%0 Journal Article %J Nature %D 2006 %T The DNA sequence, annotation and analysis of human chromosome 3. %A Donna M Muzny %A Steven E Scherer %A Kaul, Rajinder %A Wang, Jing %A Yu, Jun %A Sudbrak, Ralf %A Buhay, Christian J %A Rui Chen %A Cree, Andrew %A Ding, Yan %A Dugan-Rocha, Shannon %A Gill, Rachel %A Gunaratne, Preethi %A R. Alan Harris %A Hawes, Alicia C %A Hernandez, Judith %A Hodgson, Anne V %A Hume, Jennifer %A Jackson, Andrew %A Ziad Khan %A Kovar-Smith, Christie %A Lewis, Lora R %A Lozado, Ryan J %A Metzker, Michael L %A Milosavljevic, Aleksandar %A Miner, George R %A Morgan, Margaret B %A Nazareth, Lynne V %A Scott, Graham %A Sodergren, Erica %A Song, Xing-Zhi %A Steffen, David %A Wei, Sharon %A David A Wheeler %A Wright, Mathew W %A Kim C Worley %A Yuan, Ye %A Zhang, Zhengdong %A Adams, Charles Q %A Ansari-Lari, M Ali %A Ayele, Mulu %A Brown, Mary J %A Chen, Guan %A Chen, Zhijian %A Clendenning, James %A Clerc-Blankenburg, Kerstin P %A Chen, Runsheng %A Chen, Zhu %A Davis, Clay %A Delgado, Oliver %A Dinh, Huyen H %A Dong, Wei %A Draper, Heather %A Ernst, Stephen %A Fu, Gang %A Gonzalez-Garay, Manuel L %A Garcia, Dawn K %A Gillett, Will %A Gu, Jun %A Hao, Bailin %A Haugen, Eric %A Havlak, Paul %A He, Xin %A Hennig, Steffen %A Hu, Songnian %A Huang, Wei %A Jackson, Laronda R %A Jacob, Leni S %A Kelly, Susan H %A Kube, Michael %A Levy, Ruth %A Li, Zhangwan %A Liu, Bin %A Liu, Jing %A Liu, Wen %A Lu, Jing %A Maheshwari, Manjula %A Nguyen, Bao-Viet %A Okwuonu, Geoffrey O %A Palmeiri, Anthony %A Pasternak, Shiran %A Perez, Lesette M %A Phelps, Karen A %A Plopper, Farah J H %A Qiang, Boqin %A Raymond, Christopher %A Rodriguez, Ruben %A Saenphimmachak, Channakhone %A Santibanez, Jireh %A Shen, Hua %A Shen, Yan %A Subramanian, Sandhya %A Tabor, Paul E %A Verduzco, Daniel %A Waldron, Lenée %A Wang, Jian %A Wang, Jun %A Wang, Qiaoyan %A Williams, Gabrielle A %A Wong, Gane K-S %A Yao, Zhijian %A Zhang, Jingkun %A Zhang, Xiuqing %A Zhao, Guoping %A Zhou, Jianling %A Zhou, Yang %A Nelson, David %A Lehrach, Hans %A Reinhardt, Richard %A Naylor, Susan L %A Yang, Huanming %A Olson, Maynard %A Weinstock, George %A Richard A Gibbs %K Animals %K Base Sequence %K Chromosome Breakage %K Chromosome Inversion %K Chromosomes, Human, Pair 3 %K Contig Mapping %K CpG Islands %K DNA, Complementary %K Evolution, Molecular %K Expressed Sequence Tags %K Human Genome Project %K Humans %K Macaca mulatta %K Molecular Sequence Data %K Pan troglodytes %K Sequence Analysis, DNA %K Synteny %X

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.

%B Nature %V 440 %P 1194-8 %8 2006 Apr 27 %G eng %N 7088 %1 https://www.ncbi.nlm.nih.gov/pubmed/16641997?dopt=Abstract %R 10.1038/nature04728 %0 Journal Article %J Nature %D 2006 %T The finished DNA sequence of human chromosome 12. %A Scherer, Steven E %A Donna M Muzny %A Buhay, Christian J %A Rui Chen %A Cree, Andrew %A Ding, Yan %A Dugan-Rocha, Shannon %A Gill, Rachel %A Gunaratne, Preethi %A R. Alan Harris %A Hawes, Alicia C %A Hernandez, Judith %A Hodgson, Anne V %A Hume, Jennifer %A Jackson, Andrew %A Ziad Khan %A Kovar-Smith, Christie %A Lewis, Lora R %A Lozado, Ryan J %A Metzker, Michael L %A Milosavljevic, Aleksandar %A Miner, George R %A Montgomery, Kate T %A Morgan, Margaret B %A Nazareth, Lynne V %A Scott, Graham %A Sodergren, Erica %A Song, Xing-Zhi %A Steffen, David %A Lovering, Ruth C %A Wheeler, David A %A Worley, Kim C %A Yuan, Yi %A Zhang, Zhengdong %A Adams, Charles Q %A Ansari-Lari, M Ali %A Ayele, Mulu %A Brown, Mary J %A Chen, Guan %A Chen, Zhijian %A Clerc-Blankenburg, Kerstin P %A Davis, Clay %A Delgado, Oliver %A Dinh, Huyen H %A Draper, Heather %A Gonzalez-Garay, Manuel L %A Havlak, Paul %A Jackson, Laronda R %A Jacob, Leni S %A Kelly, Susan H %A Li, Li %A Li, Zhangwan %A Liu, Jing %A Liu, Wen %A Lu, Jing %A Maheshwari, Manjula %A Nguyen, Bao-Viet %A Okwuonu, Geoffrey O %A Pasternak, Shiran %A Perez, Lesette M %A Plopper, Farah J H %A Santibanez, Jireh %A Shen, Hua %A Tabor, Paul E %A Verduzco, Daniel %A Waldron, Lenée %A Wang, Qiaoyan %A Williams, Gabrielle A %A Zhang, Jingkun %A Zhou, Jianling %A Allen, Carlana C %A Amin, Anita G %A Anyalebechi, Vivian %A Bailey, Michael %A Barbaria, Joseph A %A Bimage, Kesha E %A Bryant, Nathaniel P %A Burch, Paula E %A Burkett, Carrie E %A Burrell, Kevin L %A Calderon, Eliana %A Cardenas, Veronica %A Carter, Kelvin %A Casias, Kristal %A Cavazos, Iracema %A Cavazos, Sandra R %A Ceasar, Heather %A Chacko, Joseph %A Chan, Sheryl N %A Chavez, Dean %A Christopoulos, Constantine %A Chu, Joseph %A Cockrell, Raynard %A Cox, Caroline D %A Dang, Michelle %A Dathorne, Stephanie R %A David, Robert %A Davis, Candi Mon'Et %A Davy-Carroll, Latarsha %A Deshazo, Denise R %A Donlin, Jeremy E %A D'Souza, Lisa %A Eaves, Kristy A %A Simons, Rain %A Emery-Cohen, Alexandra J %A Escotto, Michael %A Flagg, Nicole %A Forbes, Lisa D %A Gabisi, Abdul M %A Garza, Melissa %A Hamilton, Cerissa %A Henderson, Nicholas %A Hernandez, Omar %A Hines, Sandra %A Hogues, Marilyn E %A Huang, Mei %A Idlebird, DeVincent G %A Johnson, Rudy %A Jolivet, Angela %A Jones, Sally %A Kagan, Ryan %A King, Laquisha M %A Leal, Belita %A Lebow, Heather %A Lee, Sandra %A LeVan, Jaclyn M %A Lewis, Lakeshia C %A London, Pamela %A Lorensuhewa, Lorna M %A Loulseged, Hermela %A Lovett, Demetria A %A Lucier, Alice %A Lucier, Raymond L %A Ma, Jie %A Madu, Renita C %A Mapua, Patricia %A Martindale, Ashley D %A Martinez, Evangelina %A Massey, Elizabeth %A Mawhiney, Samantha %A Meador, Michael G %A Mendez, Sylvia %A Mercado, Christian %A Mercado, Iracema C %A Merritt, Christina E %A Miner, Zachary L %A Minja, Emmanuel %A Mitchell, Teresa %A Mohabbat, Farida %A Mohabbat, Khatera %A Montgomery, Baize %A Moore, Niki %A Morris, Sidney %A Munidasa, Mala %A Ngo, Robin N %A Nguyen, Ngoc B %A Nickerson, Elizabeth %A Nwaokelemeh, Ogechi O %A Nwokenkwo, Stanley %A Obregon, Melissa %A Oguh, Maryann %A Oragunye, Njideka %A Oviedo, Rodolfo J %A Parish, Bridgette J %A Parker, David N %A Parrish, Julia %A Parks, Kenya L %A Paul, Heidie A %A Payton, Brett A %A Perez, Agapito %A Perrin, William %A Pickens, Adam %A Primus, Eltrick L %A Pu, Ling-Ling %A Puazo, Maria %A Quiles, Miyo M %A Quiroz, Juana B %A Rabata, Dina %A Reeves, Kacy %A Ruiz, San Juana %A Shao, Hongmei %A Sisson, Ida %A Sonaike, Titilola %A Sorelle, Richard P %A Sutton, Angelica E %A Svatek, Amanda F %A Svetz, Leah Anne %A Tamerisa, Kavitha S %A Taylor, Tineace R %A Teague, Brian %A Thomas, Nicole %A Thorn, Rachel D %A Trejos, Zulma Y %A Trevino, Brenda K %A Ukegbu, Ogechi N %A Urban, Jeremy B %A Vasquez, Lydia I %A Vera, Virginia A %A Villasana, Donna M %A Wang, Ling %A Ward-Moore, Stephanie %A Warren, James T %A Wei, Xuehong %A White, Flower %A Williamson, Angela L %A Wleczyk, Regina %A Wooden, Hailey S %A Wooden, Steven H %A Yen, Jennifer %A Yoon, Lillienne %A Yoon, Vivienne %A Zorrilla, Sara E %A Nelson, David %A Kucherlapati, Raju %A Weinstock, George %A Richard A Gibbs %K Animals %K Base Composition %K Chromosomes, Human, Pair 12 %K CpG Islands %K Evolution, Molecular %K Expressed Sequence Tags %K Genes %K Humans %K Linkage Disequilibrium %K Microsatellite Repeats %K Molecular Sequence Data %K Mutagenesis, Insertional %K Pan troglodytes %K Sequence Analysis, DNA %K Sequence Deletion %K Short Interspersed Nucleotide Elements %K Synteny %X

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.

%B Nature %V 440 %P 346-51 %8 2006 Mar 16 %G eng %N 7082 %1 https://www.ncbi.nlm.nih.gov/pubmed/16541075?dopt=Abstract %R 10.1038/nature04569 %0 Journal Article %J Nature %D 2005 %T The DNA sequence of the human X chromosome. %A Ross, Mark T %A Grafham, Darren V %A Coffey, Alison J %A Steven E Scherer %A McLay, Kirsten %A Donna M Muzny %A Platzer, Matthias %A Howell, Gareth R %A Burrows, Christine %A Bird, Christine P %A Frankish, Adam %A Lovell, Frances L %A Howe, Kevin L %A Ashurst, Jennifer L %A Fulton, Robert S %A Sudbrak, Ralf %A Wen, Gaiping %A Jones, Matthew C %A Hurles, Matthew E %A Andrews, T Daniel %A Scott, Carol E %A Searle, Stephen %A Ramser, Juliane %A Whittaker, Adam %A Deadman, Rebecca %A Carter, Nigel P %A Hunt, Sarah E %A Rui Chen %A Cree, Andrew %A Gunaratne, Preethi %A Havlak, Paul %A Hodgson, Anne %A Metzker, Michael L %A Stephen Richards %A Scott, Graham %A Steffen, David %A Sodergren, Erica %A David A Wheeler %A Kim C Worley %A Ainscough, Rachael %A Ambrose, Kerrie D %A Ansari-Lari, M Ali %A Aradhya, Swaroop %A Ashwell, Robert I S %A Babbage, Anne K %A Bagguley, Claire L %A Ballabio, Andrea %A Banerjee, Ruby %A Barker, Gary E %A Barlow, Karen F %A Barrett, Ian P %A Bates, Karen N %A Beare, David M %A Beasley, Helen %A Beasley, Oliver %A Beck, Alfred %A Bethel, Graeme %A Blechschmidt, Karin %A Brady, Nicola %A Bray-Allen, Sarah %A Bridgeman, Anne M %A Brown, Andrew J %A Brown, Mary J %A Bonnin, David %A Bruford, Elspeth A %A Buhay, Christian %A Burch, Paula %A Burford, Deborah %A Burgess, Joanne %A Burrill, Wayne %A Burton, John %A Bye, Jackie M %A Carder, Carol %A Carrel, Laura %A Chako, Joseph %A Chapman, Joanne C %A Chavez, Dean %A Chen, Ellson %A Chen, Guan %A Chen, Yuan %A Chen, Zhijian %A Chinault, Craig %A Ciccodicola, Alfredo %A Clark, Sue Y %A Clarke, Graham %A Clee, Chris M %A Clegg, Sheila %A Clerc-Blankenburg, Kerstin %A Clifford, Karen %A Cobley, Vicky %A Cole, Charlotte G %A Conquer, Jen S %A Corby, Nicole %A Connor, Richard E %A David, Robert %A Davies, Joy %A Davis, Clay %A Davis, John %A Delgado, Oliver %A Deshazo, Denise %A Dhami, Pawandeep %A Ding, Yan %A Dinh, Huyen %A Dodsworth, Steve %A Draper, Heather %A Dugan-Rocha, Shannon %A Dunham, Andrew %A Dunn, Matthew %A Durbin, K James %A Dutta, Ireena %A Eades, Tamsin %A Ellwood, Matthew %A Emery-Cohen, Alexandra %A Errington, Helen %A Evans, Kathryn L %A Faulkner, Louisa %A Francis, Fiona %A Frankland, John %A Fraser, Audrey E %A Galgoczy, Petra %A Gilbert, James %A Gill, Rachel %A Glöckner, Gernot %A Gregory, Simon G %A Gribble, Susan %A Griffiths, Coline %A Grocock, Russell %A Gu, Yanghong %A Gwilliam, Rhian %A Hamilton, Cerissa %A Hart, Elizabeth A %A Hawes, Alicia %A Heath, Paul D %A Heitmann, Katja %A Hennig, Steffen %A Hernandez, Judith %A Hinzmann, Bernd %A Ho, Sarah %A Hoffs, Michael %A Howden, Phillip J %A Huckle, Elizabeth J %A Hume, Jennifer %A Hunt, Paul J %A Hunt, Adrienne R %A Isherwood, Judith %A Jacob, Leni %A Johnson, David %A Jones, Sally %A De Jong, Pieter J %A Joseph, Shirin S %A Keenan, Stephen %A Kelly, Susan %A Kershaw, Joanne K %A Ziad Khan %A Kioschis, Petra %A Klages, Sven %A Knights, Andrew J %A Kosiura, Anna %A Kovar-Smith, Christie %A Laird, Gavin K %A Langford, Cordelia %A Lawlor, Stephanie %A Leversha, Margaret %A Lewis, Lora %A Liu, Wen %A Lloyd, Christine %A Lloyd, David M %A Loulseged, Hermela %A Loveland, Jane E %A Lovell, Jamieson D %A Lozado, Ryan %A Lu, Jing %A Lyne, Rachael %A Ma, Jie %A Maheshwari, Manjula %A Matthews, Lucy H %A McDowall, Jennifer %A McLaren, Stuart %A McMurray, Amanda %A Meidl, Patrick %A Meitinger, Thomas %A Milne, Sarah %A Miner, George %A Mistry, Shailesh L %A Morgan, Margaret %A Morris, Sidney %A Müller, Ines %A Mullikin, James C %A Nguyen, Ngoc %A Nordsiek, Gabriele %A Nyakatura, Gerald %A O'Dell, Christopher N %A Okwuonu, Geoffery %A Palmer, Sophie %A Pandian, Richard %A Parker, David %A Parrish, Julia %A Pasternak, Shiran %A Patel, Dina %A Pearce, Alex V %A Pearson, Danita M %A Pelan, Sarah E %A Perez, Lesette %A Porter, Keith M %A Ramsey, Yvonne %A Reichwald, Kathrin %A Rhodes, Susan %A Ridler, Kerry A %A Schlessinger, David %A Schueler, Mary G %A Sehra, Harminder K %A Shaw-Smith, Charles %A Shen, Hua %A Sheridan, Elizabeth M %A Shownkeen, Ratna %A Skuce, Carl D %A Smith, Michelle L %A Sotheran, Elizabeth C %A Steingruber, Helen E %A Steward, Charles A %A Storey, Roy %A Swann, R Mark %A Swarbreck, David %A Tabor, Paul E %A Taudien, Stefan %A Taylor, Tineace %A Teague, Brian %A Thomas, Karen %A Thorpe, Andrea %A Timms, Kirsten %A Tracey, Alan %A Trevanion, Steve %A Tromans, Anthony C %A d'Urso, Michele %A Verduzco, Daniel %A Villasana, Donna %A Waldron, Lenée %A Wall, Melanie %A Wang, Qiaoyan %A Warren, James %A Warry, Georgina L %A Wei, Xuehong %A West, Anthony %A Whitehead, Siobhan L %A Whiteley, Mathew N %A Wilkinson, Jane E %A Willey, David L %A Williams, Gabrielle %A Williams, Leanne %A Williamson, Angela %A Williamson, Helen %A Wilming, Laurens %A Woodmansey, Rebecca L %A Wray, Paul W %A Yen, Jennifer %A Zhang, Jingkun %A Zhou, Jianling %A Zoghbi, Huda %A Zorilla, Sara %A Buck, David %A Reinhardt, Richard %A Poustka, Annemarie %A Rosenthal, André %A Lehrach, Hans %A Meindl, Alfons %A Minx, Patrick J %A Hillier, LaDeana W %A Willard, Huntington F %A Wilson, Richard K %A Waterston, Robert H %A Rice, Catherine M %A Vaudin, Mark %A Coulson, Alan %A Nelson, David L %A Weinstock, George %A Sulston, John E %A Durbin, Richard %A Hubbard, Tim %A Richard A Gibbs %A Beck, Stephan %A Rogers, Jane %A Bentley, David R %K Animals %K Antigens, Neoplasm %K Centromere %K Chromosomes, Human, X %K Chromosomes, Human, Y %K Contig Mapping %K Crossing Over, Genetic %K Dosage Compensation, Genetic %K Evolution, Molecular %K Female %K Genetic Linkage %K Genetics, Medical %K Genomics %K Humans %K Male %K Polymorphism, Single Nucleotide %K Repetitive Sequences, Nucleic Acid %K RNA %K Sequence Analysis, DNA %K Sequence Homology, Nucleic Acid %K Testis %X

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.

%B Nature %V 434 %P 325-37 %8 2005 Mar 17 %G eng %N 7031 %1 https://www.ncbi.nlm.nih.gov/pubmed/15772651?dopt=Abstract %R 10.1038/nature03440 %0 Journal Article %J Nature %D 2004 %T Genome sequence of the Brown Norway rat yields insights into mammalian evolution. %A Gibbs, Richard A %A Weinstock, George M %A Metzker, Michael L %A Muzny, Donna M %A Sodergren, Erica J %A Scherer, Steven %A Scott, Graham %A Steffen, David %A Worley, Kim C %A Burch, Paula E %A Okwuonu, Geoffrey %A Hines, Sandra %A Lewis, Lora %A DeRamo, Christine %A Delgado, Oliver %A Dugan-Rocha, Shannon %A Miner, George %A Morgan, Margaret %A Hawes, Alicia %A Gill, Rachel %A Holt, Robert A %A Adams, Mark D %A Amanatides, Peter G %A Baden-Tillson, Holly %A Barnstead, Mary %A Chin, Soo %A Evans, Cheryl A %A Ferriera, Steve %A Fosler, Carl %A Glodek, Anna %A Gu, Zhiping %A Jennings, Don %A Kraft, Cheryl L %A Nguyen, Trixie %A Pfannkoch, Cynthia M %A Sitter, Cynthia %A Sutton, Granger G %A Venter, J Craig %A Woodage, Trevor %A Smith, Douglas %A Lee, Hong-Mei %A Gustafson, Erik %A Cahill, Patrick %A Kana, Arnold %A Doucette-Stamm, Lynn %A Weinstock, Keith %A Fechtel, Kim %A Weiss, Robert B %A Dunn, Diane M %A Green, Eric D %A Blakesley, Robert W %A Bouffard, Gerard G %A De Jong, Pieter J %A Osoegawa, Kazutoyo %A Zhu, Baoli %A Marra, Marco %A Schein, Jacqueline %A Bosdet, Ian %A Fjell, Chris %A Jones, Steven %A Krzywinski, Martin %A Mathewson, Carrie %A Siddiqui, Asim %A Wye, Natasja %A McPherson, John %A Zhao, Shaying %A Fraser, Claire M %A Shetty, Jyoti %A Shatsman, Sofiya %A Geer, Keita %A Chen, Yixin %A Abramzon, Sofyia %A Nierman, William C %A Havlak, Paul H %A Chen, Rui %A Durbin, K James %A Simons, Rain %A Ren, Yanru %A Song, Xing-Zhi %A Li, Bingshan %A Liu, Yue %A Qin, Xiang %A Cawley, Simon %A Worley, Kim C %A Cooney, A J %A D'Souza, Lisa M %A Martin, Kirt %A Wu, Jia Qian %A Gonzalez-Garay, Manuel L %A Jackson, Andrew R %A Kalafus, Kenneth J %A McLeod, Michael P %A Milosavljevic, Aleksandar %A Virk, Davinder %A Volkov, Andrei %A Wheeler, David A %A Zhang, Zhengdong %A Bailey, Jeffrey A %A Eichler, Evan E %A Tuzun, Eray %A Birney, Ewan %A Mongin, Emmanuel %A Ureta-Vidal, Abel %A Woodwark, Cara %A Zdobnov, Evgeny %A Bork, Peer %A Suyama, Mikita %A Torrents, David %A Alexandersson, Marina %A Trask, Barbara J %A Young, Janet M %A Huang, Hui %A Wang, Huajun %A Xing, Heming %A Daniels, Sue %A Gietzen, Darryl %A Schmidt, Jeanette %A Stevens, Kristian %A Vitt, Ursula %A Wingrove, Jim %A Camara, Francisco %A Mar Albà, M %A Abril, Josep F %A Guigó, Roderic %A Smit, Arian %A Dubchak, Inna %A Rubin, Edward M %A Couronne, Olivier %A Poliakov, Alexander %A Hübner, Norbert %A Ganten, Detlev %A Goesele, Claudia %A Hummel, Oliver %A Kreitler, Thomas %A Lee, Young-Ae %A Monti, Jan %A Schulz, Herbert %A Zimdahl, Heike %A Himmelbauer, Heinz %A Lehrach, Hans %A Jacob, Howard J %A Bromberg, Susan %A Gullings-Handley, Jo %A Jensen-Seaman, Michael I %A Kwitek, Anne E %A Lazar, Jozef %A Pasko, Dean %A Tonellato, Peter J %A Twigger, Simon %A Ponting, Chris P %A Duarte, Jose M %A Rice, Stephen %A Goodstadt, Leo %A Beatson, Scott A %A Emes, Richard D %A Winter, Eitan E %A Webber, Caleb %A Brandt, Petra %A Nyakatura, Gerald %A Adetobi, Margaret %A Chiaromonte, Francesca %A Elnitski, Laura %A Eswara, Pallavi %A Hardison, Ross C %A Hou, Minmei %A Kolbe, Diana %A Makova, Kateryna %A Miller, Webb %A Nekrutenko, Anton %A Riemer, Cathy %A Schwartz, Scott %A Taylor, James %A Yang, Shan %A Zhang, Yi %A Lindpaintner, Klaus %A Andrews, T Dan %A Caccamo, Mario %A Clamp, Michele %A Clarke, Laura %A Curwen, Valerie %A Durbin, Richard %A Eyras, Eduardo %A Searle, Stephen M %A Cooper, Gregory M %A Batzoglou, Serafim %A Brudno, Michael %A Sidow, Arend %A Stone, Eric A %A Venter, J Craig %A Payseur, Bret A %A Bourque, Guillaume %A López-Otín, Carlos %A Puente, Xose S %A Chakrabarti, Kushal %A Chatterji, Sourav %A Dewey, Colin %A Pachter, Lior %A Bray, Nicolas %A Yap, Von Bing %A Caspi, Anat %A Tesler, Glenn %A Pevzner, Pavel A %A Haussler, David %A Roskin, Krishna M %A Baertsch, Robert %A Clawson, Hiram %A Furey, Terrence S %A Hinrichs, Angie S %A Karolchik, Donna %A Kent, William J %A Rosenbloom, Kate R %A Trumbower, Heather %A Weirauch, Matt %A Cooper, David N %A Stenson, Peter D %A Ma, Bin %A Brent, Michael %A Arumugam, Manimozhiyan %A Shteynberg, David %A Copley, Richard R %A Taylor, Martin S %A Riethman, Harold %A Mudunuri, Uma %A Peterson, Jane %A Guyer, Mark %A Felsenfeld, Adam %A Old, Susan %A Mockrin, Stephen %A Collins, Francis %K Animals %K Base Composition %K Centromere %K Chromosomes, Mammalian %K CpG Islands %K DNA Transposable Elements %K DNA, Mitochondrial %K Evolution, Molecular %K Gene Duplication %K Genome %K Genomics %K Humans %K Introns %K Male %K Mice %K Models, Molecular %K Mutagenesis %K Polymorphism, Single Nucleotide %K Rats %K Rats, Inbred BN %K Regulatory Sequences, Nucleic Acid %K Retroelements %K RNA Splice Sites %K RNA, Untranslated %K Sequence Analysis, DNA %K Telomere %X

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

%B Nature %V 428 %P 493-521 %8 2004 Apr 01 %G eng %N 6982 %1 https://www.ncbi.nlm.nih.gov/pubmed/15057822?dopt=Abstract %R 10.1038/nature02426 %0 Journal Article %J Nucleic Acids Res %D 2002 %T Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomes. %A Dederich, Debra A %A Okwuonu, Geoffrey %A Garner, Toni %A Denn, Amanda %A Sutton, Angelica %A Escotto, Michael %A Martindale, Ashley %A Delgado, Oliver %A Donna M Muzny %A Richard A Gibbs %A Metzker, Michael L %K Animals %K DNA %K Genome %K Glass %K Microspheres %K Plasmids %K Rats %K Reproducibility of Results %K Sequence Analysis, DNA %X

To meet the new challenge of generating the draft sequences of mammalian genomes, we describe the development of a novel high throughput 96-well method for the purification of plasmid DNA template using size-fractionated, acid-washed glass beads. Unlike most previously described approaches, the current method has been designed and optimized to facilitate the direct binding of alcohol-precipitated plasmid DNA to glass beads from alkaline lysed bacterial cells containing the insoluble cellular aggregate material. Eliminating the tedious step of separating the cleared lysate significantly simplifies the method and improves throughput and reliability. During a 4 month period of 96-capillary DNA sequencing of the Rattus norvegicus genome at the Baylor College of Medicine Human Genome Sequencing Center, the average success rate and read length derived from >1 800 000 plasmid DNA templates prepared by the direct lysis/glass bead method were 82.2% and 516 bases, respectively. The cost of this direct lysis/glass bead method in September 2001 was approximately 10 cents per clone, which is a significant cost saving in high throughput genomic sequencing efforts.

%B Nucleic Acids Res %V 30 %P e32 %8 2002 Apr 01 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/11917038?dopt=Abstract %R 10.1093/nar/30.7.e32