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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
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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
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3. [Untitled]

Author

Lucy Matthews, Syed Sufyan Hussain, Matthew E. Hurles, and David Willey

Subjects
Genetics, 0303 health sciences, Concerted evolution, Chromosomal rearrangement, Biology, Y chromosome, 03 medical and health sciences, 0302 clinical medicine, Evolutionary biology, Gene duplication, Human genome, Gene conversion, Homologous recombination, 030217 neurology & neurosurgery, 030304 developmental biology, Sequence (medicine)
Abstract

Background: The origins of the recombination hotspots that are a common feature of both allelic and non-allelic homologous recombination in the human genome are poorly understood. We have investigated, by comparative sequencing, the evolution of two hotspots of non-allelic homologous recombination on the Y chromosome that lie within paralogous sequences known to sponsor deletions resulting in male infertility. Results: These recombination hotspots are characterized by signatures of concerted evolution, which indicate that gene conversion between paralogs has been predominant in shaping their recent evolution. By contrast, the paralogous sequences that surround the hotspots exhibit little evidence of gene conversion. A second feature of these rearrangement hotspots is the extreme interspecific sequence divergence (around 2.5%) that places them among the most divergent orthologous sequences between humans and chimpanzees. Conclusions: Several hominid-specific gene conversion events have rendered these hotspots better substrates for chromosomal rearrangements in humans than in chimpanzees or gorillas. Monte Carlo simulations of sequence evolution suggest that extreme sequence divergence is a direct consequence of gene conversion between paralogs. We propose that the coincidence of signatures of concerted evolution and recurrent breakpoints of chromosomal rearrangement (mapped at the sequence level) may enable the identification of putative rearrangement hotspots from analysis of comparative sequences from great apes.

Published
2004
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