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1. The DNA sequence, annotation and analysis of human chromosome 3

Author

Zhengdong D. Zhang, Jun Wang, Zhu Chen, Will Gillett, George M. Weinstock, Guoping Zhao, LaRonda Jackson, Christopher K. Raymond, Manuel L. Gonzalez-Garay, Yang Zhou, Judith Hernandez, Boqin Qiang, James B. Clendenning, Zhijian J. Chen, Shannon Dugan-Rocha, Andrew R. Jackson, Zhijian Yao, Yan Shen, R. Alan Harris, Ziad Khan, Margaret Morgan, Wei Dong, Sharon Wei, Dawn Garcia, Aleksandar Milosavljevic, Maynard V. Olson, Ruben Rodriguez, Kerstin P. Clerc-Blankenburg, Ryan J. Lozado, Ralf Sudbrak, Jun Gu, Jing Kun Zhang, Heather R. Draper, Mary J. Brown, Channakhone Saenphimmachak, M. Ali Ansari-Lari, Songnian Hu, Preethi H. Gunaratne, Donna M. Muzny, Shiran Pasternak, Xing Zhi Song, Oliver Delgado, Bailin Hao, Lesette Perez, Charles Q. Adams, Michael L. Metzker, Anne Hodgson, Daniel Verduzco, Bao Viet Nguyen, Susan H. Kelly, Xin He, Jing Wang, Runsheng Chen, Karen A. Phelps, Rajinder Kaul, Guan Chen, Wei Huang, Huyen Dinh, Lenee Waldron, Paul Havlak, George Miner, Qiaoyan Wang, Ye Yuan, Rachel Gill, Anthony Palmeiri, Mathew W. Wright, Kim C. Worley, Michael Kube, Jing Liu, Clay Davis, Christian J. Buhay, Zhangwan Li, Jun Yu, Alicia Hawes, Jing Lu, Steffen Hennig, David L. Nelson, Rui Chen, Leni S. Jacob, Huanming Yang, Bin Liu, Steven E. Scherer, Christie Kovar-Smith, Jian Wang, Manjula Maheshwari, Gabrielle A. Williams, Paul E. Tabor, David A. Wheeler, Hans Lehrach, Graham R. Scott, Farah J.H. Plopper, Erica Sodergren, Wen Liu, Mulu Ayele, Richard Reinhardt, Richard A. Gibbs, Eric Haugen, Lora Lewis, Hua Shen, Gang Fu, Jianling Zhou, Xiuqing Zhang, Stephen Ernst, Geoffrey Okwuonu, Susan L. Naylor, Jennifer Hume, Ruth Levy, Andrew Cree, Yan Ding, David Steffen, Lynne V. Nazareth, Jireh Santibanez, Sandhya Subramanian, and Gane Ka-Shu Wong

Subjects
Inversion, Chromosome, Genome evolution, DNA, Complementary, Pan troglodytes, Molecular Sequence Data, Biology, Synteny, Genome, Evolution, Molecular, Chimpanzee genome project, Contig Mapping, Chromosome 19, Human Genome Project, Animals, Humans, Expressed Sequence Tags, Genetics, Multidisciplinary, Base Sequence, Chromosome Breakage, Sequence Analysis, DNA, Genome project, Macaca mulatta, Chromosome Inversion, CpG Islands, Human genome, Chromosomes, Human, Pair 3, Chromosome 21, Reference genome
Abstract

Udgivelsesdato: 2006-Apr-27 After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

Published
2006
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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. The finished DNA sequence of human chromosome 12

Author

Steven E, Scherer, Donna M, Muzny, Christian J, Buhay, Rui, Chen, Andrew, Cree, Yan, Ding, Shannon, Dugan-Rocha, Rachel, Gill, Preethi, Gunaratne, R Alan, Harris, Alicia C, Hawes, Judith, Hernandez, Anne V, Hodgson, Jennifer, Hume, Andrew, Jackson, Ziad Mohid, Khan, Christie, Kovar-Smith, Lora R, Lewis, Ryan J, Lozado, Michael L, Metzker, Aleksandar, Milosavljevic, George R, Miner, Kate T, Montgomery, Margaret B, Morgan, Lynne V, Nazareth, Graham, Scott, Erica, Sodergren, Xing-Zhi, Song, David, Steffen, Ruth C, Lovering, David A, Wheeler, Kim C, Worley, Yi, Yuan, Zhengdong, Zhang, Charles Q, Adams, M Ali, Ansari-Lari, Mulu, Ayele, Mary J, Brown, Guan, Chen, Zhijian, Chen, Kerstin P, Clerc-Blankenburg, Clay, Davis, Oliver, Delgado, Huyen H, Dinh, Heather, Draper, Manuel L, Gonzalez-Garay, Paul, Havlak, Laronda R, Jackson, Leni S, Jacob, Susan H, Kelly, Li, Li, Zhangwan, Li, Jing, Liu, Wen, Liu, Jing, Lu, Manjula, Maheshwari, Bao-Viet, Nguyen, Geoffrey O, Okwuonu, Shiran, Pasternak, Lesette M, Perez, Farah J H, Plopper, Jireh, Santibanez, Hua, Shen, Paul E, Tabor, Daniel, Verduzco, Lenee, Waldron, Qiaoyan, Wang, Gabrielle A, Williams, Jingkun, Zhang, Jianling, Zhou, Carlana C, Allen, Anita G, Amin, Vivian, Anyalebechi, Michael, Bailey, Joseph A, Barbaria, Kesha E, Bimage, Nathaniel P, Bryant, Paula E, Burch, Carrie E, Burkett, Kevin L, Burrell, Eliana, Calderon, Veronica, Cardenas, Kelvin, Carter, Kristal, Casias, Iracema, Cavazos, Sandra R, Cavazos, Heather, Ceasar, Joseph, Chacko, Sheryl N, Chan, Dean, Chavez, Constantine, Christopoulos, Joseph, Chu, Raynard, Cockrell, Caroline D, Cox, Michelle, Dang, Stephanie R, Dathorne, Robert, David, Candi Mon'Et, Davis, Latarsha, Davy-Carroll, Denise R, Deshazo, Jeremy E, Donlin, Lisa, D'Souza, Kristy A, Eaves, Amy, Egan, Alexandra J, Emery-Cohen, Michael, Escotto, Nicole, Flagg, Lisa D, Forbes, Abdul M, Gabisi, Melissa, Garza, Cerissa, Hamilton, Nicholas, Henderson, Omar, Hernandez, Sandra, Hines, Marilyn E, Hogues, Mei, Huang, DeVincent G, Idlebird, Rudy, Johnson, Angela, Jolivet, Sally, Jones, Ryan, Kagan, Laquisha M, King, Belita, Leal, Heather, Lebow, Sandra, Lee, Jaclyn M, LeVan, Lakeshia C, Lewis, Pamela, London, Lorna M, Lorensuhewa, Hermela, Loulseged, Demetria A, Lovett, Alice, Lucier, Raymond L, Lucier, Jie, Ma, Renita C, Madu, Patricia, Mapua, Ashley D, Martindale, Evangelina, Martinez, Elizabeth, Massey, Samantha, Mawhiney, Michael G, Meador, Sylvia, Mendez, Christian, Mercado, Iracema C, Mercado, Christina E, Merritt, Zachary L, Miner, Emmanuel, Minja, Teresa, Mitchell, Farida, Mohabbat, Khatera, Mohabbat, Baize, Montgomery, Niki, Moore, Sidney, Morris, Mala, Munidasa, Robin N, Ngo, Ngoc B, Nguyen, Elizabeth, Nickerson, Ogechi O, Nwaokelemeh, Stanley, Nwokenkwo, Melissa, Obregon, Maryann, Oguh, Njideka, Oragunye, Rodolfo J, Oviedo, Bridgette J, Parish, David N, Parker, Julia, Parrish, Kenya L, Parks, Heidie A, Paul, Brett A, Payton, Agapito, Perez, William, Perrin, Adam, Pickens, Eltrick L, Primus, Ling-Ling, Pu, Maria, Puazo, Miyo M, Quiles, Juana B, Quiroz, Dina, Rabata, Kacy, Reeves, San Juana, Ruiz, Hongmei, Shao, Ida, Sisson, Titilola, Sonaike, Richard P, Sorelle, Angelica E, Sutton, Amanda F, Svatek, Leah Anne, Svetz, Kavitha S, Tamerisa, Tineace R, Taylor, Brian, Teague, Nicole, Thomas, Rachel D, Thorn, Zulma Y, Trejos, Brenda K, Trevino, Ogechi N, Ukegbu, Jeremy B, Urban, Lydia I, Vasquez, Virginia A, Vera, Donna M, Villasana, Ling, Wang, Stephanie, Ward-Moore, James T, Warren, Xuehong, Wei, Flower, White, Angela L, Williamson, Regina, Wleczyk, Hailey S, Wooden, Steven H, Wooden, Jennifer, Yen, Lillienne, Yoon, Vivienne, Yoon, Sara E, Zorrilla, David, Nelson, Raju, Kucherlapati, George, Weinstock, and Richard A, Gibbs

Subjects
Pan troglodytes, Molecular Sequence Data, Biology, Synteny, Linkage Disequilibrium, Evolution, Molecular, Chromosome 16, Chromosome 19, Animals, Humans, Sequence Deletion, Short Interspersed Nucleotide Elements, Genetics, Chromosome 7 (human), Expressed Sequence Tags, Base Composition, Multidisciplinary, Chromosomes, Human, Pair 12, Sequence Analysis, DNA, Chromosome 17 (human), Mutagenesis, Insertional, Chromosome 4, Chromosome 3, Genes, Evolutionary biology, CpG Islands, Chromosome 21, Chromosome 22, Microsatellite Repeats
Abstract

Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.

Published
2005

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