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1. 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

2. The DNA sequence and comparative analysis of human chromosome 10

Author

P, Deloukas, M E, Earthrowl, D V, Grafham, M, Rubenfield, L, French, C A, Steward, S K, Sims, M C, Jones, S, Searle, C, Scott, K, Howe, S E, Hunt, T D, Andrews, J G R, Gilbert, D, Swarbreck, J L, Ashurst, A, Taylor, J, Battles, C P, Bird, R, Ainscough, J P, Almeida, R I S, Ashwell, K D, Ambrose, A K, Babbage, C L, Bagguley, J, Bailey, R, Banerjee, K, Bates, H, Beasley, S, Bray-Allen, A J, Brown, J Y, Brown, D C, Burford, W, Burrill, J, Burton, P, Cahill, D, Camire, N P, Carter, J C, Chapman, S Y, Clark, G, Clarke, C M, Clee, S, Clegg, N, Corby, A, Coulson, P, Dhami, I, Dutta, M, Dunn, L, Faulkner, A, Frankish, J A, Frankland, P, Garner, J, Garnett, S, Gribble, C, Griffiths, R, Grocock, E, Gustafson, S, Hammond, J L, Harley, E, Hart, P D, Heath, T P, Ho, B, Hopkins, J, Horne, P J, Howden, E, Huckle, C, Hynds, C, Johnson, D, Johnson, A, Kana, M, Kay, A M, Kimberley, J K, Kershaw, M, Kokkinaki, G K, Laird, S, Lawlor, H M, Lee, D A, Leongamornlert, G, Laird, C, Lloyd, D M, Lloyd, J, Loveland, J, Lovell, S, McLaren, K E, McLay, A, McMurray, M, Mashreghi-Mohammadi, L, Matthews, S, Milne, T, Nickerson, M, Nguyen, E, Overton-Larty, S A, Palmer, A V, Pearce, A I, Peck, S, Pelan, B, Phillimore, K, Porter, C M, Rice, A, Rogosin, M T, Ross, T, Sarafidou, H K, Sehra, R, Shownkeen, C D, Skuce, M, Smith, L, Standring, N, Sycamore, J, Tester, A, Thorpe, W, Torcasso, A, Tracey, A, Tromans, J, Tsolas, M, Wall, J, Walsh, H, Wang, K, Weinstock, A P, West, D L, Willey, S L, Whitehead, L, Wilming, P W, Wray, L, Young, Y, Chen, R C, Lovering, N K, Moschonas, R, Siebert, K, Fechtel, D, Bentley, R, Durbin, T, Hubbard, L, Doucette-Stamm, S, Beck, D R, Smith, and J, Rogers

Subjects
Base Composition, Multidisciplinary, Pan troglodytes, Chromosomes, Human, Pair 10, Genetics, Medical, Genetic Variation, Proteins, Exons, Genomics, Sequence Analysis, DNA, Physical Chromosome Mapping, Evolution, Molecular, Contig Mapping, Genes, Gene Duplication, Animals, Humans, CpG Islands, Pseudogenes
Abstract

The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence.

Published
2004

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

4. Genetic tagging of humpback whales

Author

Martine Bérubé, Jon Lien, David K. Mattila, Judith Allen, Tonnie P. Feddersen, Jóhann Sigurjónsson, Tim D. Smith, Anja Holm Larsen, Philip S. Hammond, Richard Sears, Hanne Jørgensen, Phillip J. Clapham, Renate Sponer, Steve Katona, Finn Larsen, Peter T. Stevick, Per J. Palsbøll, Nils Øien, Richard R. Hudson, Groningen Institute for Evolutionary Life Sciences, and Palsbøll lab

Subjects
Genetic Markers, Male, GULF, Multidisciplinary, Ecology, MEGAPTERA-NOVAEANGLIAE, Population Dynamics, Whales, DNA, MAINE, Biology, SIMPLE SEQUENCES, Abundance (ecology), Genetic marker, Evolutionary biology, Genotype, Animals, Feasibility Studies, Microsatellite, Female, Identification (biology), Atlantic Ocean, POPULATION, Microsatellite Repeats, Skin
Abstract

The ability to recognize individual animals has substantially increased our knowledge of the biology and behaviour of many taxa(1). However, not all species lend themselves to this approach, either because of insufficient phenotypic variation or because tag attachment is not feasible. The use of genetic markers ('tags') represents a viable alternative to traditional methods of individual recognition, as they are permanent and exist in all individuals. We tested the use of genetic markers as the primary means of identifying individuals in a study of humpback whales in the North Atlantic Ocean. Analysis of six microsatellite loci(2,3) among 3,060 skin samples collected throughout this ocean allowed the unequivocal identification of individuals. Analysis of 692 'recaptures', identified by their genotype, revealed individual local and migratory movements of up to 10,000 km, limited exchange among summer feeding grounds, and mixing in winter breeding areas, and also allowed the first estimates of animal abundance based solely on genotypic data. Our study demonstrates that genetic tagging is not only feasible, but generates data (for example, on sex) that can be valuable when interpreting-the results of tagging experiments.

Published
1997

5. 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

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. The DNA sequence and comparative analysis of human chromosome 20

Author

G Clarke, L M Faulkner, Jane E. Loveland, J Walsh, Kirsten McLay, G Laird, A K Babbage, J C Chapman, Sophie Palmer, C Hynds, M Earthrowl, T D Andrews, J Battles, Theologia Sarafidou, S. M. Clegg, Christine P. Bird, T P Ho, Sarah Pelan, A M Kimberley, Anthony P. West, E. Hart, Russell J. Grocock, Carol Scott, Stuart McLaren, J Lovell, M Kokkinaki, J K Kershaw, Sarah Milne, Christine Lloyd, D. M. Lloyd, R I S Ashwell, L Standring, Amanda McMurray, John Burton, A Rogosin, Yuan Chen, D Camire, Gavin K. Laird, Nigel P. Carter, David Willey, Nicholas K. Moschonas, Stephan Beck, Ruth C. Lovering, Mark T. Ross, Adam Frankish, S Lawlor, Laurens G. Wilming, I Dutta, David Bentley, Joanna Harley, R Ainscough, Matthew Jones, Susan M. Gribble, C. D. Skuce, A Thorpe, Pawandeep Dhami, L Young, Melanie M. Wall, Erik Gustafson, David Swarbreck, Douglas Smith, J Frankland, S Y Clark, C M Clee, Lucy Matthews, S Bray-Allen, A Taylor, W Burrill, Lynn Doucette-Stamm, S. Searle, Alan Tracey, J Tester, Panos Deloukas, Daniel Leongamornlert, T Nickerson, David W. Johnson, Philip Howden, Paul Wray, M. Kay, Catherine M. Rice, A Kana, H M Lee, Keith Weinstock, Kim Fechtel, Sarah E. Hunt, A I Peck, S. Whitehead, H Wang, N Sycamore, Patrick Cahill, J Bailey, Alan Coulson, E K Overton-Larty, J Y Brown, Jennifer L. Ashurst, A. V. Pearce, M Mashreghi-Mohammadi, C L Bagguley, P Garner, A J Brown, Benjamin Phillimore, W Torcasso, S Hammond, M Nguyen, J Horne, K Bates, J P Almeida, N Corby, Matthew Dunn, Darren Grafham, Ratna Shownkeen, D C Burford, A Tromans, Jane Rogers, J Garnett, Harminder Sehra, Kerstin Howe, K D Ambrose, James G. R. Gilbert, Helen Beasley, Reiner Siebert, Charles A. Steward, Chris Johnson, K M Porter, Ruby Banerjee, Marc Rubenfield, Sarah Sims, Lisa French, Paul Heath, Elizabeth J. Huckle, B Hopkins, C Griffiths, Richard Durbin, J Tsolas, Michelle Smith, and Tim Hubbard

Subjects
Genetics, Multidisciplinary, Base Sequence, Proteome, Sequence analysis, Pseudogene, Physical Chromosome Mapping, Chromosomes, Human, Pair 20, Genetic Diseases, Inborn, Computational Biology, Genetic Variation, Locus (genetics), DNA, Sequence Analysis, DNA, Biology, Contig Mapping, Mice, Gene duplication, Animals, Humans, Human genome, Chromosome 20, Segmental duplication
Abstract

The finished sequence of human chromosome 20 comprises 59,187,298 base pairs (bp) and represents 99.4% of the euchromatic DNA. A single contig of 26 megabases (Mb) spans the entire short arm, and five contigs separated by gaps totalling 320 kb span the long arm of this metacentric chromosome. An additional 234,339 bp of sequence has been determined within the pericentromeric region of the long arm. We annotated 727 genes and 168 pseudogenes in the sequence. About 64% of these genes have a 5' and a 3' untranslated region and a complete open reading frame. Comparative analysis of the sequence of chromosome 20 to whole-genome shotgun-sequence data of two other vertebrates, the mouse Mus musculus and the puffer fish Tetraodon nigroviridis, provides an independent measure of the efficiency of gene annotation, and indicates that this analysis may account for more than 95% of all coding exons and almost all genes.

Published
2002

8. 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

9. Erratum: Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome

Author

Alan Tracey, Lucy Barr, Karen Holt, Stephen J. Trevanion, Bob Plumb, Daniel Leongamornlert, Paul Wray, Carol Churcher, J. C. Davis, Ruth Gilderthorp, Christine Lloyd, Adrienne Hunt, Michelle Smith, Britt Kilian, Martina Konantz, Jeff Almeida-King, Richard M. Clark, Nick Barker, Kirsty Ambridge, Susan J. Clark, Karen Oliver, Glen Threadgold, Yong Gu, Jane E. Loveland, David Lloyd, Guy Griffiths, Ronald H.A. Plasterk, Karen McLaren, Sarah Pelan, Sarah Nichol, Kenric Leung, Rebecca Woodmansey, Sharmin Begum, Cigdem Eser, Sophie Palmer, Jacqueline Brown, Ian M Sealy, James Torrance, J Lovell, John E. Collins, Sara Widaa, A M Kimberley, A Tromans, Richard Pandian, Judith Konantz, Maria Geisler, Carlos Torroja, N Sycamore, Sancha Martin, Darren Barker, Amanda Rapp, Monte Westerfield, Silke Rudolph-Geiger, Zemin Ning, José Afonso Guerra-Assunção, Clare Riddle, Rebecca Glithero, Daniel P. Kelly, Nicholas Matthews, Pieter J. de Jong, Nigel P. Carter, Camille Berthelot, Fengtang Yang, A K Babbage, Graham Clark, Andrea Berger, Robert Andrews, C Griffiths, Jennifer Harrow, Gerd Jörg Rauch, Steve Searle, J. M. Wallis, Christa Lanz, Ruby Banerjee, William Chow, Jan Hinnerk Vogel, Matthieu Muffato, David Elliott, Mathias Teucke, Derek L. Stemple, Debbie E. Wright, Deepa Manthravadi, Gavin K. Laird, Sarah Sims, M Mashreghi-Mohammadi, David S. Saunders, Lena Karotki, P Garner, Paul Heath, Jane Rogers, Ines Gehring, J Garnett, Charles Lee, Philip Howden, John H. Postlethwait, Robert Geisler, Sarah Donaldson, Elizabeth Langley, Claire Raisen, Katherine Auger, Javier Herrero, Beiyuan Fu, Carol Scott, Zübeyde Ersan-Ürün, Mario Caccamo, Sean Humphray, Gary L A Barker, S. Whitehead, Darren Ware, Baoli Zhu, Jianxiang Chi, Jonathan Wood, Nigel Fosker, Sarah McGuire, Stephan C. Schuster, Chris Clee, Martina Oberländer, Daria Gordon, Clare Murnane, Romke Koch, Emma Gray, Beverley J. Mortimore, Harminder Sehra, Joanna Collins, Hugues Roest Crollius, Kirsten McLay, Kerstin Howe, Lauren Dyer, Christopher Stevens, Andrew D. Ellington, Kazutoyo Osoegawa, Stuart McLaren, Christopher N. Johnson, Giselle Kerry, Helen Beasley, Georgios Panagiotidis, Christiane Nüsslein Volhard, Tina Eyre, Horst Geiger, Jennifer Yen, Matthew Ellwood, Christine P. Bird, N Corby, Matthew Dunn, Darren Grafham, Günter Raddatz, Matthew Humphries, Anette Kirn, Yi Zhou, James D. Cooper, John Burton, Simon D. M. White, Anton J. Enright, Dave Willey, Tim Hubbard, Rebekah Hall, Michael Kay, Matthew D. Clark, Matthew Jones, Glenn Harden, C. D. Skuce, Lauren Robertson, Leonard I. Zon, Lucy Matthews, Jeffrey C. Barrett, Michael A. Quail, Emma J. Kenyon, Leonor T. Quintais, Benjamin Phillimore, S Hammond, Carl Henderson, Joanna Harley, Elliot Harrison, Cordelia Langford, Christopher M. Dooley, and Sean Maguire

Subjects
Max planck institute, Comparative genomics, Multidisciplinary, Reference genome sequence, biology, Evolutionary biology, Philosophy, Human genome, Bioinformatics, biology.organism_classification, Zebrafish
Abstract

Nature 496, 498–503 (2013); doi:10.1038/nature12111 In this Letter, five authors were inadvertently omitted: Sharmin Begum and Christine Lloyd from the Wellcome Trust Sanger Institute, and Christa Lanz, Gunter Raddatz and Stephan C. Schuster from the Max Planck Institute for Developmental Biology. David Elliot was incorrectly listed as David Eliot, Beverley Mortimore was incorrectly listed as Beverly Mortimer, and James D.

Published
2013

10. 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

11. Properties of cystinotic fibroblast-D98 cell hybrids studied by somatic cell hybridization

Author

Fred L. A. Becker, Jerry A. Schneider, Ocean L. Pellett, Deborah S. Hammond, and Uta Francke

Subjects
Somatic cell, Cellular differentiation, Cystinosis, Chromosome Disorders, Biology, Glucosephosphate Dehydrogenase, Hybrid Cells, Somatic Cell Hybridization, Chromosomes, Cell Line, medicine, Humans, Metabolic disease, Fibroblast, Child, Chromosome Aberrations, Multidisciplinary, Syndrome, Fibroblasts, Fanconi Syndrome, Molecular biology, Cell biology, Clone Cells, Isoenzymes, medicine.anatomical_structure, Hypoxanthines, Karyotyping, Cell hybrids, Cystine, Female
Abstract

SINCE the discovery of somatic cell hybridization1 this technique has been used primarily for studies of formal genetics, cell differentiation, and cancer2. This study represents an attempt to use this technique to study a metabolic disease in which the primary defect is unknown.

Published
1973

12. The zebrafish reference genome sequence and its relationship to the human genome.

Author

Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch GJ, White S, Chow W, Kilian B, Quintais LT, Guerra-Assunção JA, Zhou Y, Gu Y, Yen J, Vogel JH, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird GK, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliot D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper J, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley CM, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster SC, Carter NP, Harrow J, Ning Z, Herrero J, Searle SM, Enright A, Geisler R, Plasterk RH, Lee C, Westerfield M, de Jong PJ, Zon LI, Postlethwait JH, Nüsslein-Volhard C, Hubbard TJ, Roest Crollius H, Rogers J, and Stemple DL

Subjects
Animals, Chromosomes genetics, Evolution, Molecular, Female, Genes genetics, Genome, Human genetics, Genomics, Humans, Male, Meiosis genetics, Molecular Sequence Annotation, Pseudogenes genetics, Reference Standards, Sex Determination Processes genetics, Zebrafish Proteins genetics, Conserved Sequence genetics, Genome genetics, Zebrafish genetics
Abstract

Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.

Published
2013
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13. 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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14. 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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15. The DNA sequence and comparative analysis of human chromosome 10.

Author

Deloukas P, Earthrowl ME, Grafham DV, Rubenfield M, French L, Steward CA, Sims SK, Jones MC, Searle S, Scott C, Howe K, Hunt SE, Andrews TD, Gilbert JG, Swarbreck D, Ashurst JL, Taylor A, Battles J, Bird CP, Ainscough R, Almeida JP, Ashwell RI, Ambrose KD, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Bates K, Beasley H, Bray-Allen S, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Cahill P, Camire D, Carter NP, Chapman JC, Clark SY, Clarke G, Clee CM, Clegg S, Corby N, Coulson A, Dhami P, Dutta I, Dunn M, Faulkner L, Frankish A, Frankland JA, Garner P, Garnett J, Gribble S, Griffiths C, Grocock R, Gustafson E, Hammond S, Harley JL, Hart E, Heath PD, Ho TP, Hopkins B, Horne J, Howden PJ, Huckle E, Hynds C, Johnson C, Johnson D, Kana A, Kay M, Kimberley AM, Kershaw JK, Kokkinaki M, Laird GK, Lawlor S, Lee HM, Leongamornlert DA, Laird G, Lloyd C, Lloyd DM, Loveland J, Lovell J, McLaren S, McLay KE, McMurray A, Mashreghi-Mohammadi M, Matthews L, Milne S, Nickerson T, Nguyen M, Overton-Larty E, Palmer SA, Pearce AV, Peck AI, Pelan S, Phillimore B, Porter K, Rice CM, Rogosin A, Ross MT, Sarafidou T, Sehra HK, Shownkeen R, Skuce CD, Smith M, Standring L, Sycamore N, Tester J, Thorpe A, Torcasso W, Tracey A, Tromans A, Tsolas J, Wall M, Walsh J, Wang H, Weinstock K, West AP, Willey DL, Whitehead SL, Wilming L, Wray PW, Young L, Chen Y, Lovering RC, Moschonas NK, Siebert R, Fechtel K, Bentley D, Durbin R, Hubbard T, Doucette-Stamm L, Beck S, Smith DR, and Rogers J

Subjects
Animals, Base Composition, Contig Mapping, CpG Islands genetics, Evolution, Molecular, Exons genetics, Gene Duplication, Genetic Variation genetics, Genetics, Medical, Genomics, Humans, Pan troglodytes genetics, Proteins genetics, Pseudogenes genetics, Sequence Analysis, DNA, Chromosomes, Human, Pair 10 genetics, Genes, Physical Chromosome Mapping
Abstract

The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence.

Published
2004
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16. 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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17. 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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18. The DNA sequence and comparative analysis of human chromosome 20.

Author

Deloukas P, Matthews LH, Ashurst J, Burton J, Gilbert JG, Jones M, Stavrides G, Almeida JP, Babbage AK, Bagguley CL, Bailey J, Barlow KF, Bates KN, Beard LM, Beare DM, Beasley OP, Bird CP, Blakey SE, Bridgeman AM, Brown AJ, Buck D, Burrill W, Butler AP, Carder C, Carter NP, Chapman JC, Clamp M, Clark G, Clark LN, Clark SY, Clee CM, Clegg S, Cobley VE, Collier RE, Connor R, Corby NR, Coulson A, Coville GJ, Deadman R, Dhami P, Dunn M, Ellington AG, Frankland JA, Fraser A, French L, Garner P, Grafham DV, Griffiths C, Griffiths MN, Gwilliam R, Hall RE, Hammond S, Harley JL, Heath PD, Ho S, Holden JL, Howden PJ, Huckle E, Hunt AR, Hunt SE, Jekosch K, Johnson CM, Johnson D, Kay MP, Kimberley AM, King A, Knights A, Laird GK, Lawlor S, Lehvaslaiho MH, Leversha M, Lloyd C, Lloyd DM, Lovell JD, Marsh VL, Martin SL, McConnachie LJ, McLay K, McMurray AA, Milne S, Mistry D, Moore MJ, Mullikin JC, Nickerson T, Oliver K, Parker A, Patel R, Pearce TA, Peck AI, Phillimore BJ, Prathalingam SR, Plumb RW, Ramsay H, Rice CM, Ross MT, Scott CE, Sehra HK, Shownkeen R, Sims S, Skuce CD, Smith ML, Soderlund C, Steward CA, Sulston JE, Swann M, Sycamore N, Taylor R, Tee L, Thomas DW, Thorpe A, Tracey A, Tromans AC, Vaudin M, Wall M, Wallis JM, Whitehead SL, Whittaker P, Willey DL, Williams L, Williams SA, Wilming L, Wray PW, Hubbard T, Durbin RM, Bentley DR, Beck S, and Rogers J

Subjects
Animals, Base Sequence, Computational Biology, Contig Mapping, DNA, Genetic Diseases, Inborn genetics, Genetic Variation, Humans, Mice, Physical Chromosome Mapping, Proteome, Sequence Analysis, DNA, Chromosomes, Human, Pair 20
Abstract

The finished sequence of human chromosome 20 comprises 59,187,298 base pairs (bp) and represents 99.4% of the euchromatic DNA. A single contig of 26 megabases (Mb) spans the entire short arm, and five contigs separated by gaps totalling 320 kb span the long arm of this metacentric chromosome. An additional 234,339 bp of sequence has been determined within the pericentromeric region of the long arm. We annotated 727 genes and 168 pseudogenes in the sequence. About 64% of these genes have a 5' and a 3' untranslated region and a complete open reading frame. Comparative analysis of the sequence of chromosome 20 to whole-genome shotgun-sequence data of two other vertebrates, the mouse Mus musculus and the puffer fish Tetraodon nigroviridis, provides an independent measure of the efficiency of gene annotation, and indicates that this analysis may account for more than 95% of all coding exons and almost all genes.

Published
2001
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19. 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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