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1. 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

2. 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

3. 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

4. Erratum: 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, R. Banerjee, H. Beasley, G. Bethel, C. P. Bird, S. Bray-Allen, J. Y. Brown, A. J. Brown, S. P. Bryant, D. Buckley, D. C. Burford, W. D. H. Burrill, J. Burton, J. Bye, C. Carder, J. C. Chapman, S. Y. Clark, G. Clarke, C. Clee, S. M. Clegg, V. Cobley, R. E. Collier, N. Corby, G. J. Coville, J. Davies, R. Deadman, P. Dhami, O. Dovey, M. Dunn, M. Earthrowl, A. G. Ellington, H. Errington, L. M. Faulkner, 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, S. M. Gribble, 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, C. F. Langford, 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. M. oore, T. Nickerson, C. N. O'Dell, K. Oliver, A. Palmeiri, S. A. Palmer, R. D. Pandian, A. Parker, D. Patel, A. V. Pearce, A. I. Peck, S. Pelan, K. Phelps, B. J. Phillimore, R. Plumb, K. M. Porter, E. Prigmore, 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, and D. R. Bentley

Subjects
Genetics, Annotation, Multidisciplinary, Chromosome (genetic algorithm), Gribble, Biology, biology.organism_classification, DNA sequencing
Abstract

Nature 441, 315–321 (2006) We inadvertently omitted the names of the following authors: 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.

Published
2006

5. Erratum: correction: The DNA sequence of human chromosome 22

Author

Nobuyoshi Shimizu, Bruce A. Roe, S. Chissoe, and I. Dunham

Subjects
Multidisciplinary, media_common.quotation_subject, Art, Chromosome 22, Genealogy, DNA sequencing, media_common
Abstract

Nature 402, 489–495 (1999) The names of the following authors were omitted from the complete list at the end of the Article: P. Wilkinson (The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK); A. Bodenteich, K. Hartman, X. Hu, A. S. Khan, L. Lane, Y. Tilahun & H. Wright (Department of Chemistry and Biochemistry, The University of Oklahoma, 620 Parrington Oval, Room 311, Norman, Oklahoma 73019, USA).

Published
2000

6. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Author

Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, and de Jong PJ

Subjects
Chromatin genetics, Chromatin metabolism, Chromatin Immunoprecipitation, Conserved Sequence genetics, DNA Replication, Evolution, Molecular, Exons genetics, Genetic Variation genetics, Heterozygote, Histones metabolism, Humans, Pilot Projects, Protein Binding, RNA, Messenger genetics, RNA, Untranslated genetics, Transcription Factors metabolism, Transcription Initiation Site, Genome, Human genetics, Genomics, Regulatory Sequences, Nucleic Acid genetics, Transcription, Genetic genetics
Abstract

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Published
2007
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7. The DNA sequence and biological annotation of human chromosome 1.

Author

Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D, Dunham A, Scott CE, Howe KL, Woodfine K, Spencer CC, Jones MC, Gillson C, Searle S, Zhou Y, Kokocinski F, McDonald L, Evans R, Phillips K, Atkinson A, Cooper R, Jones C, Hall RE, Andrews TD, Lloyd C, Ainscough R, Almeida JP, Ambrose KD, Anderson F, Andrew RW, Ashwell RI, Aubin K, Babbage AK, Bagguley CL, Bailey J, Beasley H, Bethel G, Bird CP, Bray-Allen S, Brown JY, Brown AJ, Buckley D, Burton J, Bye J, Carder C, Chapman JC, Clark SY, Clarke G, Clee C, Cobley V, Collier RE, Corby N, Coville GJ, Davies J, Deadman R, Dunn M, Earthrowl M, Ellington AG, Errington H, Frankish A, Frankland J, French L, Garner P, Garnett J, Gay L, Ghori MR, Gibson R, Gilby LM, Gillett W, Glithero RJ, Grafham DV, Griffiths C, Griffiths-Jones S, Grocock R, Hammond S, Harrison ES, Hart E, Haugen E, Heath PD, Holmes S, Holt K, Howden PJ, Hunt AR, Hunt SE, Hunter G, Isherwood J, James R, Johnson C, Johnson D, Joy A, Kay M, Kershaw JK, Kibukawa M, Kimberley AM, King A, Knights AJ, Lad H, Laird G, Lawlor S, Leongamornlert DA, Lloyd DM, Loveland J, Lovell J, Lush MJ, Lyne R, Martin S, Mashreghi-Mohammadi M, Matthews L, Matthews NS, McLaren S, Milne S, Mistry S, Moore MJ, Nickerson T, O'Dell CN, Oliver K, Palmeiri A, Palmer SA, Parker A, Patel D, Pearce AV, Peck AI, Pelan S, Phelps K, Phillimore BJ, Plumb R, Rajan J, Raymond C, Rouse G, Saenphimmachak C, Sehra HK, Sheridan E, Shownkeen R, Sims S, Skuce CD, Smith M, Steward C, Subramanian S, Sycamore N, Tracey A, Tromans A, Van Helmond Z, Wall M, Wallis JM, White S, Whitehead SL, Wilkinson JE, Willey DL, Williams H, Wilming L, Wray PW, Wu Z, Coulson A, Vaudin M, Sulston JE, Durbin R, Hubbard T, Wooster R, Dunham I, Carter NP, McVean G, Ross MT, Harrow J, Olson MV, Beck S, Rogers J, Bentley DR, Banerjee R, Bryant SP, Burford DC, Burrill WD, Clegg SM, Dhami P, Dovey O, Faulkner LM, Gribble SM, Langford CF, Pandian RD, Porter KM, and Prigmore E

Subjects
Base Sequence, DNA Replication Timing, Disease, Gene Duplication, Genes genetics, Genetic Variation genetics, Genomics, Humans, Molecular Sequence Data, Open Reading Frames genetics, Pseudogenes genetics, Recombination, Genetic genetics, Selection, Genetic, Sequence Analysis, DNA, Chromosomes, Human, Pair 1 genetics
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
2006
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8. DNA sequence and analysis of human chromosome 9.

Author

Humphray SJ, Oliver K, Hunt AR, Plumb RW, Loveland JE, Howe KL, Andrews TD, Searle S, Hunt SE, Scott CE, Jones MC, Ainscough R, Almeida JP, Ambrose KD, Ashwell RI, Babbage AK, Babbage S, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beasley H, Beasley O, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burford D, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Chen Y, Clarke G, Clark SY, Clee CM, Clegg S, Collier RE, Corby N, Crosier M, Cummings AT, Davies J, Dhami P, Dunn M, Dutta I, Dyer LW, Earthrowl ME, Faulkner L, Fleming CJ, Frankish A, Frankland JA, French L, Fricker DG, Garner P, Garnett J, Ghori J, Gilbert JG, Glison C, Grafham DV, Gribble S, Griffiths C, Griffiths-Jones S, Grocock R, Guy J, Hall RE, Hammond S, Harley JL, Harrison ES, Hart EA, Heath PD, Henderson CD, Hopkins BL, Howard PJ, Howden PJ, Huckle E, Johnson C, Johnson D, Joy AA, Kay M, Keenan S, Kershaw JK, Kimberley AM, King A, Knights A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd C, Lloyd DM, Lovell J, Martin S, Mashreghi-Mohammadi M, Matthews L, McLaren S, McLay KE, McMurray A, Milne S, Nickerson T, Nisbett J, Nordsiek G, Pearce AV, Peck AI, Porter KM, Pandian R, Pelan S, Phillimore B, Povey S, Ramsey Y, Rand V, Scharfe M, Sehra HK, Shownkeen R, Sims SK, Skuce CD, Smith M, Steward CA, Swarbreck D, Sycamore N, Tester J, Thorpe A, Tracey A, Tromans A, Thomas DW, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Williams SA, Wilming L, Wray PW, Young L, Ashurst JL, Coulson A, Blöcker H, Durbin R, Sulston JE, Hubbard T, Jackson MJ, Bentley DR, Beck S, Rogers J, and Dunham I

Subjects
Base Composition, Euchromatin genetics, Evolution, Molecular, Female, Gene Duplication, Genes, Duplicate genetics, Genetic Variation genetics, Genetics, Medical, Genomics, Heterochromatin genetics, Humans, Male, Neoplasms genetics, Neurodegenerative Diseases genetics, Pseudogenes genetics, Sequence Analysis, DNA, Sex Determination Processes, Chromosomes, Human, Pair 9 genetics, Genes, Physical Chromosome Mapping
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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9. The DNA sequence and analysis of human chromosome 13.

Author

Dunham A, Matthews LH, Burton J, Ashurst JL, Howe KL, Ashcroft KJ, Beare DM, Burford DC, Hunt SE, Griffiths-Jones S, Jones MC, Keenan SJ, Oliver K, Scott CE, Ainscough R, Almeida JP, Ambrose KD, Andrews DT, Ashwell RI, Babbage AK, Bagguley CL, Bailey J, Bannerjee R, Barlow KF, Bates K, Beasley H, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burrill W, Carder C, Carter NP, Chapman JC, Clamp ME, Clark SY, Clarke G, Clee CM, Clegg SC, Cobley V, Collins JE, Corby N, Coville GJ, Deloukas P, Dhami P, Dunham I, Dunn M, Earthrowl ME, Ellington AG, Faulkner L, Frankish AG, Frankland J, French L, Garner P, Garnett J, Gilbert JG, Gilson CJ, Ghori J, Grafham DV, Gribble SM, Griffiths C, Hall RE, Hammond S, Harley JL, Hart EA, Heath PD, Howden PJ, Huckle EJ, Hunt PJ, Hunt AR, Johnson C, Johnson D, Kay M, Kimberley AM, King A, Laird GK, Langford CJ, Lawlor S, Leongamornlert DA, Lloyd DM, Lloyd C, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, McLaren SJ, McMurray A, Milne S, Moore MJ, Nickerson T, Palmer SA, Pearce AV, Peck AI, Pelan S, Phillimore B, Porter KM, Rice CM, Searle S, Sehra HK, Shownkeen R, Skuce CD, Smith M, Steward CA, Sycamore N, Tester J, Thomas DW, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Wilming L, Wray PW, Wright MW, Young L, Coulson A, Durbin R, Hubbard T, Sulston JE, Beck S, Bentley DR, Rogers J, and Ross MT

Subjects
Chromosome Mapping, Genetics, Medical, Humans, Pseudogenes genetics, RNA, Untranslated genetics, Sequence Analysis, DNA, Chromosomes, Human, Pair 13 genetics, Genes genetics, Physical Chromosome Mapping
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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10. The DNA sequence and analysis of human chromosome 6.

Author

Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, Gilbert JG, Clamp ME, Bethel G, Milne S, Ainscough R, Almeida JP, Ambrose KD, Andrews TD, Ashwell RI, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beare DM, Beasley H, Beasley O, Bird CP, Blakey S, Bray-Allen S, Brook J, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Clark SY, Clark G, Clee CM, Clegg S, Cobley V, Collier RE, Collins JE, Colman LK, Corby NR, Coville GJ, Culley KM, Dhami P, Davies J, Dunn M, Earthrowl ME, Ellington AE, Evans KA, Faulkner L, Francis MD, Frankish A, Frankland J, French L, Garner P, Garnett J, Ghori MJ, Gilby LM, Gillson CJ, Glithero RJ, Grafham DV, Grant M, Gribble S, Griffiths C, Griffiths M, Hall R, Halls KS, Hammond S, Harley JL, Hart EA, Heath PD, Heathcott R, Holmes SJ, Howden PJ, Howe KL, Howell GR, Huckle E, Humphray SJ, Humphries MD, Hunt AR, Johnson CM, Joy AA, Kay M, Keenan SJ, Kimberley AM, King A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd CR, Lloyd DM, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, Maslen GL, Matthews L, McCann OT, McLaren SJ, McLay K, McMurray A, Moore MJ, Mullikin JC, Niblett D, Nickerson T, Novik KL, Oliver K, Overton-Larty EK, Parker A, Patel R, Pearce AV, Peck AI, Phillimore B, Phillips S, Plumb RW, Porter KM, Ramsey Y, Ranby SA, Rice CM, Ross MT, Searle SM, Sehra HK, Sheridan E, Skuce CD, Smith S, Smith M, Spraggon L, Squares SL, Steward CA, Sycamore N, Tamlyn-Hall G, Tester J, Theaker AJ, Thomas DW, Thorpe A, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, White SS, Whitehead SL, Whittaker H, Wild A, Willey DJ, Wilmer TE, Wood JM, Wray PW, Wyatt JC, Young L, Younger RM, Bentley DR, Coulson A, Durbin R, Hubbard T, Sulston JE, Dunham I, Rogers J, and Beck S

Subjects
Animals, Exons genetics, Genetic Diseases, Inborn genetics, HLA-B Antigens genetics, Humans, Pseudogenes genetics, RNA, Transfer genetics, Sequence Analysis, DNA, Chromosomes, Human, Pair 6 genetics, Genes genetics, Physical Chromosome Mapping
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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11. A first-generation linkage disequilibrium map of human chromosome 22.

Author

Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lõhmussaar E, Zernant J, Tõnisson N, Remm M, Mägi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR, and Dunham I

Subjects
Founder Effect, Gene Frequency, Haplotypes genetics, Humans, Pedigree, Polymorphism, Genetic genetics, Recombination, Genetic, Chromosome Mapping, Chromosomes, Human, Pair 22 genetics, Linkage Disequilibrium genetics
Abstract

DNA sequence variants in specific genes or regions of the human genome are responsible for a variety of phenotypes such as disease risk or variable drug response. These variants can be investigated directly, or through their non-random associations with neighbouring markers (called linkage disequilibrium (LD)). Here we report measurement of LD along the complete sequence of human chromosome 22. Duplicate genotyping and analysis of 1,504 markers in Centre d'Etude du Polymorphisme Humain (CEPH) reference families at a median spacing of 15 kilobases (kb) reveals a highly variable pattern of LD along the chromosome, in which extensive regions of nearly complete LD up to 804 kb in length are interspersed with regions of little or no detectable LD. The LD patterns are replicated in a panel of unrelated UK Caucasians. There is a strong correlation between high LD and low recombination frequency in the extant genetic map, suggesting that historical and contemporary recombination rates are similar. This study demonstrates the feasibility of developing genome-wide maps of LD.

Published
2002
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12. 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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13. The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X.

Author

Bentley DR, Deloukas P, Dunham A, French L, Gregory SG, Humphray SJ, Mungall AJ, Ross MT, Carter NP, Dunham I, Scott CE, Ashcroft KJ, Atkinson AL, Aubin K, Beare DM, Bethel G, Brady N, Brook JC, Burford DC, Burrill WD, Burrows C, Butler AP, Carder C, Catanese JJ, Clee CM, Clegg SM, Cobley V, Coffey AJ, Cole CG, Collins JE, Conquer JS, Cooper RA, Culley KM, Dawson E, Dearden FL, Durbin RM, de Jong PJ, Dhami PD, Earthrowl ME, Edwards CA, Evans RS, Gillson CJ, Ghori J, Green L, Gwilliam R, Halls KS, Hammond S, Harper GL, Heathcott RW, Holden JL, Holloway E, Hopkins BL, Howard PJ, Howell GR, Huckle EJ, Hughes J, Hunt PJ, Hunt SE, Izmajlowicz M, Jones CA, Joseph SS, Laird G, Langford CF, Lehvaslaiho MH, Leversha MA, McCann OT, McDonald LM, McDowall J, Maslen GL, Mistry D, Moschonas NK, Neocleous V, Pearson DM, Phillips KJ, Porter KM, Prathalingam SR, Ramsey YH, Ranby SA, Rice CM, Rogers J, Rogers LJ, Sarafidou T, Scott DJ, Sharp GJ, Shaw-Smith CJ, Smink LJ, Soderlund C, Sotheran EC, Steingruber HE, Sulston JE, Taylor A, Taylor RG, Thorpe AA, Tinsley E, Warry GL, Whittaker A, Whittaker P, Williams SH, Wilmer TE, Wooster R, and Wright CL

Subjects
Humans, Chromosomes, Human, Pair 1, Chromosomes, Human, Pair 10, Chromosomes, Human, Pair 13, Chromosomes, Human, Pair 20, Chromosomes, Human, Pair 6, Contig Mapping, Genome, Human, X Chromosome
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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14. 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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15. 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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