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1. A haplotype map of the human genome

Author

Mark Leppert, Aravinda Chakravarti, Charmaine D.M. Royal, Sarah S. Murray, Renzong Qiu, Panos Deloukas, Renwu Wang, David A. Hinds, Barbara E. Stranger, Xiaoli Tang, Huanming Yang, John W. Belmont, Nigel P. Carter, Huy Nguyen, William Mak, Kazuto Kato, Shiran Pasternak, Chaohua Li, Jeffrey C. Barrett, Lon R. Cardon, Vincent Ferretti, Atsushi Nagashima, Peter E. Chen, Stephen F. Schaffner, Hongbo Fu, Zhu Chen, Siqi Liu, John Burton, Paul Hardenbol, Gudmundur A. Thorisson, Yusuke Nakamura, Mark Griffiths, Imtiaz Yakub, Eiko Suda, Gonçalo R. Abecasis, Carl S. Kashuk, Qingrun Zhang, Yoshimitsu Fukushima, Karen Kennedy, Sarah E. Hunt, Yi Wang, Norio Niikawa, Ichiro Matsuda, Lynn F. Zacharia, Lalitha Krishnan, Zhen Wang, Stéphanie Roumy, C M Clee, David J. Cutler, Albert V. Smith, Lincoln Stein, Simon Myers, Jane Peterson, Jun Zhou, Yozo Ohnishi, Weihua Guan, Matthew Stephens, Xiaoyan Xiong, Julian Maller, Houcan Zhang, Pui-Yan Kwok, Mark S. Guyer, Liuda Ziaugra, Jonathan Witonsky, Matthew C. Jones, Stacey Gabriel, You-Qiang Song, Daochang An, Haifeng Wang, Gilean McVean, Lawrence M. Sung, Zhijian Yao, Yan Shen, Yangfan Liu, George M. Weinstock, Ludmila Pawlikowska, Erica Sodergren, Mark T. Ross, Andrew Boudreau, Toshihiro Tanaka, Thomas D. Willis, Weitao Hu, Kelly A. Frazer, Li Jin, Robert W. Plumb, Paul I.W. de Bakker, Hongbin Zhao, Wei Lin, Sarah Sims, Richard A. Gibbs, Maura Faggart, Michael Feolo, Dennis G. Ballinger, Xun Chu, Lucinda Fulton, Marcos Delgado, Ellen Winchester, Wei Huang, Fuli Yu, Christianne R. Bird, Shaun Purcell, Jessica Roy, Dongmei Cai, Launa M. Galver, Bartha Maria Knoppers, Emmanouil T. Dermitzakis, Gao Yang, Takashi Morizono, Rachel Barry, Kirsten McLay, Daryl J. Thomas, Steve McCarroll, Jonathan Marchini, Daniel J. Richter, Andy Peiffer, Patricia Taillon-Miller, Richard K. Wilson, Stephen Kwok-Wing Tsui, Jian-Bing Fan, Lisa D. Brooks, Laura L. Stuve, Paul L'Archevêque, David M. Evans, Clémentine Sallée, Peter Donnelly, Hong Xue, Hui Zhao, Charles N. Rotimi, Jean E. McEwen, J. Tze Fei Wong, Hao Pan, Alastair Kent, Brendan Blumenstiel, Qing Li, Weiwei Sun, L. Kang, Colin Freeman, John Stewart, Chibuzor Nkwodimmah, Morris W. Foster, Don Powell, Leonardo Bottolo, Raymond D. Miller, Stephen T. Sherry, Francis S. Collins, Donna M. Muzny, Jun Yu, Ike Ajayi, Hua Han, Pardis C. Sabeti, Hongguang Wang, Takahisa Kawaguchi, Tatsuhiko Tsunoda, Guy Bellemare, Zhaohui S. Qin, H. B. Hu, Jane Rogers, Thomas J. Hudson, Mark J. Daly, Andrew P. Morris, Supriya Gupta, Ming Xiao, Patrick Varilly, Nick Patterson, Akihiro Sekine, Chris C. A. Spencer, Jonathan Morrison, Missy Dixon, Paul K.H. Tam, Jian Wang, Matthew Defelice, Susana Eyheramendy, Michael Shi, Yungang He, Ellen Wright Clayton, Richa Saxena, Heather M. Munro, Arthur L. Holden, Yayun Shen, Christine P. Bird, Bruce W. Birren, Itsik Pe'er, David R. Bentley, Lynne V. Nazareth, Pamela Whittaker, Pak C. Sham, Amy L. Camargo, David A. Wheeler, Koji Saeki, Martin Godbout, David Altshuler, Liang Xu, Ying Wang, David Willey, Alexandre Montpetit, Shin Lin, Michael S. Phillips, Changqing Zeng, Clement Adebamowo, John C. Wallenburg, Mark S. Chee, Ben Fry, Erich Stahl, Melissa Parkin, Rhian Gwilliam, Andrei Verner, Patrick J. Nailer, Lap-Chee Tsui, Bo Zhang, Fanny Chagnon, David R. Cox, Jack Spiegel, Jamie Moore, Vivian Ota Wang, Patricia A. Marshall, Takuya Kitamoto, Bruce S. Weir, Darryl Macer, Geraldine M. Clarke, Robert C. Onofrio, Mary M.Y. Waye, Wei Wang, Suzanne M. Leal, James C. Mullikin, Toyin Aniagwu, Daniel C. Koboldt, Mary Goyette, Martin Leboeuf, Isaac F. Adewole, Ruth Jamieson, Arnold Oliphant, Jessica Watkin, and Jean François Olivier

Subjects
Linkage disequilibrium, Biology, DNA, Mitochondrial, Polymorphism, Single Nucleotide, Article, Linkage Disequilibrium, Structural variation, Gene Frequency, Humans, Selection, Genetic, International HapMap Project, Genetic association, Haplotypes - genetics, Recombination, Genetic, Genetics, Chromosomes, Human, Y, Multidisciplinary, Genome, Human, DNA, Mitochondrial - genetics, Haplotype, Tag SNP, Polymorphism, Single Nucleotide - genetics, Haplotypes, Human genome, Haplotype estimation, Chromosomes, Human, Y - genetics
Abstract

Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution. © 2005 Nature Publishing Group., link_to_OA_fulltext

Published
2005

2. The DNA sequence of the human X chromosome

Author

Gernot Glöckner, Karen Thomas, Christine Lloyd, Huda Y. Zoghbi, Adrienne Hunt, Fiona Francis, Annemarie Poustka, George M. Weinstock, Xuehong Wei, Alan Tracey, Gabriele Nordsiek, Ines Müller, Graham Clarke, Oliver Beasley, John Sulston, Alfred Beck, Christian J. Buhay, Thomas Meitinger, Manjula Maheshwari, Yvonne Ramsey, Kirsten McLay, Shannon Dugan-Rocha, James G. R. Gilbert, Louisa Faulkner, Sidney Morris, Margaret Morgan, Huntington F. Willard, Leni S. Jacob, Hermela Loulseged, K M Porter, T. Daniel Andrews, Cordelia Langford, Paul Wray, Guan Chen, Juliane Ramser, Nigel P. Carter, Georgina Warry, Ruby Banerjee, Graeme Bethel, LaDeana W. Hillier, Anne Hodgson, Stephen M. J. Searle, K F Barlow, David R. Bentley, Paul E. Tabor, Kathryn L. Evans, Russell J. Grocock, Rebecca Woodmansey, Alex V Pearce, Christie Kovar-Smith, Angela Williamson, Dean Chavez, Roy Storey, Kevin L. Howe, Zhijian J. Chen, Lesette Perez, Richard A. Gibbs, Michele D'Urso, Karen N Bates, Jackie Bye, Shirin S. Joseph, Bernd Hinzmann, Paul Heath, Susan H. Kelly, Jennifer Hume, Paula E. Burch, David Buck, Mark T. Ross, David A. Wheeler, Matthew C. Jones, A K Babbage, Erica Sodergren, Sophie Palmer, Jie Ma, Elizabeth C. Sotheran, Margaret A. Leversha, Cerissa Hamilton, Hans Lehrach, Swaroop Aradhya, Michael L. Metzker, S. M. Clegg, Elizabeth J. Huckle, Audrey Fraser, Sarah Bray-Allen, C. D. Skuce, Petra Galgoczy, Richard K. Wilson, Patrick Minx, Richard E Connor, Tamsin Eades, Alfons Meindl, Michelle Smith, John M. Davis, André Rosenthal, Stuart McLaren, Geoffery Okwuonu, M. Vaudin, Laura Carrel, Ryan J. Lozado, Harminder Sehra, Richard Pandian, Sue Y Clark, Anna Kosiura, Wen Liu, Simon G. Gregory, A Tromans, Alexandra Emery-Cohen, Charles Shaw-Smith, Donna Villasana, Joseph Chako, Katja Heitmann, Robert G. David, Jennifer L. Ashurst, Craig Chinault, S Lawlor, Paul Havlak, Jane E. Loveland, Lucy Matthews, Jianling Zhou, S. Whitehead, Paul Hunt, E Sheridan, Richard Reinhardt, Tim Hubbard, Mary G. Schueler, Patrick Meidl, Helen Beasley, David Beare, Donna M. Muzny, Kerry A Ridler, Joanne C Chapman, Jennifer McDowall, Andrew Dunham, Anne Bridgeman, Gabrielle Williams, Amanda McMurray, Stefan Taudien, Matthew E. Hurles, Helen Williamson, Preethi H. Gunaratne, Alfredo Ciccodicola, R Ainscough, Alison J. Coffey, Charlotte G. Cole, Stephan Beck, Frances L Lovell, Alan Coulson, Qiaoyan Wang, Sally Jones, Charles A. Steward, Michael Hoffs, Kim C. Worley, Sarah Pelan, David Bonnin, David Schlessinger, Mathew N Whiteley, Graham Scott, Christopher N O'Dell, Tineace Taylor, Susan Rhodes, Anthony P. West, E. Hart, Ian P. Barrett, Andrea Thorpe, D. Pearson, Huyen Dinh, Susan M. Gribble, Andrew J Knights, Laurens G. Wilming, N Corby, Steven E. Scherer, Pawandeep Dhami, Gerald Nyakatura, J Lovell, M. Ali Ansari-Lari, Kerstin P. Clerc-Blankenburg, David Swarbreck, Sara Zorilla, Yanghong Gu, Karin Blechschmidt, Matthew Dunn, Andrew Brown, Kirsten M. Timms, Darren Grafham, Yan Ding, Elspeth A. Bruford, Leanne Williams, Melanie M. Wall, Hua Shen, Dina Patel, Joanne K Kershaw, Rachel Gill, Yuan Chen, Joy Davies, D C Burford, John Burton, Vicky Cobley, R I S Ashwell, Nicola Brady, Ellson Y. Chen, Ngoc Nguyen, Gaiping Wen, Gavin K. Laird, Julia E. Parrish, Carol Scott, C Griffiths, Ratna Shownkeen, Ralf Sudbrak, Denise R. DeShazo, Shiran Pasternak, Ireena Dutta, Brian Teague, Rachael Lyne, David Parker, Jane Rogers, Steve Dodsworth, Mary J. Brown, Gary E Barker, Steve Trevanion, Joanne Burgess, Jane E. Wilkinson, James T. Warren, Jen S. Conquer, R Mark Swann, Oliver Delgado, Heather R. Draper, Shailesh L Mistry, Chris Clee, Richard Durbin, Karen Clifford, John Frankland, Sarah E. Hunt, David Steffen, Christine Burrows, Daniel Verduzco, C Carder, Robert H. Waterston, Stephen Richards, Andrea Ballabio, Catherine M. Rice, David Willey, Helen Errington, Andrew Cree, K. James Durbin, Lora Lewis, D. M. Lloyd, Helen E. Steingruber, Adam Whittaker, K D Ambrose, Rhian Gwilliam, Adam Frankish, Robert S. Fulton, Judith Hernandez, Claire L Bagguley, Pieter J. de Jong, Jennifer Yen, Matthew Ellwood, Christine P. Bird, Rui Chen, Sarah Milne, Clay Davis, Alicia Hawes, Jing Lu, Sven Klages, David L. Nelson, Wayne Burrill, Jingkun Zhang, Judith Isherwood, Kathrin Reichwald, Lenee Waldron, Rebecca Deadman, Steffen Hennig, Ziad Khan, Sarah Ho, Matthias Platzer, Gareth R. Howell, Stephen Keenan, Petra Kioschis, Phillip J Howden, George Miner, David W. Johnson, and James C. Mullikin

Subjects
Male, Genetic Linkage, Genetics, Medical, Centromere, HUMAN GENOME SEQUENCE, Biology, Y chromosome, Polymorphism, Single Nucleotide, Article, Evolution, Molecular, Contig Mapping, Chromosome 16, Antigens, Neoplasm, Dosage Compensation, Genetic, Sequence Homology, Nucleic Acid, Chromosome 19, Testis, Animals, Humans, Crossing Over, Genetic, X chromosome, Repetitive Sequences, Nucleic Acid, Genetics, Chromosomes, Human, X, Chromosomes, Human, Y, Multidisciplinary, INACTIVATION CENTER, LINKED MENTAL-RETARDATION, Genomics, Sequence Analysis, DNA, REPEAT HYPOTHESIS, MAMMALIAN Y-CHROMOSOME, Chromosome 4, Chromosome 3, RNA, Female, Chromosome 21, Chromosome 22
Abstract

The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

Published
2005

3. DNA sequence and analysis of human chromosome 9

Author

L K Colman, S S White, R Heathcott, K D Ambrose, C Griffiths, C L Bagguley, Christine Lloyd, Jim Davies, James G. R. Gilbert, Richard Durbin, Carol Scott, Rebekah Hall, Graeme Bethel, Adrienne Hunt, C Carder, A Tromans, G Tamlyn-Hall, Jane Rogers, J Garnett, L M Faulkner, J C Chapman, Benjamin Phillimore, M Grant, A Wild, Christopher J. Gillson, S Hammond, A K Babbage, Sophie Palmer, C. D. Skuce, V. Cobley, Margaret A. Leversha, Robert W. Plumb, J. M. Wallis, Lucy Matthews, Sarah E. Smith, Mark Griffiths, Karen Oliver, J Tester, Christopher M. Johnson, M Earthrowl, K L Novik, Graeme T Clark, Kirsten McLay, Michelle Smith, R M Younger, T Nickerson, K F Barlow, A. King, S. M. Clegg, Mark T. Ross, K M Culley, R. E. Collier, K Bates, Nigel P. Carter, Sarah E. Hunt, Matthew Humphries, Kevin L. Howe, R Ainscough, Matthew Jones, J P Almeida, Laurens G. Wilming, R Patel, C M Clee, A M Kimberley, David Niblett, Gareth Maslen, Jane E. Loveland, Pawandeep Dhami, J C Wyatt, Philip Howden, Harminder Sehra, N Corby, Stephan Beck, Andrew J. Mungall, Cordelia Langford, Mohammed J. R. Ghori, O. T. McCann, Sarah Milne, Ian Dunham, C A Edwards, J Y Brown, Matthew Dunn, A J Theaker, Darren Grafham, Alan Tracey, S. Searle, Anne Parker, John Burton, Amanda McMurray, H Whittaker, R I S Ashwell, M Mashreghi-Mohammadi, P Garner, A J Brown, O. Beasley, Michele Clamp, A Thorpe, Daniel Leongamornlert, Alan Coulson, Y. Ramsey, Paul Wray, N Sycamore, Helen Beasley, M. J F Moore, Dave Willey, K M Porter, S Y Clark, A I Peck, Tim Hubbard, D. M. Lloyd, David R. Bentley, A Joy, Joanna Harley, L Spraggon, J Lovell, Anthony P. West, E. Hart, Adam Frankish, M. Kay, Catherine M. Rice, Matthew D. Francis, S A Ranby, Duncan W. Thomas, Elizabeth J. Huckle, T. E. Wilmer, Sean Humphray, L Young, W Burrill, David Beare, B Tubby, S Lawlor, E Sheridan, Susan M. Gribble, J Frankland, A E Ellington, Charles A. Steward, K S Halls, Roger Horton, Melanie M. Wall, James C. Mullikin, D C Burford, S. Holmes, L M Gilby, T D Andrews, Christine P. Bird, Gareth R. Howell, Stephen Keenan, Joanna Collins, S. Squares, Ruby Banerjee, Jennifer L. Ashurst, Sarah Sims, S Bray-Allen, Lisa French, G. J. Coville, Paul Heath, A. V. Pearce, S. Whitehead, Sancha Martin, J Bailey, J Brook, Darren Barker, Rebecca Glithero, Jonathan Wood, E K Overton-Larty, K A Evans, S. Blakey, John Sulston, Gavin K. Laird, Sam Phillips, and S J McLaren

Subjects
Male, Genetics, Medical, Biology, Article, Euchromatin, Evolution, Molecular, Chromosome 15, Chromosome 16, Genes, Duplicate, Gene Duplication, Heterochromatin, Neoplasms, Chromosome 19, Humans, Chromosome 13, Genetics, Base Composition, Multidisciplinary, Genetic Variation, Neurodegenerative Diseases, Genomics, Sequence Analysis, DNA, Sex Determination Processes, Physical Chromosome Mapping, Chromosome 17 (human), Genes, Chromosome 3, Female, Chromosomes, Human, Pair 9, Chromosome 21, Chromosome 22, Pseudogenes
Abstract

Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6–8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.

Published
2004

4. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes

Author

Lina Chen, Mingming Jia, Mark Maddison, Claire Hardy, Henry Knott, Jenny Andrews, Bill Wondergem, Karl Dykema, Patrick S. Tarpey, Syd Barthorpe, Meng-Lay Lin, Michael R. Stratton, Sok Kean Khoo, Lucy Stebbings, Sarah Edkins, Laura Mudie, Gemma Buck, Adam Butler, Calli Latimer, Helen Davies, Tatiana Mironenko, David Petillo, David T. Jones, John Anema, Jon W. Teague, Bin Tean Teh, Dave Beare, Simon A. Forbes, Catherine Leroy, Kirsten McLay, Simon Maguire, Gurpreet Tang, Kelly Turrell, P. Andrew Futreal, Graham R. Bignell, Aarjunan Rajasingham, David J. McBride, King Wai Lau, Christopher Greenman, Erin Pleasance, Chai Yin Kok, Andrew Menzies, Richard J. Kahnoski, Gillian L. Dalgliesh, Raffaella Smith, Peter J. Campbell, Rebecca Shepherd, Philip J. Stephens, Lee Mulderrig, Kyle A. Furge, and Sarah O’Meara

Subjects
Histone H3 Lysine 4, Biology, medicine.disease_cause, Histones, 03 medical and health sciences, Histone H3, 0302 clinical medicine, SETD2, Genes, Neurofibromatosis 2, medicine, Humans, Cancer epigenetics, Carcinoma, Renal Cell, 030304 developmental biology, Genetics, Histone Demethylases, 0303 health sciences, Mutation, Multidisciplinary, Cancer, Nuclear Proteins, Oxidoreductases, N-Demethylating, Histone-Lysine N-Methyltransferase, Sequence Analysis, DNA, medicine.disease, Cell Hypoxia, Chromatin, Kidney Neoplasms, 3. Good health, Gene Expression Regulation, Neoplastic, Histone, 030220 oncology & carcinogenesis, Histone methyltransferase, biology.protein
Abstract

Clear cell renal cell carcinoma (ccRCC) is the most common form of adult kidney cancer, characterized by the presence of inactivating mutations in the VHL gene in most cases, and by infrequent somatic mutations in known cancer genes. To determine further the genetics of ccRCC, we have sequenced 101 cases through 3,544 protein-coding genes. Here we report the identification of inactivating mutations in two genes encoding enzymes involved in histone modification-SETD2, a histone H3 lysine 36 methyltransferase, and JARID1C (also known as KDM5C), a histone H3 lysine 4 demethylase-as well as mutations in the histone H3 lysine 27 demethylase, UTX (KMD6A), that we recently reported. The results highlight the role of mutations in components of the chromatin modification machinery in human cancer. Furthermore, NF2 mutations were found in non-VHL mutated ccRCC, and several other probable cancer genes were identified. These results indicate that substantial genetic heterogeneity exists in a cancer type dominated by mutations in a single gene, and that systematic screens will be key to fully determining the somatic genetic architecture of cancer.

Published
2009

5. Initial sequencing and comparative analysis of the mouse genome

Author

Laura Elnitski, David B. Jaffe, Jia Li, Marina Alexandersson, Michael J. Morgan, Shiaw Pyng Yang, Robert Baertsch, Claire M. Wade, John Tromp, Michael C. Zody, Terrence S. Furey, Emma Overton-Larty, Stephen D. Brown, Scott Schwartz, Diane M. Dunn, J. P. Leger, Kris A. Wetterstrand, David Torrents, Ratna Shownkeen, Brian Schultz, Kim C. Worley, Richard D. Emes, John Mayer, Tom Landers, Beverley Meredith, Carol Scott, R. J. Weber, Sean R. Eddy, David Kulp, Jun Kawai, J Bailey, Fan Hsu, Diana L. Kolbe, Kirsten McLay, Marc Botcherby, Richard Mott, Tracie L. Miner, Jill P. Mesirov, Cristyn Kells, Michael A. Quail, Melanie M. Wall, Alistair G. Rust, Josep F. Abril, Ian F Korf, Peter An, Roderic Guigó, Abel Ureta-Vidal, Evan Mauceli, L. Steven Johnson, Arian F.A. Smit, Arkadiusz Kasprzyk, Michael C. Wendl, Deanna M. Church, Francis S. Collins, Wayne N. Frankel, Pallavi Eswara, Bin Ma, Robert H. Waterston, Stylianos E. Antonarakis, Edward M. Rubin, John Douglas Mcpherson, Andrew Sheridan, Megan McCarthy, Ming Li, Colin N. Dewey, Justin Deri, Rosie Levine, Matthew Jones, Sheila Dodge, Richard R. Copley, Leo Goodstadt, Shan Yang, Donna Maglott, Jamey Wierzbowski, Nick Goldman, Evgeny M. Zdobnov, Simon G. Gregory, C M Clee, Steven Leonard, Elaine R. Mardis, Simon C. Potter, Sarah Sims, Richard A. Gibbs, Mark S. Guyer, Francesca Chiaromonte, Susan Lucas, Mark Diekhans, Steve Searle, Rachel Ainscough, Jane Peterson, Emmanouil T. Dermitzakis, Robert Nicol, Lucy Matthews, Guy Slater, Adam Felsenfeld, Karen Foley, Lucinda Fulton, Tim Hubbard, Richard K. Wilson, Deana W. LaHillier, W. Richard McCombie, Johanna Thompson, Robert David, John Attwood, Anthony P. West, Jane Rogers, Evan Keibler, Lisa Cook, Raju Kucherlapati, Steven Seaman, William E. Nash, Ian J. Jackson, Jonathan Singer, Axin Hua, Tina Graves, Ted Sharpe, Dudley Wyman, Bruce W. Birren, Stuart McLaren, David Willey, A Joy, Douglas Smith, Alexandre Reymond, Paul Flicek, Simon Cawley, Richa Agarwala, Diane Gage, Evanne Trevaskis, Ginger A. Fewell, Michael R. Brent, Tracy C. Ponce, W. James Kent, Timothy Holzer, Eduardo Eyras, Michael J. O’Connor, Webb Miller, Donna M. Muzny, Andrew von Niederhausern, Inna Dubchak, Eitan E. Winter, Catherine Ucla, Arne Stabenau, Michael N. Nhan, Piero Carninci, Michele Clamp, Pavel A. Pevzner, James Meldrim, Tim Cutts, R. D. Campbell, Joy Davies, Wratko Hlavina, Elinor K. Karlsson, David Haussler, John Burton, Peer Bork, Nicole Stange-Thomann, Mikita Suyama, Mark J. Daly, Ewan Birney, Edward J. Kulbokas, Craig Pohl, James C. Mullikin, Chad Nusbaum, Genís Parra, Jade P. Vinson, Yoshihide Hayashizaki, Sante Gnerre, Eric Berry, Daniel G. Brown, Asif T. Chinwalla, Emmanuel Mongin, Robert B. Weiss, Raymond Wheeler, Andrew Kirby, Yasushi Okazaki, Lior Pachter, Ross C. Hardison, Brian Spencer, Carol J. Bult, Joanne O. Nelson, Pankaj K. Agarwal, Darren Grafham, Gustavo Glusman, Thomas A. Jones, Glenn Tesler, Simon Whelan, James Cuff, Robert S. Fulton, K F Barlow, Jörg Schultz, Matthias S. Schwartz, Alex Poliakov, Jonathan Butler, Bruce A. Roe, Angela S. Hinrichs, Alan Coulson, Kate Montgomery, Eric D. Green, Stephan Beck, Val Curwen, Krishna M. Roskin, Robert W. Plumb, Chris P. Ponting, Ralph Santos, Victor Sapojnikov, Nicolas Bray, Kymberlie H. Pepin, Charles W. Sugnet, Olivier Couronne, Ivica Letunic, Sophie Williams, Kimberly D. Delehaunty, Kerstin Lindblad-Toh, Zemin Ning, Karen Oliver, Toby Bloom, Michael Kamal, Nicholas J. Dickens, Eric S. Lander, Christine Lloyd, Donna Karolchik, Adrienne Hunt, Antonarakis, Stylianos, Couronne, Olivier, Dermitzakis, Emmanouil, and Zdobnov, Evgeny

Subjects
RNA, Untranslated, Proteome, Untranslated/genetics, Genome, Transgenic, Repetitive Sequences, Mice, Models, Neoplasms, Conserved Sequence, ddc:616, Genetics, Mice, Knockout, Base Composition, Multidisciplinary, Sex Chromosomes, Pseudogenes/genetics, Genomics, Multigene Family/genetics, Physical Chromosome Mapping, Neoplasms/genetics, CpG Islands/genetics, Proteome/genetics, Genetic Variation/genetics, Multigene Family, Mice/classification/ genetics, Models, Animal, Conserved Sequence/genetics, Sequence Analysis, Pseudogenes, Human, Genome evolution, Evolution, Sequence analysis, Knockout, Quantitative Trait Loci, Mice, Transgenic, Sex Chromosomes/genetics, Computational biology, Biology, Synteny, Chromosomes, Evolution, Molecular, Nucleic Acid/genetics, Genetic, Species Specificity, Mammalian/ genetics, Animals, Humans, Genes/genetics, Selection, Genetic, Selection, Repetitive Sequences, Nucleic Acid, Comparative genomics, Animal, Genome, Human, Molecular, Genetic Variation, DNA, Sequence Analysis, DNA, Chromosomes, Mammalian, Gene Expression Regulation, Genes, Mutagenesis, RNA, Human genome, CpG Islands, Quantitative Trait Loci/genetics, Reference genome
Abstract

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

Published
2002

6. The DNA sequence and comparative analysis of human chromosome 20

Author

G Clarke, L M Faulkner, Jane E. Loveland, J Walsh, Kirsten McLay, G Laird, A K Babbage, J C Chapman, Sophie Palmer, C Hynds, M Earthrowl, T D Andrews, J Battles, Theologia Sarafidou, S. M. Clegg, Christine P. Bird, T P Ho, Sarah Pelan, A M Kimberley, Anthony P. West, E. Hart, Russell J. Grocock, Carol Scott, Stuart McLaren, J Lovell, M Kokkinaki, J K Kershaw, Sarah Milne, Christine Lloyd, D. M. Lloyd, R I S Ashwell, L Standring, Amanda McMurray, John Burton, A Rogosin, Yuan Chen, D Camire, Gavin K. Laird, Nigel P. Carter, David Willey, Nicholas K. Moschonas, Stephan Beck, Ruth C. Lovering, Mark T. Ross, Adam Frankish, S Lawlor, Laurens G. Wilming, I Dutta, David Bentley, Joanna Harley, R Ainscough, Matthew Jones, Susan M. Gribble, C. D. Skuce, A Thorpe, Pawandeep Dhami, L Young, Melanie M. Wall, Erik Gustafson, David Swarbreck, Douglas Smith, J Frankland, S Y Clark, C M Clee, Lucy Matthews, S Bray-Allen, A Taylor, W Burrill, Lynn Doucette-Stamm, S. Searle, Alan Tracey, J Tester, Panos Deloukas, Daniel Leongamornlert, T Nickerson, David W. Johnson, Philip Howden, Paul Wray, M. Kay, Catherine M. Rice, A Kana, H M Lee, Keith Weinstock, Kim Fechtel, Sarah E. Hunt, A I Peck, S. Whitehead, H Wang, N Sycamore, Patrick Cahill, J Bailey, Alan Coulson, E K Overton-Larty, J Y Brown, Jennifer L. Ashurst, A. V. Pearce, M Mashreghi-Mohammadi, C L Bagguley, P Garner, A J Brown, Benjamin Phillimore, W Torcasso, S Hammond, M Nguyen, J Horne, K Bates, J P Almeida, N Corby, Matthew Dunn, Darren Grafham, Ratna Shownkeen, D C Burford, A Tromans, Jane Rogers, J Garnett, Harminder Sehra, Kerstin Howe, K D Ambrose, James G. R. Gilbert, Helen Beasley, Reiner Siebert, Charles A. Steward, Chris Johnson, K M Porter, Ruby Banerjee, Marc Rubenfield, Sarah Sims, Lisa French, Paul Heath, Elizabeth J. Huckle, B Hopkins, C Griffiths, Richard Durbin, J Tsolas, Michelle Smith, and Tim Hubbard

Subjects
Genetics, Multidisciplinary, Base Sequence, Proteome, Sequence analysis, Pseudogene, Physical Chromosome Mapping, Chromosomes, Human, Pair 20, Genetic Diseases, Inborn, Computational Biology, Genetic Variation, Locus (genetics), DNA, Sequence Analysis, DNA, Biology, Contig Mapping, Mice, Gene duplication, Animals, Humans, Human genome, Chromosome 20, Segmental duplication
Abstract

The finished sequence of human chromosome 20 comprises 59,187,298 base pairs (bp) and represents 99.4% of the euchromatic DNA. A single contig of 26 megabases (Mb) spans the entire short arm, and five contigs separated by gaps totalling 320 kb span the long arm of this metacentric chromosome. An additional 234,339 bp of sequence has been determined within the pericentromeric region of the long arm. We annotated 727 genes and 168 pseudogenes in the sequence. About 64% of these genes have a 5' and a 3' untranslated region and a complete open reading frame. Comparative analysis of the sequence of chromosome 20 to whole-genome shotgun-sequence data of two other vertebrates, the mouse Mus musculus and the puffer fish Tetraodon nigroviridis, provides an independent measure of the efficiency of gene annotation, and indicates that this analysis may account for more than 95% of all coding exons and almost all genes.

Published
2002

7. Erratum: Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome

Author

Alan Tracey, Lucy Barr, Karen Holt, Stephen J. Trevanion, Bob Plumb, Daniel Leongamornlert, Paul Wray, Carol Churcher, J. C. Davis, Ruth Gilderthorp, Christine Lloyd, Adrienne Hunt, Michelle Smith, Britt Kilian, Martina Konantz, Jeff Almeida-King, Richard M. Clark, Nick Barker, Kirsty Ambridge, Susan J. Clark, Karen Oliver, Glen Threadgold, Yong Gu, Jane E. Loveland, David Lloyd, Guy Griffiths, Ronald H.A. Plasterk, Karen McLaren, Sarah Pelan, Sarah Nichol, Kenric Leung, Rebecca Woodmansey, Sharmin Begum, Cigdem Eser, Sophie Palmer, Jacqueline Brown, Ian M Sealy, James Torrance, J Lovell, John E. Collins, Sara Widaa, A M Kimberley, A Tromans, Richard Pandian, Judith Konantz, Maria Geisler, Carlos Torroja, N Sycamore, Sancha Martin, Darren Barker, Amanda Rapp, Monte Westerfield, Silke Rudolph-Geiger, Zemin Ning, José Afonso Guerra-Assunção, Clare Riddle, Rebecca Glithero, Daniel P. Kelly, Nicholas Matthews, Pieter J. de Jong, Nigel P. Carter, Camille Berthelot, Fengtang Yang, A K Babbage, Graham Clark, Andrea Berger, Robert Andrews, C Griffiths, Jennifer Harrow, Gerd Jörg Rauch, Steve Searle, J. M. Wallis, Christa Lanz, Ruby Banerjee, William Chow, Jan Hinnerk Vogel, Matthieu Muffato, David Elliott, Mathias Teucke, Derek L. Stemple, Debbie E. Wright, Deepa Manthravadi, Gavin K. Laird, Sarah Sims, M Mashreghi-Mohammadi, David S. Saunders, Lena Karotki, P Garner, Paul Heath, Jane Rogers, Ines Gehring, J Garnett, Charles Lee, Philip Howden, John H. Postlethwait, Robert Geisler, Sarah Donaldson, Elizabeth Langley, Claire Raisen, Katherine Auger, Javier Herrero, Beiyuan Fu, Carol Scott, Zübeyde Ersan-Ürün, Mario Caccamo, Sean Humphray, Gary L A Barker, S. Whitehead, Darren Ware, Baoli Zhu, Jianxiang Chi, Jonathan Wood, Nigel Fosker, Sarah McGuire, Stephan C. Schuster, Chris Clee, Martina Oberländer, Daria Gordon, Clare Murnane, Romke Koch, Emma Gray, Beverley J. Mortimore, Harminder Sehra, Joanna Collins, Hugues Roest Crollius, Kirsten McLay, Kerstin Howe, Lauren Dyer, Christopher Stevens, Andrew D. Ellington, Kazutoyo Osoegawa, Stuart McLaren, Christopher N. Johnson, Giselle Kerry, Helen Beasley, Georgios Panagiotidis, Christiane Nüsslein Volhard, Tina Eyre, Horst Geiger, Jennifer Yen, Matthew Ellwood, Christine P. Bird, N Corby, Matthew Dunn, Darren Grafham, Günter Raddatz, Matthew Humphries, Anette Kirn, Yi Zhou, James D. Cooper, John Burton, Simon D. M. White, Anton J. Enright, Dave Willey, Tim Hubbard, Rebekah Hall, Michael Kay, Matthew D. Clark, Matthew Jones, Glenn Harden, C. D. Skuce, Lauren Robertson, Leonard I. Zon, Lucy Matthews, Jeffrey C. Barrett, Michael A. Quail, Emma J. Kenyon, Leonor T. Quintais, Benjamin Phillimore, S Hammond, Carl Henderson, Joanna Harley, Elliot Harrison, Cordelia Langford, Christopher M. Dooley, and Sean Maguire

Subjects
Max planck institute, Comparative genomics, Multidisciplinary, Reference genome sequence, biology, Evolutionary biology, Philosophy, Human genome, Bioinformatics, biology.organism_classification, Zebrafish
Abstract

Nature 496, 498–503 (2013); doi:10.1038/nature12111 In this Letter, five authors were inadvertently omitted: Sharmin Begum and Christine Lloyd from the Wellcome Trust Sanger Institute, and Christa Lanz, Gunter Raddatz and Stephan C. Schuster from the Max Planck Institute for Developmental Biology. David Elliot was incorrectly listed as David Eliot, Beverley Mortimore was incorrectly listed as Beverly Mortimer, and James D.

Published
2013

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