikita
AU - Torrents, David
AU - Waterston, Robert H.
AU - Wilson, Richard K.
N1 - Funding Information: Acknowledgements The authors would like to thank the staff, past and present, of the Washington University Genome Sequencing Center as well as the following laboratories that contributed sequence segments to the final chromosome 2 and 4 sequence: the Broad Institute of MIT; Stanford DNA Sequencing and Technology Development Center; the Sanger Centre; National Yang-Ming University in Taipei; Genoscope; Baylor College of Medicine; the Joint Genome Institute; University of Washington Multimegabase Sequencing Center; DOE Joint Genome Institute; and Roswell Park Cancer Institute. We thank T. Hubbard, J. Ashurst, J. Gilbert and S. Keenan for Ensembl pipeline assistance. We thank the Broad Institute of MIT, Harvard and Agencourt Bioscience for making a preliminary assembly of dog genome sequence available to us. We thank the Zebrafish Sequencing Group at the Sanger Centre for the Danio rerio preliminary protein set. We thank the International HapMap Consortium and their sponsors for use of their data and J. Mullikin for help with alignment of their data to the human genome. We thank the Chimpanzee Genome Sequencing Consortium for use of the chimpanzee sequence data. The authors would also like to acknowledge the efforts of the HUGO Gene Nomenclature Committee. Finally, the authors acknowledge the National Human Genome Research Institute for funding this work. Copyright: Copyright 2008 Elsevier B.V., All rights reserved.
PY - 2005/4/7
Y1 - 2005/4/7
N2 - Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.
AB - Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.
UR - http://www.scopus.com/inward/record.url?scp=20244378058&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=20244378058&partnerID=8YFLogxK
U2 - 10.1038/nature03466
DO - 10.1038/nature03466
M3 - Article
C2 - 15815621
AN - SCOPUS:20244378058
VL - 434
SP - 724
EP - 731
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7034
ER -