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1. 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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2. 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
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3. The DNA sequence and analysis of human chromosome 13

Author

A, Dunham, L H, Matthews, J, Burton, J L, Ashurst, K L, Howe, K J, Ashcroft, D M, Beare, D C, Burford, S E, Hunt, S, Griffiths-Jones, M C, Jones, S J, Keenan, K, Oliver, C E, Scott, R, Ainscough, J P, Almeida, K D, Ambrose, D T, Andrews, R I S, Ashwell, A K, Babbage, C L, Bagguley, J, Bailey, R, Bannerjee, K F, Barlow, K, Bates, H, Beasley, C P, Bird, S, Bray-Allen, A J, Brown, J Y, Brown, W, Burrill, C, Carder, N P, Carter, J C, Chapman, M E, Clamp, S Y, Clark, G, Clarke, C M, Clee, S C M, Clegg, V, Cobley, J E, Collins, N, Corby, G J, Coville, P, Deloukas, P, Dhami, I, Dunham, M, Dunn, M E, Earthrowl, A G, Ellington, L, Faulkner, A G, Frankish, J, Frankland, L, French, P, Garner, J, Garnett, J G R, Gilbert, C J, Gilson, J, Ghori, D V, Grafham, S M, Gribble, C, Griffiths, R E, Hall, S, Hammond, J L, Harley, E A, Hart, P D, Heath, P J, Howden, E J, Huckle, P J, Hunt, A R, Hunt, C, Johnson, D, Johnson, M, Kay, A M, Kimberley, A, King, G K, Laird, C J, Langford, S, Lawlor, D A, Leongamornlert, D M, Lloyd, C, Lloyd, J E, Loveland, J, Lovell, S, Martin, M, Mashreghi-Mohammadi, S J, McLaren, A, McMurray, S, Milne, M J F, Moore, T, Nickerson, S A, Palmer, A V, Pearce, A I, Peck, S, Pelan, B, Phillimore, K M, Porter, C M, Rice, S, Searle, H K, Sehra, R, Shownkeen, C D, Skuce, M, Smith, C A, Steward, N, Sycamore, J, Tester, D W, Thomas, A, Tracey, A, Tromans, B, Tubby, M, Wall, J M, Wallis, A P, West, S L, Whitehead, D L, Willey, L, Wilming, P W, Wray, M W, Wright, L, Young, A, Coulson, R, Durbin, T, Hubbard, J E, Sulston, S, Beck, D R, Bentley, J, Rogers, and M T, Ross

Subjects
RNA, Untranslated, Multidisciplinary, Chromosomes, Human, Pair 13, Genes, Genetics, Medical, Chromosome Mapping, Humans, Sequence Analysis, DNA, Physical Chromosome Mapping, Pseudogenes, Article
Abstract

Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.

Published
2004
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4. The DNA sequence and biological annotation of human chromosome 1

Author

S G, Gregory, K F, Barlow, K E, McLay, R, Kaul, D, Swarbreck, A, Dunham, C E, Scott, K L, Howe, K, Woodfine, C C A, Spencer, M C, Jones, C, Gillson, S, Searle, Y, Zhou, F, Kokocinski, L, McDonald, R, Evans, K, Phillips, A, Atkinson, R, Cooper, C, Jones, R E, Hall, T D, Andrews, C, Lloyd, R, Ainscough, J P, Almeida, K D, Ambrose, F, Anderson, R W, Andrew, R I S, Ashwell, K, Aubin, A K, Babbage, C L, Bagguley, J, Bailey, H, Beasley, G, Bethel, C P, Bird, S, Bray-Allen, J Y, Brown, A J, Brown, D, Buckley, J, Burton, J, Bye, C, Carder, J C, Chapman, S Y, Clark, G, Clarke, C, Clee, V, Cobley, R E, Collier, N, Corby, G J, Coville, J, Davies, R, Deadman, M, Dunn, M, Earthrowl, A G, Ellington, H, Errington, A, Frankish, J, Frankland, L, French, P, Garner, J, Garnett, L, Gay, M R J, Ghori, R, Gibson, L M, Gilby, W, Gillett, R J, Glithero, D V, Grafham, C, Griffiths, S, Griffiths-Jones, R, Grocock, S, Hammond, E S I, Harrison, E, Hart, E, Haugen, P D, Heath, S, Holmes, K, Holt, P J, Howden, A R, Hunt, S E, Hunt, G, Hunter, J, Isherwood, R, James, C, Johnson, D, Johnson, A, Joy, M, Kay, J K, Kershaw, M, Kibukawa, A M, Kimberley, A, King, A J, Knights, H, Lad, G, Laird, S, Lawlor, D A, Leongamornlert, D M, Lloyd, J, Loveland, J, Lovell, M J, Lush, R, Lyne, S, Martin, M, Mashreghi-Mohammadi, L, Matthews, N S W, Matthews, S, McLaren, S, Milne, S, Mistry, M J F, Moore, T, Nickerson, C N, O'Dell, K, Oliver, A, Palmeiri, S A, Palmer, A, Parker, D, Patel, A V, Pearce, A I, Peck, S, Pelan, K, Phelps, B J, Phillimore, R, Plumb, J, Rajan, C, Raymond, G, Rouse, C, Saenphimmachak, H K, Sehra, E, Sheridan, R, Shownkeen, S, Sims, C D, Skuce, M, Smith, C, Steward, S, Subramanian, N, Sycamore, A, Tracey, A, Tromans, Z, Van Helmond, M, Wall, J M, Wallis, S, White, S L, Whitehead, J E, Wilkinson, D L, Willey, H, Williams, L, Wilming, P W, Wray, Z, Wu, A, Coulson, M, Vaudin, J E, Sulston, R, Durbin, T, Hubbard, R, Wooster, I, Dunham, N P, Carter, G, McVean, M T, Ross, J, Harrow, M V, Olson, S, Beck, J, Rogers, D R, Bentley, R, Banerjee, S P, Bryant, D C, Burford, W D H, Burrill, S M, Clegg, P, Dhami, O, Dovey, L M, Faulkner, S M, Gribble, C F, Langford, R D, Pandian, K M, Porter, and E, Prigmore

Subjects
Sequence analysis, DNA Replication Timing, Molecular Sequence Data, Locus (genetics), Biology, Structural variation, Open Reading Frames, Chromosome 19, Gene Duplication, Humans, Disease, Selection, Genetic, Genetics, Recombination, Genetic, Multidisciplinary, Gene map, Base Sequence, Genetic Variation, Genome project, Genomics, Sequence Analysis, DNA, Genes, Chromosomes, Human, Pair 1, Human genome, Chromosome 21, Pseudogenes
Abstract

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.

Published
2005

5. Human chromosome 11 DNA sequence and analysis including novel gene identification

Author

Takehiko Itoh, Christopher Seaman, K F Barlow, Jane Rogers, Hideki Noguchi, Chad Nusbaum, Masahira Hattori, Michael Fitzgerald, Michael C. Zody, Evan E. Eichler, Yasushi Totoki, Robert Nicol, Andrew Zimmer, Carrie Sougnez, Yoshiyuki Sakaki, Elspeth A. Bruford, David B. Jaffe, Bruce W. Birren, Kurt LaButti, Atsushi Toyoda, Asao Fujiyama, Ken Dewar, Christina A. Cuomo, Dae-Won Kim, Tadayuki Takeda, Xinwei She, Xiaoping Yang, Todd D. Taylor, Toby Bloom, Christine Lloyd, Hong Seog Park, Yoko Kuroki, Eric S. Lander, and Jean L. Chang

Subjects
Genetics, Multidisciplinary, Chromosomes, Human, Pair 11, Molecular Sequence Data, Gene Expression, DNA, Sequence Analysis, DNA, Biology, Physical Chromosome Mapping, Receptors, Odorant, Chromosome 17 (human), Chromosome 15, Chromosome 16, Genes, Chromosome 19, Gene density, Humans, Chromosome 20, Chromosome 21, Chromosome 22
Abstract

Chromosome 11, although average in size, is one of the most gene- and disease-rich chromosomes in the human genome. Initial gene annotation indicates an average gene density of 11.6 genes per megabase, including 1,524 protein-coding genes, some of which were identified using novel methods, and 765 pseudogenes. One-quarter of the protein-coding genes shows overlap with other genes. Of the 856 olfactory receptor genes in the human genome, more than 40% are located in 28 single- and multi-gene clusters along this chromosome. Out of the 171 disorders currently attributed to the chromosome, 86 remain for which the underlying molecular basis is not yet known, including several mendelian traits, cancer and susceptibility loci. The high-quality data presented here--nearly 134.5 million base pairs representing 99.8% coverage of the euchromatic sequence--provide scientists with a solid foundation for understanding the genetic basis of these disorders and other biological phenomena.

Published
2005

6. The DNA sequence and analysis of human chromosome 6

Author

A. J. Mungall, S. A. Palmer, S. K. Sims, C. A. Edwards, J. L. Ashurst, L. Wilming, M. C. Jones, R. Horton, S. E. Hunt, C. E. Scott, J. G. R. Gilbert, M. E. Clamp, G. Bethel, S. Milne, R. Ainscough, J. P. Almeida, K. D. Ambrose, T. D. Andrews, R. I. S. Ashwell, A. K. Babbage, C. L. Bagguley, J. Bailey, R. Banerjee, D. J. Barker, K. F. Barlow, K. Bates, D. M. Beare, H. Beasley, O. Beasley, C. P. Bird, S. Blakey, S. Bray-Allen, J. Brook, A. J. Brown, J. Y. Brown, D. C. Burford, W. Burrill, J. Burton, C. Carder, N. P. Carter, J. C. Chapman, S. Y. Clark, G. Clark, C. M. Clee, S. Clegg, V. Cobley, R. E. Collier, J. E. Collins, L. K. Colman, N. R. Corby, G. J. Coville, K. M. Culley, P. Dhami, J. Davies, M. Dunn, M. E. Earthrowl, A. E. Ellington, K. A. Evans, L. Faulkner, M. D. Francis, A. Frankish, J. Frankland, L. French, P. Garner, J. Garnett, M. J. R. Ghori, L. M. Gilby, C. J. Gillson, R. J. Glithero, D. V. Grafham, M. Grant, S. Gribble, C. Griffiths, M. Griffiths, R. Hall, K. S. Halls, S. Hammond, J. L. Harley, E. A. Hart, P. D. Heath, R. Heathcott, S. J. Holmes, P. J. Howden, K. L. Howe, G. R. Howell, E. Huckle, S. J. Humphray, M. D. Humphries, A. R. Hunt, C. M. Johnson, A. A. Joy, M. Kay, S. J. Keenan, A. M. Kimberley, A. King, G. K. Laird, C. Langford, S. Lawlor, D. A. Leongamornlert, M. Leversha, C. R. Lloyd, D. M. Lloyd, J. E. Loveland, J. Lovell, S. Martin, M. Mashreghi-Mohammadi, G. L. Maslen, L. Matthews, O. T. McCann, S. J. McLaren, K. McLay, A. McMurray, M. J. F. Moore, J. C. Mullikin, D. Niblett, T. Nickerson, K. L. Novik, K. Oliver, E. K. Overton-Larty, A. Parker, R. Patel, A. V. Pearce, A. I. Peck, B. Phillimore, S. Phillips, R. W. Plumb, K. M. Porter, Y. Ramsey, S. A. Ranby, C. M. Rice, M. T. Ross, S. M. Searle, H. K. Sehra, E. Sheridan, C. D. Skuce, S. Smith, M. Smith, L. Spraggon, S. L. Squares, C. A. Steward, N. Sycamore, G. Tamlyn-Hall, J. Tester, A. J. Theaker, D. W. Thomas, A. Thorpe, A. Tracey, A. Tromans, B. Tubby, M. Wall, J. M. Wallis, A. P. West, S. S. White, S. L. Whitehead, H. Whittaker, A. Wild, D. J. Willey, T. E. Wilmer, J. M. Wood, P. W. Wray, J. C. Wyatt, L. Young, R. M. Younger, D. R. Bentley, A. Coulson, R. Durbin, T. Hubbard, J. E. Sulston, I. Dunham, J. Rogers, and S. Beck

Subjects
Multidisciplinary, Genes, RNA, Transfer, HLA-B Antigens, Genetic Diseases, Inborn, Animals, Humans, Chromosomes, Human, Pair 6, Exons, Sequence Analysis, DNA, Physical Chromosome Mapping, Pseudogenes
Abstract

Chromosome 6 is a metacentric chromosome that constitutes about 6% of the human genome. The finished sequence comprises 166,880,988 base pairs, representing the largest chromosome sequenced so far. The entire sequence has been subjected to high-quality manual annotation, resulting in the evidence-supported identification of 1,557 genes and 633 pseudogenes. Here we report that at least 96% of the protein-coding genes have been identified, as assessed by multi-species comparative sequence analysis, and provide evidence for the presence of further, otherwise unsupported exons/genes. Among these are genes directly implicated in cancer, schizophrenia, autoimmunity and many other diseases. Chromosome 6 harbours the largest transfer RNA gene cluster in the genome; we show that this cluster co-localizes with a region of high transcriptional activity. Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome.

Published
2003

7. 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

8. The DNA sequence of human chromosome 22

Author

L. Song, D. M. Lloyd, R. M. Swann, Ian F Korf, Lucinda Fulton, Carol Soderlund, I. D. Martyn, A. King, W Burrill, H. Wu, Y. Ramsey, Tracy Rohlfing, Mark T. Ross, Robert S. Fulton, L. Spragon, Darek Kedra, Laurens G. Wilming, Lisa Edelmann, James G. R. Gilbert, L. Williams, L. Chu, K. Fleming, J. Burgess, S. Shaull, M. N. Whiteley, Phil Latreille, Y. Qian, Ian Dunham, Dan Layman, Jennifer Lewis, A. C.C. Wong, Nobuyoshi Shimizu, Noriaki Aoki, Melanie M. Wall, Margaret A. Leversha, Ingegerd Fransson, M. Vaudin, Takashi Sasaki, Bernice E. Morrow, Graeme T Clark, S. Lewis, S. M. Clegg, H. Ramsay, A M Kimberley, S. J. Dodsworth, Melvin I. Simon, Stephan Beck, D. Conroy, Joseph A. Murray, Michele Clamp, Jan P. Dumanski, Christine Lloyd, Joseph L. McClay, P. Hu, Genwei Zhang, Adrienne Hunt, Steve Kenton, Antony V. Cox, Tina Graves, T. Nguyen, Lesley J. Rogers, Kazuhiko Kawasaki, Luc J. Smink, C. Dockree, J. M. Fey, J. C. Davis, U. J. Kim, Nigel P. Carter, Philip Ozersky, R. W. Heathcott, Richard Durbin, Ai Shintani, J Bailey, S. Bourne, Feng Chen, Harminder Sehra, Sulagna C. Saitta, G. Hall-Tamlyn, Charmain L. Wright, A. A. Garner, T. Do, Jane Rogers, Rebekah Hall, Joseph A. Bedell, Shuichi Asakawa, K Bates, J P Almeida, C. Hall, R. Pavitt, Charlotte G. Cole, K. Hinds, N Corby, V. Cobley, D. Pearson, Beverly S. Emanuel, C. Odell, Carl E.G. Bruder, Darren Grafham, Hiroki Kurahashi, Cordelia Langford, Dave Willey, T. E. Wilmer, David R. Bentley, I. Tapia, Hiroaki Shizuya, Myriam Peyrard, Tamim H. Shaikh, J K Kershaw, F. Fang, LaDeana W. Hillier, P. Loh, C L Bagguley, Tim Hubbard, John Sulston, Z. Wang, Kazunori Shibuya, R. E. Collier, Melanie E. Goward, K F Barlow, Richard Bruskiewich, M. L. Budarf, Yuan Chen, Kathryn L. Evans, Sarah E. Hunt, Judy S. Crabtree, Benjamin Phillimore, Stuart McLaren, M Mashreghi-Mohammadi, S. Chissoe, D. Willingham, J. Hawkins, Huaqin Pan, Q. Wang, Michelle Smith, H. Bradshaw, C. Walker, C. D. Skuce, Jim White, Amanda McMurray, Lucy Matthews, John Burton, Patricia Wohldmann, G. Bemis, O. Beasley, Robert H. Waterston, David W. Johnson, Elaine R. Mardis, H. Williamson, D. Buck, Yuhang Wang, Andrew D. Ellington, Zijin Du, Eyal Seroussi, Susumu Mitsuyama, A. Wamsley, Joanne O. Nelson, Y. Yoshizaki, K. P. O'Brien, H. I. Lao, R. Connor, S. Smalley, Anne Bridgeman, R Ainscough, Matthew Jones, Elisabeth Dawson, Joanna Collins, Pawandeep Dhami, S. Holmes, S. Phan, L. Ray, Angela Dorman, O. T. McCann, Christine P. Bird, Sarah Milne, Q. Ren, B. J. Mortimore, Carol Scott, Lisa French, Shuk-Mei Ho, G. J. Coville, Richard K. Wilson, Patrick Minx, Ziyun Yao, Jun Kudoh, David Beare, Charles A. Steward, Hongshing Lai, Alexander Johnson, Scott M. Williams, Robert W. Plumb, M. Zhan, Y. Fu, A. V. Pearce, S. Blakey, D. Goela, Gavin K. Laird, N. Miller, Matt Cordes, Kymberlie H. Pepin, Sam Phillips, David Bentley, Stéphane Deschamps, A. Do, Shaoping Lin, Shinsei Minoshima, Bruce A. Roe, Axin Hua, S. Qi, C Carder, Paul Scheet, Mark Griffiths, A K Babbage, J. M. Wallis, Heather E. McDermid, Eda Malaj, D. Sloan, and K. Kemp

Subjects
Multidisciplinary, Sequence analysis, Chromosomes, Human, Pair 22, Molecular Sequence Data, Nucleic acid sequence, Gene Dosage, Chromosome Mapping, Computational biology, DNA, Sequence Analysis, DNA, Biology, ENCODE, Genome, Complete sequence, Mice, Species Specificity, Human Genome Project, Animals, Humans, Human genome, Sequence (medicine), Genomic organization, Repetitive Sequences, Nucleic Acid
Abstract

Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.

Published
1999

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