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1. Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Author

Hillier, LaDeana 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., and Wilson, Richard K.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): LaDeana W. Hillier [1]; Tina A. Graves [1]; Robert S. Fulton [1]; Lucinda A. Fulton [1]; Kymberlie H. Pepin [1]; Patrick Minx [1]; Caryn Wagner-McPherson [1]; Dan Layman [1]; [...]

Published
2005
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2. The DNA sequence of human chromosome 7

Author

Hillier, LaDeana W., Fulton, Robert S., Fulton, Lucinda A., Graves, Tina A., Pepin, Kymberlie H., Wagner-McPherson, Caryn, Layman, Dan, Maas, Jason, Jaeger, Sara, Walker, Rebecca, Wylie, Kristine, Sekhon, Mandeep, Becker, Michael C., O'Laughlin, Michelle D., Schaller, Mark E., Fewell, Ginger A., Delehaunty, Kimberly D., Miner, Tracie L., Nash, William E., Cordes, Matt, Du, Hui, Sun, Hui, Edwards, Jennifer, Bradshaw-Cordum, Holland, Ali, Johar, Andrews, Stephanie, Isak, Amber, VanBrunt, Andrew, Nguyen, Christine, Du, Feiyu, Lamar, Betty, Courtney, Laura, Kalicki, Joelle, Ozersky, Philip, Bielicki, Lauren, Scott, Kelsi, Holmes, Andrea, Harkins, Richard, Harris, Anthony, Strong, Cynthia Madsen, Hou, Shunfang, Tomlinson, Chad, Dauphin-Kohlberg, Sara, Kozlowicz-Reilly, Amy, Leonard, Shawn, Rohlfing, Theresa, Rock, Susan M., Tin-Wollam, Aye-Mon, Abbott, Amanda, Minx, Patrick, Maupin, Rachel, Strowmatt, Catrina, Latreille, Phil, Miller, Nancy, Johnson, Doug, Murray, Jennifer, Woessner, Jeffrey P., Wendl, Michael C., Yang, Shiaw-Pyng, Schultz, Brian R., Wallis, John W., Spieth, John, Bieri, Tamberlyn A., Nelson, Joanne O., Berkowicz, Nicolas, Wohldmann, Patricia E., Cook, Lisa L., Hickenbotham, Matthew T., Eldred, James, Williams, Donald, Bedell, Joseph A., Mardis, Elaine R., Clifton, Sandra W., Chissoe, Stephanie L., Marra, Marco A., Raymond, Christopher, Haugen, Eric, Gillett, Will, Zhou, Yang, James, Rose, Phelps, Karen, Iadanoto, Shawn, Bubb, Kerry, Simms, Elizabeth, Levy, Ruth, Clendenning, James, Kaul, Rajinder, Kent, W. James, Furey, Terrence S., Baertsch, Robert A., Brent, Michael R., Keibler, Evan, Flicek, Paul, Bork, Peer, Suyama, Mikita, Bailey, Jeffrey A., Portnoy, Matthew E., Torrents, David, Chinwalla, Asif T., Gish, Warren R., Eddy, Sean R., McPherson, John D., Olson, Maynard V., Eichler, Evan E., Green, Eric D., Waterston, Robert H., and Wilson, Richard K.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): LaDeana W. Hillier [1]; Robert S. Fulton [1]; Lucinda A. Fulton [1]; Tina A. Graves [1]; Kymberlie H. Pepin [1]; Caryn Wagner-McPherson [1]; Dan Layman [1]; Jason Maas [1]; [...]

Published
2003
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3. The DNA sequence of human chromosome 7

Author

Robert Baertsch, Karen A. Phelps, Lisa Cook, Joelle Kalicki, Michelle O'Laughlin, Kerry L. Bubb, David Torrents, Kristine M. Wylie, Andrew Vanbrunt, Mark E. Schaller, Dan Layman, Kelsi Scott, LaDeana W. Hillier, Marco A. Marra, Caryn Wagner-McPherson, Cindy Strong, Phil Latreille, Hui Sun, Maynard V. Olson, Holland Bradshaw-Cordum, Amanda Abbott, Robert S. Fulton, Nicolas Berkowicz, Richard Harkins, Asif T. Chinwalla, Rajinder Kaul, William E. Nash, Chad Tomlinson, Susan M. Rock, Patricia Wohldmann, Paul Flicek, Elaine R. Mardis, Catrina Strowmatt, James M. Eldred, Betty Lamar, Christopher K. Raymond, Michael C. Wendl, Lauren Bielicki, Shawn Leonard, John Douglas Mcpherson, Christine Nguyen, Jennifer Murray, Michael C. Becker, Lucinda Fulton, Amber Isak, Will Gillett, Matt Cordes, James B. Clendenning, Kymberlie H. Pepin, Mandeep Sekhon, Eric Haugen, Feiyu Du, Theresa Rohlfing, Kimberly D. Delehaunty, Nancy Miller, Amy Kozlowicz-Reilly, Eric D. Green, W. James Kent, Tamberlyn Bieri, Peer Bork, Richard K. Wilson, Patrick Minx, John Spieth, Evan E. Eichler, Shawn Iadanoto, Terrence S. Furey, Matthew E. Portnoy, Shunfang Hou, R. James, Warren Gish, Brian Schultz, Doug Johnson, Philip Ozersky, Jennifer Edwards, Stephanie L. Chissoe, Jeffrey A. Bailey, Tracie L. Miner, Jason Maas, Andrea Holmes, Sandra W. Clifton, Sara Jaeger, Tina Graves, Ruth Levy, Joseph A. Bedell, Ginger A. Fewell, Mikita Suyama, Shiaw-Pyng Yang, Sean R. Eddy, Rebecca S. Walker, Aye-Mon Tin-Wollam, Hui Du, Evan Keibler, Matthew T. Hickenbotham, Sara Dauphin-Kohlberg, Robert H. Waterston, Yang Zhou, Stephanie Andrews, Johar Ali, John W. Wallis, Michael R. Brent, Rachel Maupin, Donald Williams, Elizabeth Simms, Laura Courtney, Anthony R. Harris, Jeffrey Woessner, and Joanne O. Nelson

Subjects
Williams Syndrome, Chromosome 7 (human), Genetics, RNA, Untranslated, Multidisciplinary, Base Sequence, Sequence analysis, Pseudogene, Molecular Sequence Data, Proteins, Sequence Analysis, DNA, Genome project, Biology, Physical Chromosome Mapping, Conserved sequence, Sequence-tagged site, Mice, Sequence logo, Species Specificity, Gene Duplication, Consensus sequence, Animals, Humans, Chromosomes, Human, Pair 7, Pseudogenes
Abstract

Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame.

Published
2003

4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Author

Xinwei She, Sara Dauphin-Kohlberg, Robert H. Waterston, Patricia Wohldmann, Joelle Kalicki, Ivan Ovcharenko, Shawn Leonard, Scott Kruchowski, Ernest Goyea, William Haakenson, Scott Abbott, Catrina Fronick, Aniko Sabo, Maria Cedroni, Edward A. Belter, Hui Du, Asif T. Chinwalla, Kelly Mead, Michael C. Wendl, Rachel Maupin, Amber Isak, David R. Cox, Tamberlyn Bieri, LaDeana W. Hillier, Lee Trani, Neenu Grewal, Aye Mon Tin-Wollam, Rick Meyer, Lachlan G. Oddy, Lucinda Fulton, Li Ding, Richard M. Myers, Neha Shah, Colin Kremitzki, Tracie L. Miner, Holland Bradshaw-Cordum, Tina Graves, Glendoria Elliott, Matthew T. Hickenbotham, Wesley C. Warren, Mandeep Sekhon, Anu Desai, Jason Carter, Thomas Erb, Webb Miller, Prashant R. Sinha, Richard K. Wilson, Krista Haglund, John Spieth, Craig Pohl, Lisa Cook, John Douglas Mcpherson, Patrick Minx, Susan M. Rock, Ginger A. Fewell, Thomas A. Jones, Michael C. Becker, Yoram Shotland, Chunyan Wang, Jason Waligorski, Kyung Kim, Nicolas Berkowicz, Amy Kozlowicz-Reilly, Johar Ali, Xiaoqiu Huang, Shiaw Pyng Yang, Sean R. Eddy, Mikita Suyama, Francesca D. Ciccarelli, Martin Yoakum, John W. Wallis, Kristine M. Wylie, Maxim Radionenko, Donald Williams, Richard Harkins, Terrence S. Furey, Jacqueline E. Snider, Michael D. McLellan, Andrea Holmes, Shunfang Hou, Johanna Thompson, Andrew Van Brunt, Hui Sun, Teresa Davidson, Rekha Meyer, Feiyu Du, Jennifer Randall-Maher, Chad Tomlinson, Jon R. Armstrong, Robert S. Fulton, William E. Nash, Philip Ozersky, Marc Cotton, Sandra W. Clifton, Elisa Izaurralde, Lauren Caruso, Joanne O. Nelson, James M. Eldred, Sharhonda Swearengen-Shahid, Marco A. Marra, Caryn Wagner-McPherson, Cindy Strong, David Torrents, Phil Latreille, Peer Bork, Elaine R. Mardis, Andrew Levy, Evan E. Eichler, Laura Courtney, Anthony R. Harris, Jeremy Schmutz, Christine Nguyen, Dan Layman, James Taylor, Matt Cordes, Joseph T. Strong, Kimberly D. Delehaunty, Kymberlie H. Pepin, Scott Martinka, Tony Gaige, Charlene Pearman, and John R. Osborne

Subjects
Primates, RNA, Untranslated, Centromere, Molecular Sequence Data, Biology, Euchromatin, Chromosome 16, Chromosome 19, Gene Duplication, Animals, Humans, RNA, Messenger, Conserved Sequence, Genetics, Expressed Sequence Tags, Recombination, Genetic, Base Composition, Multidisciplinary, Polymorphism, Genetic, Base Sequence, Genetic Variation, Proteins, Genomics, Sequence Analysis, DNA, Physical Chromosome Mapping, Chromosome 17 (human), Chromosome 4, Chromosome 3, Chromosomes, Human, Pair 2, CpG Islands, Chromosome 20, Chromosomes, Human, Pair 4, Chromosome 21, Chromosome 22, Pseudogenes
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.

Published
2004

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