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5 results on '"Andrew Dunham"'

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. A physical map of the human genome

Author

Anuradha Madan, S. Naylor, Kami Dixon, Wonhee Jang, John Douglas Mcpherson, Asao Fujiyama, Simon G. Gregory, Jacquelyn R. Idol, Takashi Sasaki, David Haussler, Hong Seok Park, Jun Kudoh, Ai Shintani, Erica Sodergren, Barbara J. Trask, Norma J. Nowak, Gerald Nyakatura, Gregory D. Schuler, Shinsei Minoshima, Raluca Yonescu, J. Harley Gorrell, Roland Heilig, Vivian G. Cheung, Steve Scherer, Kazunori Shibuya, Hsiu Chuan Chen, Olivia Velasquez, Scot Kennedy, Leroy Hood, Richard Reinhardt, Lucía Ramírez, Richard M. Myers, Atsushi Toyoda, Tetsushi Yada, Nobuyoshi Shimizu, Eric D. Green, Dawn Garcia, Owen T. McCann, Kate Montgomery, Asif T. Chinwalla, Elaine R. Mardis, Peter Seranski, Valerie Maduro, W. James Kent, Cynthia Friedman, Kazutoyo Osoegawa, Carol Scott, Juliane Ramser, Marco A. Marra, Caryn Wagner-McPherson, William B. Barbazuk, Thomas Reid, Mandeep Sekhon, Lee Rowen, Nancy E. Stone, Richard A. Gibbs, Lisa French, Trevor Hawkins, J. de Jong, Jin Shang, Tamara A. Kucaba, Robert H. Waterston, Adam Whittaker, Jeremy Schmutz, Richard K. Wilson, Kristine M. Wylie, Masahira Hattori, Atsushi Shimizu, Ilan R. Kirsch, Jean Weissenbach, Céline Hoff, Julie R. Korenberg, Markus Schilhabel, Sanja Rogic, David R. Bentley, Shuichi Asakawa, Paul E. Tabor, Terrence S. Furey, Kerstin P. Clerc-Blankenburg, Raju Kucherlapati, Joseph J. Catanese, Shizhen Qin, Annemarie Poustka, Suzanne Emerling, Reiner Siebert, Brigitte Schlegelberger, Hans Lehrach, Monica Dors, Thomas Brüls, Hillary Massa, R Evans, Steven J.M. Jones, Gernot Gloeckner, Elbert Branscomb, Andrew Dunham, Jane L. Holden, Xiao Ning Chen, Ashley Miller, Jan Fang Cheng, André Rosenthal, John W. Wallis, Eunice Lee, Gaiping Wen, Sean Humphray, Carol Soderlund, Robert S. Fulton, Yoshiyuki Sakaki, David R. Cox, Norman A. Doggett, Kazuhiko Kawasaki, Anne S. Olsen, Graeme Bethel, and LaDeana W. Hillier

Subjects
Genetics, Cancer genome sequencing, Whole genome sequencing, Chromosomes, Artificial, Bacterial, Multidisciplinary, Contig, Genome, Human, Computational biology, Genome project, Biology, ENCODE, DNA Fingerprinting, Genome, Chimpanzee genome project, Contig Mapping, Gene Duplication, Humans, Cloning, Molecular, In Situ Hybridization, Fluorescence, Repetitive Sequences, Nucleic Acid, Reference genome
Abstract

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

Published
2001
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3. Contigs Built with Fingerprints, Markers, and FPC V4.7

Author

Lisa French, Andrew Dunham, Sean Humphray, and Carol Soderlund

Subjects
Genetic Markers, Databases, Factual, DNA Fragmentation, Computational biology, Biology, Contig Mapping, Methods, Genetics, Humans, Computer Simulation, Genetics (clinical), Internet, Models, Statistical, Chromosomes, Human, Pair 13, Contig, Gene map, Chromosomes, Human, Pair 10, Physical Chromosome Mapping, Computational Biology, food and beverages, Numerical Analysis, Computer-Assisted, DNA Fingerprinting, Human sequence, Fingerprint database, DNA profiling, Chromosomes, Human, Pair 9, Software
Abstract

Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.

Published
2000
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4. High-Resolution Landmark Framework for the Sequence-Ready Mapping of Xq23–q26.1

Author

Gareth Maslen, Elizabeth C. Sotheran, Rhian Gwilliam, Pawandeep Dhami, Margaret A. Leversha, Carol Scott, S. M. Clegg, Mark T. Ross, Alison J. Coffey, Andrew Dunham, Sarah E. Hunt, David R. Bentley, Gareth R. Howell, Elizabeth J. Huckle, Cari Soderlund, Helen E. Steingruber, and Paul Hunt

Subjects
Genetic Markers, Yeast artificial chromosome, Letter, X Chromosome, Sequence analysis, Computational biology, Biology, Contig Mapping, Genetics, medicine, Humans, Chromosomes, Artificial, Yeast, In Situ Hybridization, Fluorescence, Genetics (clinical), X chromosome, medicine.diagnostic_test, Contig, Chromosome Mapping, Sequence Analysis, DNA, Electrophoresis, Gel, Pulsed-Field, Blotting, Southern, Genetic marker, Female, Human genome, Fluorescence in situ hybridization
Abstract

We have established a landmark framework map over 20–25 Mb of the long arm of the human X chromosome using yeast artificial chromosome (YAC) clones. The map has approximately one landmark per 45 kb of DNA and stretches from DXS7531 in proximal Xq23 to DXS895 in proximal Xq26, connecting to published framework maps on its proximal and distal sides. There are three gaps in the framework map resulting from the failure to obtain clone coverage from the YAC resources available. Estimates of the maximum sizes of these gaps have been obtained. The four YAC contigs have been positioned and oriented using somatic-cell hybrids and fluorescence in situ hybridization, and the largest is estimated to cover ∼15 Mb of DNA. The framework map is being used to assemble a sequence-ready map in large-insert bacterial clones, as part of an international effort to complete the sequence of the X chromosome. PAC and BAC contigs currently cover 18 Mb of the region, and from these, 12 Mb of finished sequence is available.

Published
1999
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5. The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X

Author

Nigel P. Carter, Ian Dunham, A. L. Atkinson, Jaime Hughes, M. Izmajlowicz, Richard Durbin, Mark T. Ross, Soumi Joseph, Adam Butler, G. L. Harper, Louise McDonald, Rohan Taylor, W. D. Burrill, Graeme Bethel, S. R. Prathalingam, David R. Bentley, Theologia Sarafidou, Vassos Neocleous, John Sulston, F. L. Dearden, C. M. Rice, E. C. Sotheran, Carol A. Edwards, S. M. Clegg, N. Brady, T. E. Wilmer, B. L. Hopkins, G. L. Maslen, Simon G. Gregory, Owen T. McCann, Andrew J. Mungall, M.A. Leversha, Elisabeth Dawson, K. J. Phillips, R Evans, A. A. Thorpe, C M Clee, Cordelia Langford, E. J. Huckle, Helen E. Steingruber, Carol Scott, Y. H. Ramsey, John E. Collins, Gareth R. Howell, Adam Whittaker, M. E. Earthrowl, M. H. Lehvaslaiho, Pamela Whittaker, G. Laird, J. C. Brook, D. J. Scott, K. J. Ashcroft, S. H. Williams, Georgina Warry, Nicholas K. Moschonas, D. M. Pearson, K. S. Halls, C. L. Wright, R. W. Heathcott, C. Carder, Jane L. Holden, D. C. Burford, S. A. Ranby, P. J. Howard, K. Aubin, K. M. Porter, E. Holloway, R. A. Cooper, A. J. Coffey, David Beare, J. J. Catanese, C. A. Jones, J. S. Conquer, J. Ghori, E. J. Tinsley, Lisa French, Charlotte G. Cole, P. D. Dhami, K. M. Culley, Christopher J. Gillson, Sarah E. Hunt, Rhian Gwilliam, Panagiotis Deloukas, V. Cobley, Carol Soderlund, A. Taylor, G. J. Sharp, Luc J. Smink, S. Hammond, Andrew Dunham, L. J. Rogers, D. Mistry, Richard Wooster, P. J. De Jong, Jane Rogers, P. J. Hunt, L D Green, C. J. Shaw-Smith, Jennifer McDowall, C. Burrows, and Sean Humphray

Subjects
Genetics, Multidisciplinary, X Chromosome, Contig, Gene map, Chromosomes, Human, Pair 13, Chromosomes, Human, Pair 10, Genome, Human, Chromosomes, Human, Pair 20, food and beverages, Chromosome, Computational biology, Biology, Genome, Contig Mapping, Gene mapping, Chromosomes, Human, Pair 1, Humans, Chromosomes, Human, Pair 6, X chromosome, Genomic organization
Abstract

We constructed maps for eight chromosomes (1, 6, 9, 10, 13, 20, X and (previously) 22), representing one-third of the genome, by building landmark maps, isolating bacterial clones and assembling contigs. By this approach, we could establish the long-range organization of the maps early in the project, and all contig extension, gap closure and problem-solving was simplified by containment within local regions. The maps currently represent more than 94% of the euchromatic (gene-containing) regions of these chromosomes in 176 contigs, and contain 96% of the chromosome-specific markers in the human gene map. By measuring the remaining gaps, we can assess chromosome length and coverage in sequenced clones.

Published
2001

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