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8 results on '"I, Dunham"'

1. Finishing the finished human chromosome 22 sequence.

Author

Cole CG, McCann OT, Collins JE, Oliver K, Willey D, Gribble SM, Yang F, McLaren K, Rogers J, Ning Z, Beare DM, and Dunham I

Subjects
Base Sequence, Chromosome Mapping, Chromosomes, Artificial, Bacterial genetics, Humans, Chromosomes, Human, Pair 22, Genome, Human, Sequence Analysis, DNA
Abstract

Background: Although the human genome sequence was declared complete in 2004, the sequence was interrupted by 341 gaps of which 308 lay in an estimated approximately 28 Mb of euchromatin. While these gaps constitute only approximately 1% of the sequence, knowledge of the full complement of human genes and regulatory elements is incomplete without their sequences., Results: We have used a combination of conventional chromosome walking (aided by the availability of end sequences) in fosmid and bacterial artificial chromosome (BAC) libraries, whole chromosome shotgun sequencing, comparative genome analysis and long PCR to finish 8 of the 11 gaps in the initial chromosome 22 sequence. In addition, we have patched four regions of the initial sequence where the original clones were found to be deleted, or contained a deletion allele of a known gene, with a further 126 kb of new sequence. Over 1.018 Mb of new sequence has been generated to extend into and close the gaps, and we have annotated 16 new or extended gene structures and one pseudogene., Conclusion: Thus, we have made significant progress to completing the sequence of the euchromatic regions of human chromosome 22 using a combination of detailed approaches. Our experience suggests that substantial work remains to close the outstanding gaps in the human genome sequence.

Published
2008
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2. Initial sequencing and analysis of the human genome.

Author

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, and Szustakowki J

Subjects
Animals, Chromosome Mapping, Conserved Sequence, CpG Islands, DNA Transposable Elements, Databases, Factual, Drug Industry, Evolution, Molecular, Forecasting, GC Rich Sequence, Gene Duplication, Genes, Genetic Diseases, Inborn, Genetics, Medical, Humans, Mutation, Private Sector, Proteins genetics, Proteome, Public Sector, RNA genetics, Repetitive Sequences, Nucleic Acid, Species Specificity, Genome, Human, Human Genome Project, Sequence Analysis, DNA methods
Abstract

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Published
2001
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3. An SNP map of human chromosome 22.

Author

Mullikin JC, Hunt SE, Cole CG, Mortimore BJ, Rice CM, Burton J, Matthews LH, Pavitt R, Plumb RW, Sims SK, Ainscough RM, Attwood J, Bailey JM, Barlow K, Bruskiewich RM, Butcher PN, Carter NP, Chen Y, Clee CM, Coggill PC, Davies J, Davies RM, Dawson E, Francis MD, Joy AA, Lamble RG, Langford CF, Macarthy J, Mall V, Moreland A, Overton-Larty EK, Ross MT, Smith LC, Steward CA, Sulston JE, Tinsley EJ, Turney KJ, Willey DL, Wilson GD, McMurray AA, Dunham I, Rogers J, and Bentley DR

Subjects
Cell Line, Chromosome Mapping methods, Evaluation Studies as Topic, Gene Library, Genome, Human, Humans, Sequence Alignment, Chromosomes, Human, Pair 22, Polymorphism, Single Nucleotide, Sequence Analysis, DNA methods
Abstract

The human genome sequence will provide a reference for measuring DNA sequence variation in human populations. Sequence variants are responsible for the genetic component of individuality, including complex characteristics such as disease susceptibility and drug response. Most sequence variants are single nucleotide polymorphisms (SNPs), where two alternate bases occur at one position. Comparison of any two genomes reveals around 1 SNP per kilobase. A sufficiently dense map of SNPs would allow the detection of sequence variants responsible for particular characteristics on the basis that they are associated with a specific SNP allele. Here we have evaluated large-scale sequencing approaches to obtaining SNPs, and have constructed a map of 2,730 SNPs on human chromosome 22. Most of the SNPs are within 25 kilobases of a transcribed exon, and are valuable for association studies. We have scaled up the process, detecting over 65,000 SNPs in the genome as part of The SNP Consortium programme, which is on target to build a map of 1 SNP every 5 kilobases that is integrated with the human genome sequence and that is freely available in the public domain.

Published
2000
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4. The DNA sequence of human chromosome 22.

Author

Dunham I, Shimizu N, Roe BA, Chissoe S, Hunt AR, Collins JE, Bruskiewich R, Beare DM, Clamp M, Smink LJ, Ainscough R, Almeida JP, Babbage A, Bagguley C, Bailey J, Barlow K, Bates KN, Beasley O, Bird CP, Blakey S, Bridgeman AM, Buck D, Burgess J, Burrill WD, and O'Brien KP

Subjects
Animals, Chromosome Mapping methods, DNA, Gene Dosage, Humans, Mice, Molecular Sequence Data, Repetitive Sequences, Nucleic Acid, Species Specificity, Chromosomes, Human, Pair 22, Human Genome Project, Sequence Analysis, DNA
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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5. Physical mapping of chromosome 6: a strategy for the rapid generation of sequence-ready contigs.

Author

Mungall AJ, Edwards CA, Ranby SA, Humphray SJ, Heathcott RW, Clee CM, East CL, Holloway E, Butler AP, Langford CF, Gwilliam R, Rice KM, Maslen GL, Carter NP, Ross MT, Deloukas P, Bentley DR, and Dunham I

Subjects
Cloning, Molecular, DNA Fingerprinting methods, DNA, Complementary, Gene Expression, Genetic Markers, Genetic Vectors, Humans, Chromosome Mapping methods, Chromosomes, Human, Pair 6 genetics, Sequence Analysis, DNA methods
Abstract

The development of radiation hybrid (RH) mapping (Cox et al., 1990) and the availability of large numbers of STS markers, together with extensive bacterial clone resources provided a means to accelerate the process of mapping a human chromosome and preparing bacterial clone contigs ready to sequence. Our aim is to construct physical clone maps covering those regions of chromosome 6 that are not currently extensively mapped, and use these to determine the DNA sequence of the whole chromosome. We report here a strategy which initially involves establishing a high density framework map using RH mapping. The framework markers are then used for the identification of bacterial genomic clones covering the chromosome. The bacterial clones are analysed by restriction enzyme fingerprinting and STS-content analysis to identify sequence-ready contigs. Contig gap closure will also be performed by clone walking.

Published
1996
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6. 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

7. 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

8. 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

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