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1. Next Generation Sequencing in Newborn Screening in the United Kingdom National Health Service

Author

Julia C. van Campen, Elizabeth S. A. Sollars, Rebecca C. Thomas, Clare M. Bartlett, Antonio Milano, Matthew D. Parker, Jennifer Dawe, Peter R. Winship, Gerrard Peck, Darren Grafham, Richard J. Kirk, James R. Bonham, Anne C. Goodeve, and Ann Dalton

Subjects
newborn screening, next generation sequencing, automation, Pediatrics, RJ1-570
Abstract

Next generation DNA sequencing (NGS) has the potential to improve the diagnostic and prognostic utility of newborn screening programmes. This study assesses the feasibility of automating NGS on dried blood spot (DBS) DNA in a United Kingdom National Health Service (UK NHS) laboratory. An NGS panel targeting the entire coding sequence of five genes relevant to disorders currently screened for in newborns in the UK was validated on DBS DNA. An automated process for DNA extraction, NGS and bioinformatics analysis was developed. The process was tested on DBS to determine feasibility, turnaround time and cost. The analytical sensitivity of the assay was 100% and analytical specificity was 99.96%, with a mean 99.5% concordance of variant calls between DBS and venous blood samples in regions with ≥30× coverage (96.8% across all regions; all variant calls were single nucleotide variants (SNVs), with indel performance not assessed). The pipeline enabled processing of up to 1000 samples a week with a turnaround time of four days from receipt of sample to reporting. This study concluded that it is feasible to automate targeted NGS on routine DBS samples in a UK NHS laboratory setting, but it may not currently be cost effective as a first line test.

Published
2019
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2. Modernizing reference genome assemblies.

Author

Deanna M Church, Valerie A Schneider, Tina Graves, Katherine Auger, Fiona Cunningham, Nathan Bouk, Hsiu-Chuan Chen, Richa Agarwala, William M McLaren, Graham R S Ritchie, Derek Albracht, Milinn Kremitzki, Susan Rock, Holland Kotkiewicz, Colin Kremitzki, Aye Wollam, Lee Trani, Lucinda Fulton, Robert Fulton, Lucy Matthews, Siobhan Whitehead, Will Chow, James Torrance, Matthew Dunn, Glenn Harden, Glen Threadgold, Jonathan Wood, Joanna Collins, Paul Heath, Guy Griffiths, Sarah Pelan, Darren Grafham, Evan E Eichler, George Weinstock, Elaine R Mardis, Richard K Wilson, Kerstin Howe, Paul Flicek, and Tim Hubbard

Subjects
Biology (General), QH301-705.5
Published
2011
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3. Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin.

Author

Melissa K Boles, Bonney M Wilkinson, Laurens G Wilming, Bin Liu, Frank J Probst, Jennifer Harrow, Darren Grafham, Kathryn E Hentges, Lanette P Woodward, Andrea Maxwell, Karen Mitchell, Michael D Risley, Randy Johnson, Karen Hirschi, James R Lupski, Yosuke Funato, Hiroaki Miki, Pablo Marin-Garcia, Lucy Matthews, Alison J Coffey, Anne Parker, Tim J Hubbard, Jane Rogers, Allan Bradley, David J Adams, and Monica J Justice

Subjects
Genetics, QH426-470
Abstract

An accurate and precisely annotated genome assembly is a fundamental requirement for functional genomic analysis. Here, the complete DNA sequence and gene annotation of mouse Chromosome 11 was used to test the efficacy of large-scale sequencing for mutation identification. We re-sequenced the 14,000 annotated exons and boundaries from over 900 genes in 41 recessive mutant mouse lines that were isolated in an N-ethyl-N-nitrosourea (ENU) mutation screen targeted to mouse Chromosome 11. Fifty-nine sequence variants were identified in 55 genes from 31 mutant lines. 39% of the lesions lie in coding sequences and create primarily missense mutations. The other 61% lie in noncoding regions, many of them in highly conserved sequences. A lesion in the perinatal lethal line l11Jus13 alters a consensus splice site of nucleoredoxin (Nxn), inserting 10 amino acids into the resulting protein. We conclude that point mutations can be accurately and sensitively recovered by large-scale sequencing, and that conserved noncoding regions should be included for disease mutation identification. Only seven of the candidate genes we report have been previously targeted by mutation in mice or rats, showing that despite ongoing efforts to functionally annotate genes in the mammalian genome, an enormous gap remains between phenotype and function. Our data show that the classical positional mapping approach of disease mutation identification can be extended to large target regions using high-throughput sequencing.

Published
2009
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4. Next Generation Sequencing in Newborn Screening in the United Kingdom National Health Service

Author

Rebecca C. Thomas, Jennifer Dawe, Gerrard Peck, P. R. Winship, James R. Bonham, Elizabeth S. A. Sollars, Matthew Parker, Clare M. Bartlett, Anne Goodeve, Julia van Campen, Darren Grafham, Antonio Milano, Ann Dalton, and Richard J. Kirk

Subjects
0301 basic medicine, medicine.medical_specialty, Concordance, 030105 genetics & heredity, Turnaround time, DNA sequencing, Article, 03 medical and health sciences, Immunology and Microbiology (miscellaneous), medicine, Indel, automation, next generation sequencing, Newborn screening, business.industry, newborn screening, lcsh:RJ1-570, Obstetrics and Gynecology, lcsh:Pediatrics, National health service, DNA extraction, 3. Good health, Dried blood spot, 030104 developmental biology, Pediatrics, Perinatology and Child Health, Emergency medicine, business
Abstract

Next generation DNA sequencing (NGS) has the potential to improve the diagnostic and prognostic utility of newborn screening programmes. This study assesses the feasibility of automating NGS on dried blood spot (DBS) DNA in a United Kingdom National Health Service (UK NHS) laboratory. An NGS panel targeting the entire coding sequence of five genes relevant to disorders currently screened for in newborns in the UK was validated on DBS DNA. An automated process for DNA extraction, NGS and bioinformatics analysis was developed. The process was tested on DBS to determine feasibility, turnaround time and cost. The analytical sensitivity of the assay was 100% and analytical specificity was 99.96%, with a mean 99.5% concordance of variant calls between DBS and venous blood samples in regions with &ge, 30&times, coverage (96.8% across all regions, all variant calls were single nucleotide variants (SNVs), with indel performance not assessed). The pipeline enabled processing of up to 1000 samples a week with a turnaround time of four days from receipt of sample to reporting. This study concluded that it is feasible to automate targeted NGS on routine DBS samples in a UK NHS laboratory setting, but it may not currently be cost effective as a first line test.

Published
2019
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5. The DNA sequence of the human X chromosome

Author

Gernot Glöckner, Karen Thomas, Christine Lloyd, Huda Y. Zoghbi, Adrienne Hunt, Fiona Francis, Annemarie Poustka, George M. Weinstock, Xuehong Wei, Alan Tracey, Gabriele Nordsiek, Ines Müller, Graham Clarke, Oliver Beasley, John Sulston, Alfred Beck, Christian J. Buhay, Thomas Meitinger, Manjula Maheshwari, Yvonne Ramsey, Kirsten McLay, Shannon Dugan-Rocha, James G. R. Gilbert, Louisa Faulkner, Sidney Morris, Margaret Morgan, Huntington F. Willard, Leni S. Jacob, Hermela Loulseged, K M Porter, T. Daniel Andrews, Cordelia Langford, Paul Wray, Guan Chen, Juliane Ramser, Nigel P. Carter, Georgina Warry, Ruby Banerjee, Graeme Bethel, LaDeana W. Hillier, Anne Hodgson, Stephen M. J. Searle, K F Barlow, David R. Bentley, Paul E. Tabor, Kathryn L. Evans, Russell J. Grocock, Rebecca Woodmansey, Alex V Pearce, Christie Kovar-Smith, Angela Williamson, Dean Chavez, Roy Storey, Kevin L. Howe, Zhijian J. Chen, Lesette Perez, Richard A. Gibbs, Michele D'Urso, Karen N Bates, Jackie Bye, Shirin S. Joseph, Bernd Hinzmann, Paul Heath, Susan H. Kelly, Jennifer Hume, Paula E. Burch, David Buck, Mark T. Ross, David A. Wheeler, Matthew C. Jones, A K Babbage, Erica Sodergren, Sophie Palmer, Jie Ma, Elizabeth C. Sotheran, Margaret A. Leversha, Cerissa Hamilton, Hans Lehrach, Swaroop Aradhya, Michael L. Metzker, S. M. Clegg, Elizabeth J. Huckle, Audrey Fraser, Sarah Bray-Allen, C. D. Skuce, Petra Galgoczy, Richard K. Wilson, Patrick Minx, Richard E Connor, Tamsin Eades, Alfons Meindl, Michelle Smith, John M. Davis, André Rosenthal, Stuart McLaren, Geoffery Okwuonu, M. Vaudin, Laura Carrel, Ryan J. Lozado, Harminder Sehra, Richard Pandian, Sue Y Clark, Anna Kosiura, Wen Liu, Simon G. Gregory, A Tromans, Alexandra Emery-Cohen, Charles Shaw-Smith, Donna Villasana, Joseph Chako, Katja Heitmann, Robert G. David, Jennifer L. Ashurst, Craig Chinault, S Lawlor, Paul Havlak, Jane E. Loveland, Lucy Matthews, Jianling Zhou, S. Whitehead, Paul Hunt, E Sheridan, Richard Reinhardt, Tim Hubbard, Mary G. Schueler, Patrick Meidl, Helen Beasley, David Beare, Donna M. Muzny, Kerry A Ridler, Joanne C Chapman, Jennifer McDowall, Andrew Dunham, Anne Bridgeman, Gabrielle Williams, Amanda McMurray, Stefan Taudien, Matthew E. Hurles, Helen Williamson, Preethi H. Gunaratne, Alfredo Ciccodicola, R Ainscough, Alison J. Coffey, Charlotte G. Cole, Stephan Beck, Frances L Lovell, Alan Coulson, Qiaoyan Wang, Sally Jones, Charles A. Steward, Michael Hoffs, Kim C. Worley, Sarah Pelan, David Bonnin, David Schlessinger, Mathew N Whiteley, Graham Scott, Christopher N O'Dell, Tineace Taylor, Susan Rhodes, Anthony P. West, E. Hart, Ian P. Barrett, Andrea Thorpe, D. Pearson, Huyen Dinh, Susan M. Gribble, Andrew J Knights, Laurens G. Wilming, N Corby, Steven E. Scherer, Pawandeep Dhami, Gerald Nyakatura, J Lovell, M. Ali Ansari-Lari, Kerstin P. Clerc-Blankenburg, David Swarbreck, Sara Zorilla, Yanghong Gu, Karin Blechschmidt, Matthew Dunn, Andrew Brown, Kirsten M. Timms, Darren Grafham, Yan Ding, Elspeth A. Bruford, Leanne Williams, Melanie M. Wall, Hua Shen, Dina Patel, Joanne K Kershaw, Rachel Gill, Yuan Chen, Joy Davies, D C Burford, John Burton, Vicky Cobley, R I S Ashwell, Nicola Brady, Ellson Y. Chen, Ngoc Nguyen, Gaiping Wen, Gavin K. Laird, Julia E. Parrish, Carol Scott, C Griffiths, Ratna Shownkeen, Ralf Sudbrak, Denise R. DeShazo, Shiran Pasternak, Ireena Dutta, Brian Teague, Rachael Lyne, David Parker, Jane Rogers, Steve Dodsworth, Mary J. Brown, Gary E Barker, Steve Trevanion, Joanne Burgess, Jane E. Wilkinson, James T. Warren, Jen S. Conquer, R Mark Swann, Oliver Delgado, Heather R. Draper, Shailesh L Mistry, Chris Clee, Richard Durbin, Karen Clifford, John Frankland, Sarah E. Hunt, David Steffen, Christine Burrows, Daniel Verduzco, C Carder, Robert H. Waterston, Stephen Richards, Andrea Ballabio, Catherine M. Rice, David Willey, Helen Errington, Andrew Cree, K. James Durbin, Lora Lewis, D. M. Lloyd, Helen E. Steingruber, Adam Whittaker, K D Ambrose, Rhian Gwilliam, Adam Frankish, Robert S. Fulton, Judith Hernandez, Claire L Bagguley, Pieter J. de Jong, Jennifer Yen, Matthew Ellwood, Christine P. Bird, Rui Chen, Sarah Milne, Clay Davis, Alicia Hawes, Jing Lu, Sven Klages, David L. Nelson, Wayne Burrill, Jingkun Zhang, Judith Isherwood, Kathrin Reichwald, Lenee Waldron, Rebecca Deadman, Steffen Hennig, Ziad Khan, Sarah Ho, Matthias Platzer, Gareth R. Howell, Stephen Keenan, Petra Kioschis, Phillip J Howden, George Miner, David W. Johnson, and James C. Mullikin

Subjects
Male, Genetic Linkage, Genetics, Medical, Centromere, HUMAN GENOME SEQUENCE, Biology, Y chromosome, Polymorphism, Single Nucleotide, Article, Evolution, Molecular, Contig Mapping, Chromosome 16, Antigens, Neoplasm, Dosage Compensation, Genetic, Sequence Homology, Nucleic Acid, Chromosome 19, Testis, Animals, Humans, Crossing Over, Genetic, X chromosome, Repetitive Sequences, Nucleic Acid, Genetics, Chromosomes, Human, X, Chromosomes, Human, Y, Multidisciplinary, INACTIVATION CENTER, LINKED MENTAL-RETARDATION, Genomics, Sequence Analysis, DNA, REPEAT HYPOTHESIS, MAMMALIAN Y-CHROMOSOME, Chromosome 4, Chromosome 3, RNA, Female, Chromosome 21, Chromosome 22
Abstract

The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

Published
2005
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6. DNA sequence and analysis of human chromosome 9

Author

L K Colman, S S White, R Heathcott, K D Ambrose, C Griffiths, C L Bagguley, Christine Lloyd, Jim Davies, James G. R. Gilbert, Richard Durbin, Carol Scott, Rebekah Hall, Graeme Bethel, Adrienne Hunt, C Carder, A Tromans, G Tamlyn-Hall, Jane Rogers, J Garnett, L M Faulkner, J C Chapman, Benjamin Phillimore, M Grant, A Wild, Christopher J. Gillson, S Hammond, A K Babbage, Sophie Palmer, C. D. Skuce, V. Cobley, Margaret A. Leversha, Robert W. Plumb, J. M. Wallis, Lucy Matthews, Sarah E. Smith, Mark Griffiths, Karen Oliver, J Tester, Christopher M. Johnson, M Earthrowl, K L Novik, Graeme T Clark, Kirsten McLay, Michelle Smith, R M Younger, T Nickerson, K F Barlow, A. King, S. M. Clegg, Mark T. Ross, K M Culley, R. E. Collier, K Bates, Nigel P. Carter, Sarah E. Hunt, Matthew Humphries, Kevin L. Howe, R Ainscough, Matthew Jones, J P Almeida, Laurens G. Wilming, R Patel, C M Clee, A M Kimberley, David Niblett, Gareth Maslen, Jane E. Loveland, Pawandeep Dhami, J C Wyatt, Philip Howden, Harminder Sehra, N Corby, Stephan Beck, Andrew J. Mungall, Cordelia Langford, Mohammed J. R. Ghori, O. T. McCann, Sarah Milne, Ian Dunham, C A Edwards, J Y Brown, Matthew Dunn, A J Theaker, Darren Grafham, Alan Tracey, S. Searle, Anne Parker, John Burton, Amanda McMurray, H Whittaker, R I S Ashwell, M Mashreghi-Mohammadi, P Garner, A J Brown, O. Beasley, Michele Clamp, A Thorpe, Daniel Leongamornlert, Alan Coulson, Y. Ramsey, Paul Wray, N Sycamore, Helen Beasley, M. J F Moore, Dave Willey, K M Porter, S Y Clark, A I Peck, Tim Hubbard, D. M. Lloyd, David R. Bentley, A Joy, Joanna Harley, L Spraggon, J Lovell, Anthony P. West, E. Hart, Adam Frankish, M. Kay, Catherine M. Rice, Matthew D. Francis, S A Ranby, Duncan W. Thomas, Elizabeth J. Huckle, T. E. Wilmer, Sean Humphray, L Young, W Burrill, David Beare, B Tubby, S Lawlor, E Sheridan, Susan M. Gribble, J Frankland, A E Ellington, Charles A. Steward, K S Halls, Roger Horton, Melanie M. Wall, James C. Mullikin, D C Burford, S. Holmes, L M Gilby, T D Andrews, Christine P. Bird, Gareth R. Howell, Stephen Keenan, Joanna Collins, S. Squares, Ruby Banerjee, Jennifer L. Ashurst, Sarah Sims, S Bray-Allen, Lisa French, G. J. Coville, Paul Heath, A. V. Pearce, S. Whitehead, Sancha Martin, J Bailey, J Brook, Darren Barker, Rebecca Glithero, Jonathan Wood, E K Overton-Larty, K A Evans, S. Blakey, John Sulston, Gavin K. Laird, Sam Phillips, and S J McLaren

Subjects
Male, Genetics, Medical, Biology, Article, Euchromatin, Evolution, Molecular, Chromosome 15, Chromosome 16, Genes, Duplicate, Gene Duplication, Heterochromatin, Neoplasms, Chromosome 19, Humans, Chromosome 13, Genetics, Base Composition, Multidisciplinary, Genetic Variation, Neurodegenerative Diseases, Genomics, Sequence Analysis, DNA, Sex Determination Processes, Physical Chromosome Mapping, Chromosome 17 (human), Genes, Chromosome 3, Female, Chromosomes, Human, Pair 9, Chromosome 21, Chromosome 22, Pseudogenes
Abstract

Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6–8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.

Published
2004
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7. Comparative and functional analyses of LYL1 loci establish marsupial sequences as a model for phylogenetic footprinting☆ ☆Sequence data from this article have been deposited with the DDBJ/EMBL/GenBank Data Libraries under Accession No. AL731834

Author

Frank Grützner, Sarah Kinston, Anthony R. Green, Berthold Göttgens, Jane Rogers, Darren Grafham, Jennifer A. Marshall Graves, Michael A Chapman, Christine P. Bird, and Fadi J. Charchar

Subjects
DNA binding site, Genetics, genomic DNA, biology, Sequence analysis, Dunnart, Phylogenetic footprinting, biology.organism_classification, Enhancer, Genome, Gene
Abstract

Comparative genomic sequence analysis is a powerful technique for identifying regulatory regions in genomic DNA. However, its utility largely depends on the evolutionary distances between the species involved. Here we describe the screening of a genomic BAC library from the stripe-faced dunnart, Sminthopsis macroura, formerly known as the narrow-footed marsupial mouse. We isolated a clone containing the LYL1 locus, completely sequenced the 60.6-kb insert, and compared it with orthologous human and mouse sequences. Noncoding homology was substantially reduced in the human/dunnart analysis compared with human/mouse, yet we could readily identify all promoters and exons. Human/mouse/dunnart alignments of the LYL1 candidate promoter allowed us to identify putative transcription factor binding sites, revealing a pattern highly reminiscent of critical regulatory regions of the LYL1 paralogue, SCL. This newly identified LYL1 promoter showed strong activity in myeloid progenitor cells and was bound in vivo by Fli1, Elf1, and Gata2—transcription factors all previously shown to bind to the SCL stem cell enhancer. This study represents the first large-scale comparative analysis involving marsupial genomic sequence and demonstrates that such comparisons provide a powerful approach to characterizing mammalian regulatory elements.

Published
2003
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8. Transcriptional Regulation of the Stem Cell Leukemia Gene (SCL) — Comparative Analysis of Five Vertebrate SCL Loci

Author

Jane Rogers, Berthold Göttgens, James G. R. Gilbert, Michael A Chapman, Anthony R. Green, Bjarne Knudsen, Linda M. Barton, Angus M. Sinclair, Darren Grafham, and David R. Bentley

Subjects
Genetics, Letter, animal structures, Sequence analysis, fungi, Phylogenetic footprinting, Biology, biology.organism_classification, Homology (biology), Conserved sequence, hemic and lymphatic diseases, Enhancer, Gene, Transcription factor, Zebrafish, Genetics (clinical)
Abstract

The stem cell leukemia (SCL) gene encodes a bHLH transcription factor with a pivotal role in hematopoiesis and vasculogenesis and a pattern of expression that is highly conserved between mammals and zebrafish. Here we report the isolation and characterization of the zebrafish SCL locus together with the identification of three neighboring genes, IER5,MAP17, and MUPP1. This region spans 68 kb and comprises the longest zebrafish genomic sequence currently available for comparison with mammalian, chicken, and pufferfish sequences. Our data show conserved synteny between zebrafish and mammalian SCL and MAP17 loci, thus suggesting the likely genomic domain necessary for the conserved pattern ofSCL expression. Long-range comparative sequence analysis/phylogenetic footprinting was used to identify noncoding conserved sequences representing candidate transcriptional regulatory elements. The SCL promoter/enhancer, exon 1, and the poly(A) region were highly conserved, but no homology to other known mouseSCL enhancers was detected in the zebrafish sequence. A combined homology/structure analysis of the poly(A) region predicted consistent structural features, suggesting a conserved functional role in mRNA regulation. Analysis of the SCL promoter/enhancer revealed five motifs, which were conserved from zebrafish to mammals, and each of which is essential for the appropriate pattern or level ofSCL transcription.[The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: N. Tanese.]

Published
2002
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9. The pig X and Y chromosomes: structure, sequence and evolution

Author

Benjamin M. Skinner, Jonathan Wood, Philip Howden, Carol Churcher, Peter J.I. Ellis, Carole A. Sargent, Daria Gordon, William Chow, Denise Carvalho-Silva, Nabeel A. Affara, Giselle Kerry, James G. R. Gilbert, Bee Ling Ng, Heidi Hauser, Glen Threadgold, Toby Hunt, Thomas Wileman, Javier Herrero, Kerstin Howe, Jane E. Loveland, Jo Harley, Chris Tyler-Smith, William Cheng, Siobhan Austin-Guest, Beiyuan Fu, Kim Lachani, Sandra Louzada, Matthew Hardy, Matthew Dunn, Darren Grafham, Daniel Kelly, James Kerwin, Kathryn Beal, Jen Harrow, Fengtang Yang, Skinner, Benjamin [0000-0002-7152-1167], Sargent, Carole [0000-0002-4205-3085], and Apollo - University of Cambridge Repository

Subjects
Resource, 0301 basic medicine, Male, X Chromosome, Swine, Molecular Sequence Data, Gene Conversion, Gene Expression, Genomics, Biology, Y chromosome, Evolution, Molecular, 03 medical and health sciences, Chromosome 16, Dogs, 0302 clinical medicine, Chromosome 19, Y Chromosome, Gene Order, Genetics, Animals, Humans, Gene family, Gene conversion, QH426, Gene, Genetics (clinical), X chromosome, Gene Library, 030304 developmental biology, QL, 0303 health sciences, Base Sequence, Chromosome, Sequence Analysis, DNA, Chromosomes, Mammalian, Chromosome 17 (human), Fosmid, 030104 developmental biology, Chromosome 4, Chromosome 3, Cats, Female, Chromosome 21, Sequence Alignment, 030217 neurology & neurosurgery
Abstract

We have generated an improved assembly and gene annotation of the pig X chromosome, and a first draft assembly of the pig Y chromosome, by sequencing BAC and fosmid clones, and incorporating information from optical mapping and fibre-FISH. The X chromosome carries 1,014 annotated genes, 689 of which are protein-coding. Gene order closely matches that found in Primates (including humans) and Carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X chromosome were absent from the pig (e.g. the cancer/testis antigen family) or inactive (e.g. AWAT1), and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y chromosome assembly focussed on two clusters of male-specific low-copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. The long arm of the chromosome is almost entirely repetitive, containing previously characterised sequences. Many of the ancestral X-related genes previously reported in at least one mammalian Y chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes - both single copy and amplified - on the pig Y, to compare the pig X and Y chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y chromosome evolution.

Published
2014
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10. Next Generation Sequencing in the National Health Service England: A Pipeline that Completely Agrees with Sanger

Author

Jennifer Dawe, Isabel M. Nesbitt, K Elizabeth Allen, Ann Dalton, Kevin Blighe, Darren Grafham, and Nicholas J. Beauchamp

Subjects
Sanger sequencing, Cancer Research, business.industry, Gold standard (test), National health service, computer.software_genre, Pipeline (software), Data science, DNA sequencing, Patient care, symbols.namesake, Oncology, symbols, Medicine, Diagnostic laboratory, Data mining, business, computer
Abstract

As next generation sequencing (NGS) technology has already become a regular fixture in research, it is now time for clinical environments to also reap the benefits of such technology. Indeed, the rich promise of NGS has the potential to be translated into improved patient care. However, there is still doubt about the widespread use of NGS in clinical diagnostics. Before implementation, there must be consensus on which analytical pipeline to use, with follow-up confirmation of variants with the gold standard: Sanger sequencing. Here, we present a NGS analytical pipeline that has complete agreement on 341 variants with Sanger sequencing and that is already being used in our clinical diagnostic laboratory in the National Health Service England for the regular screening of inherited, pathogenic variants. Details on our NGS and other services can be found at http://www.sheffieldchildrens.nhs.uk/our-services/sheffield-diagnostic-genetics-service/. Our pipeline broadly follows the ‘best practices’ guidelines set by the GATK at the Broad Institute, with a novel added approach involving randomly selecting subsets of reads and later merging variants called from each. This allows for falsenegatives to be eliminated with a high level of confidence. Moreover, modeling reduced depth of coverage reveals that 30X is the point at which false-positives are eliminated with >99.9% confidence. Our results allude to a fine balance between read-depth and error, and we believe that our pipeline will increase confidence in NGS and permit its gradual enrollment in clinical diagnostic laboratories.

Published
2014
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11. Characterization ofSCML1,a New Gene in Xp22, with Homology to Developmental Polycomb Genes

Author

J. Durham, Mark T. Ross, Dorothy Trump, A. A. B. Bergen, Susannah M. Walpole, Darren Grafham, J.T. den Dunnen, P. van der Bent, Mark Vaudin, G.J.B. van Ommen, R. Pavitt, E. van de Vosse, Alexia Nicolaou, A. Cahn, John R.W. Yates, J. Wilkinson, and Other departments

Subjects
Genetics, DNA, Complementary, X Chromosome, Base Sequence, Molecular Sequence Data, Retinal Degeneration, Polycomb-Group Proteins, Eye Diseases, Hereditary, Biology, Homology (biology), Repressor Proteins, genomic DNA, Exon, Exon trapping, Animals, Humans, Amino Acid Sequence, Homeotic gene, Hox gene, Gene, Regulator gene
Abstract

Using exon trapping, we have identified a new human gene in Xp22 encoding a 3-kb mRNA. Expression of this RNA is detectable in a range of tissues but is most pronounced in skeletal muscle and heart. The gene, designated “sex comb on midleg-like-1” ( SCML1 ), maps 14 kb centromeric of marker DXS418, between DXS418 and DXS7994, and is transcribed from telomere to centromere. SCML1 spans 18 kb of genomic DNA, consists of six exons, and has a 624-bp open reading frame. The predicted 27-kDa SCML1 protein contains two domains that each have a high homology to two Drosophila transcriptional repressors of the polycomb group (PcG) genes and their homologues in mouse and human. PcG genes are known to be involved in the regulation of homeotic genes, and the mammalian homologues of the PcG genes repress the expression of Hox genes. SCML1 appears to be a new human member of this gene group and may play an important role in the control of embryonal development.

Published
1998
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12. The zebrafish reference genome sequence and its relationship to the human genome

Author

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

Subjects
Genetics, 0303 health sciences, Genome evolution, Multidisciplinary, Gene prediction, Pseudogene, Genome project, Biology, biology.organism_classification, Genome, Article, 03 medical and health sciences, 0302 clinical medicine, Gene density, Zebrafish, 030217 neurology & neurosurgery, 030304 developmental biology, Reference genome
Abstract

Zebrafish have become a popular organism for the study of vertebrate gene function1,2. 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 disease3–5. 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 genes6, 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

13. Modernizing reference genome assemblies

Author

Fiona Cunningham, Elaine R. Mardis, Colin Kremitzki, Derek Albracht, Robert S. Fulton, Richa Agarwala, Tim Hubbard, Glen Threadgold, Hsiu Chuan Chen, Holland Kotkiewicz, S. Whitehead, Nathan Bouk, Jonathan Wood, Katherine Auger, William Chow, Glenn Harden, Lee Trani, Milinn Kremitzki, William M. McLaren, Guy Griffiths, Lucy Matthews, Susan M. Rock, Kerstin Howe, Tina Graves, Paul Heath, Richard K. Wilson, Matthew Dunn, Darren Grafham, Joanna Collins, Evan E. Eichler, Graham R. S. Ritchie, Valerie A. Schneider, Paul Flicek, James Torrance, Lucinda Fulton, Aye Wollam, George M. Weinstock, Sarah Pelan, and Deanna M. Church

Subjects
QH301-705.5, International Cooperation, MEDLINE, Library science, Human genomics, Biology, Genome Complexity, Genomic databases, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Genomic Medicine, Community Page, Databases, Genetic, Humans, Genome Sequencing, Biology (General), 030304 developmental biology, Genetics, 0303 health sciences, General Immunology and Microbiology, Genome complexity, National library, Genome, Human, General Neuroscience, Genomics, 3. Good health, European molecular biology laboratory, 030220 oncology & carcinogenesis, Pacific biosciences, General Agricultural and Biological Sciences, Reference genome
Abstract

I have read the journal's policy and have the following conflicts: Paul Flicek is married to the deputy editor of PLoS Medicine, Melissa Norton. Evan Eichler is on the board of Pacific Biosciences. Support for this work came from the Intramural Research Program of the NIH, The National Library of Medicine, the European Molecular Biology Laboratory, the Wellcome Trust (grant number 077198), and the Howard Hughes Medical Institute (EEE). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Published
2011

15. Sequence Finishing on New Platforms

Author

Darren Grafham and Andries J. van Tonder

Subjects
Genetics, DNA sequencer, Massive parallel sequencing, Shotgun sequencing, Hybrid genome assembly, Computational biology, Biology, Genome, DNA sequencing, ABI Solid Sequencing, Illumina dye sequencing
Abstract

In the past five years, next generation sequencing (NGS) technology platforms have been released and have become the tool of choice for sequencing genomes. Methods for sequence finishing have had to be updated to deal with the issues created by NGS platforms. Finishing begins with the assembling of the reads produced by the sequencing machines before computational gap closure is attempted. Remaining gaps are identified and suitable experimental techniques such as polymerase chain reactions are used to close these. Until recently, the aim for many genome sequencing projects has been to fully finish genomes. However, due to the time and cost associated with finishing, the majority of future genomes will only reach a high-quality draft. New genome standards have had to be defined to better reflect the types of sequencing now being undertaken. Improvements to the current generation of sequencing machines along with the advent of the third-generation technologies means that new ways of dealing with the data volume will need to be sought. Key Concepts: Next generation sequencing platforms have generated new issues for sequence finishing, which have required novel solutions. Genome standards have had to be updated to better reflect NGS data. Keywords: next generation sequencing; finishing; Roche (R) 454 Life Science Genome Sequencer; Illumina (R) Genome Analyzer II; Applied Bioystems (R) SOLiD system; DNA; PCR

Published
2011
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16. Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin

Author

Andrea Maxwell, Kathryn E. Hentges, Alison J. Coffey, Karen Mitchell, Randy L. Johnson, David J. Adams, Karen K. Hirschi, Bonney Wilkinson, Lucy Matthews, Frank J. Probst, Darren Grafham, Lanette S. Woodward, Pablo Marin-Garcia, Hiroaki Miki, Jennifer Harrow, Allan Bradley, Tim Hubbard, Laurens G. Wilming, Bin Liu, Melissa K. Boles, Jane Rogers, Monica J. Justice, Michael D. Risley, James R. Lupski, Anne Parker, Yosuke Funato, Bradley, Allan [0000-0002-2349-8839], and Apollo - University of Cambridge Repository

Subjects
Cancer Research, Computational Biology/Comparative Sequence Analysis, medicine.disease_cause, Conserved sequence, Developmental Biology/Molecular Development, Mice, 0302 clinical medicine, Developmental Biology/Developmental Molecular Mechanisms, Missense mutation, Evolutionary Biology/Genomics, Genetics (clinical), Genetics, 0303 health sciences, Mutation, Splice site mutation, Genetics and Genomics/Functional Genomics, Chromosome Mapping, Nuclear Proteins, Exons, 3. Good health, Biochemistry/Molecular Evolution, Genetics and Genomics/Gene Discovery, Genetics and Genomics/Comparative Genomics, Oxidoreductases, Research Article, lcsh:QH426-470, Genetics and Genomics/Animal Genetics, Sequence analysis, Evolutionary Biology/Developmental Molecular Mechanisms, Cell Biology/Developmental Molecular Mechanisms, Molecular Biology/Molecular Evolution, Biology, Computational Biology/Molecular Genetics, 03 medical and health sciences, medicine, Animals, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Evolutionary Biology/Evolutionary and Comparative Genetics, Point mutation, Gene Expression Profiling, Mice, Mutant Strains, lcsh:Genetics, Ethylnitrosourea, Genes, Lethal, Large-Scale Sequencing, 030217 neurology & neurosurgery, Computational Biology/Genomics
Abstract

An accurate and precisely annotated genome assembly is a fundamental requirement for functional genomic analysis. Here, the complete DNA sequence and gene annotation of mouse Chromosome 11 was used to test the efficacy of large-scale sequencing for mutation identification. We re-sequenced the 14,000 annotated exons and boundaries from over 900 genes in 41 recessive mutant mouse lines that were isolated in an N-ethyl-N-nitrosourea (ENU) mutation screen targeted to mouse Chromosome 11. Fifty-nine sequence variants were identified in 55 genes from 31 mutant lines. 39% of the lesions lie in coding sequences and create primarily missense mutations. The other 61% lie in noncoding regions, many of them in highly conserved sequences. A lesion in the perinatal lethal line l11Jus13 alters a consensus splice site of nucleoredoxin (Nxn), inserting 10 amino acids into the resulting protein. We conclude that point mutations can be accurately and sensitively recovered by large-scale sequencing, and that conserved noncoding regions should be included for disease mutation identification. Only seven of the candidate genes we report have been previously targeted by mutation in mice or rats, showing that despite ongoing efforts to functionally annotate genes in the mammalian genome, an enormous gap remains between phenotype and function. Our data show that the classical positional mapping approach of disease mutation identification can be extended to large target regions using high-throughput sequencing., Author Summary Here we show that tiny DNA lesions can be found in huge amounts of DNA sequence data, similar to finding a needle in a haystack. These lesions identify many new candidates for disease genes associated with birth defects, infertility, and growth. Further, our data suggest that we know very little about what mammalian genes do. Sequencing methods are becoming cheaper and faster. Therefore, our strategy, shown here for the first time, will become commonplace.

Published
2009

17. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage

Author

James R. Lupski, Xiaohong Liu, Sante Gnerre, Bruce W. Birren, Nicole R. Allen, James G. R. Gilbert, Pawel Stankiewicz, Tashi Lokyitsang, Jane E. Loveland, Amr Abouelleil, John E. Major, Manuel Garber, Steven A. McCarroll, April Cook, Mark L. Borowsky, Annie Lui, David C. Schwartz, Jonathan Butler, Christine Nicholson, Chad Nusbaum, Atanas Mihalev, Laurens G. Wilming, Catherine Hosage Norman, Daniel S. Hagopian, Jessica A. Lehoczky, Robert Nicol, David Swarbreck, Cindy Nguyen, Varsha K. Khodiyar, Ted Sharpe, Gavin K. Laird, Evan Mauceli, Russell J. Grocock, Jane Rogers, S. Searle, Charles Shaw-Smith, Michael C. Zody, Toby Bloom, Boris Bugalter, David B. Jaffe, Pieter J. de Jong, Jean L. Chang, Kazutoyo Osoegawa, Michael Kamal, Sinéad B. O'Leary, Steven A. Goldstein, David J. Adams, Richard Gibson, Jennifer Harrow, Sean Humphray, Chao-Kung Chen, Michael Fitzgerald, Allan Bradley, Ken Dewar, Charles A. Steward, Eric S. Lander, E. Hart, David DeCaprio, Nabil Hafez, Matthew C. Jones, Darren Grafham, Tim Hubbard, Vijay Venkataraman, Jonathan M. Mudge, Charles A. Whittaker, Kurt LaButti, Andrew Zimmer, Christina A. Cuomo, Xiaoping Yang, Benjamin Corum, Sarah Young, Pendexter Macdonald, Lucy Matthews, and Weimin Bi

Subjects
Genetics, Base Composition, Multidisciplinary, Sequence Analysis, DNA, Biology, Synteny, Article, Chromosome 17 (human), Evolution, Molecular, Mice, Chromosome 4, Chromosome 16, Long Interspersed Nucleotide Elements, Chromosome 19, Gene Duplication, Animals, Humans, Chromosome 21, Chromosome 22, Chromosomal inversion, Segmental duplication, Chromosomes, Human, Pair 17, Short Interspersed Nucleotide Elements
Abstract

Chromosome 17 is unusual among the human chromosomes in many respects. It is the largest human autosome with orthology to only a single mouse chromosome1, mapping entirely to the distal half of mouse chromosome 11. Chromosome 17 is rich in protein-coding genes, having the second highest gene density in the genome2,3. It is also enriched in segmental duplications, ranking third in density among the autosomes4. Here we report a finished sequence for human chromosome 17, as well as a structural comparison with the finished sequence for mouse chromosome 11, the first finished mouse chromosome. Comparison of the orthologous regions reveals striking differences. In contrast to the typical pattern seen in mammalian evolution5,6, the human sequence has undergone extensive intrachromosomal rearrangement, whereas the mouse sequence has been remarkably stable. Moreover, although the human sequence has a high density of segmental duplication, the mouse sequence has a very low density. Notably, these segmental duplications correspond closely to the sites of structural rearrangement, demonstrating a link between duplication and rearrangement. Examination of the main classes of duplicated segments provides insight into the dynamics underlying expansion of chromosome-specific, low-copy repeats in the human genome.

Published
2006

18. Canine RPGRIP1 mutation establishes cone-rod dystrophy in miniature longhaired dachshunds as a homologue of human Leber congenital amaurosis

Author

Cathryn S. Mellersh, Susan H. Blanton, Mark Vaudin, Oliver P. Forman, Keith C. Barnett, Darren Grafham, J. Sampson, Louise Pettitt, Matthew M. Binns, Edward Ryder, N. G. Holmes, and Mike Boursnell

Subjects
genetic structures, 040301 veterinary sciences, DNA Mutational Analysis, Locus (genetics), Optic Atrophy, Hereditary, Leber, Biology, Leber congenital amaurosis, Canine, 0403 veterinary science, 03 medical and health sciences, Exon, Dogs, Retinitis pigmentosa, medicine, Genetics, Animals, Humans, RPGRIP1, Child, Gene, 030304 developmental biology, Synteny, Chromosomes, Human, Pair 14, 0303 health sciences, Dystrophy, Chromosome, Infant, Proteins, 04 agricultural and veterinary sciences, Exons, medicine.disease, eye diseases, Pedigree, Cone–rod dystrophy, Cytoskeletal Proteins, Disease Models, Animal, Mutagenesis, Insertional, Codon, Nonsense, Child, Preschool, Retinal Dystrophies
Abstract

Cone–rod dystrophy 1 (cord1) is a recessive condition that occurs naturally in miniature longhaired dachshunds (MLHDs). We mapped the cord1 locus to a region of canine chromosome CFA15 that is syntenic with a region of human chromosome 14 (HSA14q11.2) containing the retinitis pigmentosa GTPase regulator-interacting protein 1 (RPGRIP1) gene. Mutations in RPGRIP1 have been shown to cause Leber congenital amaurosis, a group of retinal dystrophies that represent the most common genetic causes of congenital visual impairment in infants and children. Using the newly available canine genome sequence we sequenced RPGRIP1 in affected and carrier MLHDs and identified a 44-nucleotide insertion in exon 2 that alters the reading frame and introduces a premature stop codon. All affected and carrier dogs within an extended inbred pedigree were homozygous and heterozygous, respectively, for the mutation. We conclude the mutation is responsible for cord1 and demonstrate that this canine disease is a valuable model for exploring disease mechanisms and potential therapies for human Leber congenital amaurosis.

Published
2005

20. Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags

Author

Haizhou Tang, James K. Bonfield, Jane Rogers, Christopher Hyland, Ian M. Overton, Matthew D. Francis, Ewan Birney, Simon J. Hubbard, William Brown, Joan Burnside, Darren Grafham, Sam Griffiths-Jones, Michael D. R. Croning, Kevin J. Beattie, Carol Scott, Robert L. Davies, Sean Humphray, Elizabeth R. Farrell, Ruth Taylor, Stuart A. Wilson, Paul E. Boardman, Stuart McLaren, and Cheryll Tickle

Subjects
animal structures, DNA, Complementary, RNA, Untranslated, Transcription, Genetic, Sequence analysis, Sequence alignment, Biology, Transcriptome, Chicken Special/Resources, Complementary DNA, Genetics, Ensembl, Animals, Humans, Genomic library, Cloning, Molecular, Gene, Genetics (clinical), Gene Library, Expressed Sequence Tags, Expressed sequence tag, Computational Biology, Sequence Analysis, DNA, MicroRNAs, Chickens, Sequence Alignment
Abstract

We present an analysis of the chicken (Gallus gallus) transcriptome based on the full insert sequences for 19,626 cDNAs, combined with 485,337 EST sequences. The cDNA data set has been functionally annotated and describes a minimum of 11,929 chicken coding genes, including the sequence for 2260 full-length cDNAs together with a collection of noncoding (nc) cDNAs that have been stringently filtered to remove untranslated regions of coding mRNAs. The combined collection of cDNAs and ESTs describe 62,546 clustered transcripts and provide transcriptional evidence for a total of 18,989 chicken genes, including 88% of the annotated Ensembl gene set. Analysis of the ncRNAs reveals a set that is highly conserved in chickens and mammals, including sequences for 14 pri-miRNAs encoding 23 different miRNAs. The data sets described here provide a transcriptome toolkit linked to physical clones for bioinformaticians and experimental biologists who wish to use chicken systems as a low-cost, accessible alternative to mammals for the analysis of vertebrate development, immunology, and cell biology.

Published
2004
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21. BAC finishing strategies

Author

Christine, Bird and Darren, Grafham

Subjects
Chromosomes, Artificial, Bacterial, Contig Mapping, Base Sequence, Genome, Human, Software Design, Humans, Nucleic Acid Conformation, Sequence Analysis, DNA, Cloning, Molecular, Databases, Nucleic Acid, DNA Primers, Plasmids
Published
2004

23. Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci

Author

Jane Rogers, Anthony R. Green, Ian J. Donaldson, James G. R. Gilbert, Darren Grafham, Berthold Göttgens, and Michael A Chapman

Subjects
Genetic Markers, Web server, Molecular Sequence Data, Lyases, Genomics, Sequence alignment, Locus (genetics), Computational biology, Biology, computer.software_genre, Genome, Online Systems, Mice, Dogs, Databases, Genetic, Genetics, Animals, Humans, Genetics (clinical), Internet, Leukemia, Genome, Human, Resources, Rats, DNA binding site, Research Design, Pairwise comparison, Human genome, computer, Sequence Alignment, Genes, Neoplasm
Abstract

Comparative analysis of genomic sequences is becoming a standard technique for studying gene regulation. However, only a limited number of tools are currently available for the analysis of multiple genomic sequences. An extensive data set for the testing and training of such tools is provided by the SCL gene locus. Here we have expanded the data set to eight vertebrate species by sequencing the dog SCL locus and by annotating the dog and rat SCL loci. To provide a resource for the bioinformatics community, all SCL sequences and functional annotations, comprising a collation of the extensive experimental evidence pertaining to SCL regulation, have been made available via a Web server. A Web interface to new tools specifically designed for the display and analysis of multiple sequence alignments was also implemented. The unique SCL data set and new sequence comparison tools allowed us to perform a rigorous examination of the true benefits of multiple sequence comparisons. We demonstrate that multiple sequence alignments are, overall, superior to pairwise alignments for identification of mammalian regulatory regions. In the search for individual transcription factor binding sites, multiple alignments markedly increase the signal-to-noise ratio compared to pairwise alignments.

Published
2004

24. Comparative and functional analyses of LYL1 loci establish marsupial sequences as a model for phylogenetic footprinting

Author

Michael A, Chapman, Fadi J, Charchar, Sarah, Kinston, Christine P, Bird, Darren, Grafham, Jane, Rogers, Frank, Grützner, Jennifer A Marshall, Graves, Anthony R, Green, and Berthold, Göttgens

Subjects
Base Sequence, Models, Genetic, Sequence Homology, Amino Acid, Molecular Sequence Data, Chromosome Mapping, DNA, Neoplasm Proteins, DNA-Binding Proteins, Marsupialia, Sequence Homology, Nucleic Acid, Basic Helix-Loop-Helix Transcription Factors, Animals, Amino Acid Sequence, Promoter Regions, Genetic, Phylogeny
Abstract

Comparative genomic sequence analysis is a powerful technique for identifying regulatory regions in genomic DNA. However, its utility largely depends on the evolutionary distances between the species involved. Here we describe the screening of a genomic BAC library from the stripe-faced dunnart, Sminthopsis macroura, formerly known as the narrow-footed marsupial mouse. We isolated a clone containing the LYL1 locus, completely sequenced the 60.6-kb insert, and compared it with orthologous human and mouse sequences. Noncoding homology was substantially reduced in the human/dunnart analysis compared with human/mouse, yet we could readily identify all promoters and exons. Human/mouse/dunnart alignments of the LYL1 candidate promoter allowed us to identify putative transcription factor binding sites, revealing a pattern highly reminiscent of critical regulatory regions of the LYL1 paralogue, SCL. This newly identified LYL1 promoter showed strong activity in myeloid progenitor cells and was bound in vivo by Fli1, Elf1, and Gata2-transcription factors all previously shown to bind to the SCL stem cell enhancer. This study represents the first large-scale comparative analysis involving marsupial genomic sequence and demonstrates that such comparisons provide a powerful approach to characterizing mammalian regulatory elements.

Published
2003

25. Initial sequencing and comparative analysis of the mouse genome

Author

Laura Elnitski, David B. Jaffe, Jia Li, Marina Alexandersson, Michael J. Morgan, Shiaw Pyng Yang, Robert Baertsch, Claire M. Wade, John Tromp, Michael C. Zody, Terrence S. Furey, Emma Overton-Larty, Stephen D. Brown, Scott Schwartz, Diane M. Dunn, J. P. Leger, Kris A. Wetterstrand, David Torrents, Ratna Shownkeen, Brian Schultz, Kim C. Worley, Richard D. Emes, John Mayer, Tom Landers, Beverley Meredith, Carol Scott, R. J. Weber, Sean R. Eddy, David Kulp, Jun Kawai, J Bailey, Fan Hsu, Diana L. Kolbe, Kirsten McLay, Marc Botcherby, Richard Mott, Tracie L. Miner, Jill P. Mesirov, Cristyn Kells, Michael A. Quail, Melanie M. Wall, Alistair G. Rust, Josep F. Abril, Ian F Korf, Peter An, Roderic Guigó, Abel Ureta-Vidal, Evan Mauceli, L. Steven Johnson, Arian F.A. Smit, Arkadiusz Kasprzyk, Michael C. Wendl, Deanna M. Church, Francis S. Collins, Wayne N. Frankel, Pallavi Eswara, Bin Ma, Robert H. Waterston, Stylianos E. Antonarakis, Edward M. Rubin, John Douglas Mcpherson, Andrew Sheridan, Megan McCarthy, Ming Li, Colin N. Dewey, Justin Deri, Rosie Levine, Matthew Jones, Sheila Dodge, Richard R. Copley, Leo Goodstadt, Shan Yang, Donna Maglott, Jamey Wierzbowski, Nick Goldman, Evgeny M. Zdobnov, Simon G. Gregory, C M Clee, Steven Leonard, Elaine R. Mardis, Simon C. Potter, Sarah Sims, Richard A. Gibbs, Mark S. Guyer, Francesca Chiaromonte, Susan Lucas, Mark Diekhans, Steve Searle, Rachel Ainscough, Jane Peterson, Emmanouil T. Dermitzakis, Robert Nicol, Lucy Matthews, Guy Slater, Adam Felsenfeld, Karen Foley, Lucinda Fulton, Tim Hubbard, Richard K. Wilson, Deana W. LaHillier, W. Richard McCombie, Johanna Thompson, Robert David, John Attwood, Anthony P. West, Jane Rogers, Evan Keibler, Lisa Cook, Raju Kucherlapati, Steven Seaman, William E. Nash, Ian J. Jackson, Jonathan Singer, Axin Hua, Tina Graves, Ted Sharpe, Dudley Wyman, Bruce W. Birren, Stuart McLaren, David Willey, A Joy, Douglas Smith, Alexandre Reymond, Paul Flicek, Simon Cawley, Richa Agarwala, Diane Gage, Evanne Trevaskis, Ginger A. Fewell, Michael R. Brent, Tracy C. Ponce, W. James Kent, Timothy Holzer, Eduardo Eyras, Michael J. O’Connor, Webb Miller, Donna M. Muzny, Andrew von Niederhausern, Inna Dubchak, Eitan E. Winter, Catherine Ucla, Arne Stabenau, Michael N. Nhan, Piero Carninci, Michele Clamp, Pavel A. Pevzner, James Meldrim, Tim Cutts, R. D. Campbell, Joy Davies, Wratko Hlavina, Elinor K. Karlsson, David Haussler, John Burton, Peer Bork, Nicole Stange-Thomann, Mikita Suyama, Mark J. Daly, Ewan Birney, Edward J. Kulbokas, Craig Pohl, James C. Mullikin, Chad Nusbaum, Genís Parra, Jade P. Vinson, Yoshihide Hayashizaki, Sante Gnerre, Eric Berry, Daniel G. Brown, Asif T. Chinwalla, Emmanuel Mongin, Robert B. Weiss, Raymond Wheeler, Andrew Kirby, Yasushi Okazaki, Lior Pachter, Ross C. Hardison, Brian Spencer, Carol J. Bult, Joanne O. Nelson, Pankaj K. Agarwal, Darren Grafham, Gustavo Glusman, Thomas A. Jones, Glenn Tesler, Simon Whelan, James Cuff, Robert S. Fulton, K F Barlow, Jörg Schultz, Matthias S. Schwartz, Alex Poliakov, Jonathan Butler, Bruce A. Roe, Angela S. Hinrichs, Alan Coulson, Kate Montgomery, Eric D. Green, Stephan Beck, Val Curwen, Krishna M. Roskin, Robert W. Plumb, Chris P. Ponting, Ralph Santos, Victor Sapojnikov, Nicolas Bray, Kymberlie H. Pepin, Charles W. Sugnet, Olivier Couronne, Ivica Letunic, Sophie Williams, Kimberly D. Delehaunty, Kerstin Lindblad-Toh, Zemin Ning, Karen Oliver, Toby Bloom, Michael Kamal, Nicholas J. Dickens, Eric S. Lander, Christine Lloyd, Donna Karolchik, Adrienne Hunt, Antonarakis, Stylianos, Couronne, Olivier, Dermitzakis, Emmanouil, and Zdobnov, Evgeny

Subjects
RNA, Untranslated, Proteome, Untranslated/genetics, Genome, Transgenic, Repetitive Sequences, Mice, Models, Neoplasms, Conserved Sequence, ddc:616, Genetics, Mice, Knockout, Base Composition, Multidisciplinary, Sex Chromosomes, Pseudogenes/genetics, Genomics, Multigene Family/genetics, Physical Chromosome Mapping, Neoplasms/genetics, CpG Islands/genetics, Proteome/genetics, Genetic Variation/genetics, Multigene Family, Mice/classification/ genetics, Models, Animal, Conserved Sequence/genetics, Sequence Analysis, Pseudogenes, Human, Genome evolution, Evolution, Sequence analysis, Knockout, Quantitative Trait Loci, Mice, Transgenic, Sex Chromosomes/genetics, Computational biology, Biology, Synteny, Chromosomes, Evolution, Molecular, Nucleic Acid/genetics, Genetic, Species Specificity, Mammalian/ genetics, Animals, Humans, Genes/genetics, Selection, Genetic, Selection, Repetitive Sequences, Nucleic Acid, Comparative genomics, Animal, Genome, Human, Molecular, Genetic Variation, DNA, Sequence Analysis, DNA, Chromosomes, Mammalian, Gene Expression Regulation, Genes, Mutagenesis, RNA, Human genome, CpG Islands, Quantitative Trait Loci/genetics, Reference genome
Abstract

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

Published
2002

26. 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

27. Regulation of the stem cell leukemia (SCL) gene: a tale of two fishes

Author

David Bentley, James G. R. Gilbert, Linda M. Barton, Martin Gering, Anthony R. Green, Roger Patient, Jane Rogers, Berthold Göttgens, and Darren Grafham

Subjects
animal structures, Molecular Sequence Data, Locus (genetics), Biology, behavioral disciplines and activities, Animals, Genetically Modified, immune system diseases, Proto-Oncogene Proteins, hemic and lymphatic diseases, Genes, Regulator, Basic Helix-Loop-Helix Transcription Factors, Animals, Amino Acid Sequence, Enhancer, Zebrafish, Gene, T-Cell Acute Lymphocytic Leukemia Protein 1, Genetics, Regulation of gene expression, Gene Rearrangement, Reporter gene, Multidisciplinary, Basic helix-loop-helix, Reverse Transcriptase Polymerase Chain Reaction, Helix-Loop-Helix Motifs, fungi, Fishes, Chromosome Mapping, Gene Expression Regulation, Developmental, Gene rearrangement, Biological Sciences, Zebrafish Proteins, biology.organism_classification, DNA-Binding Proteins, Gene Expression Regulation, Female, Transcription Factors
Abstract

The stem cell leukemia ( SCL ) gene encodes a tissue-specific basic helix–loop–helix (bHLH) protein with a pivotal role in hemopoiesis and vasculogenesis. Several enhancers have been identified within the murine SCL locus that direct reporter gene expression to subdomains of the normal SCL expression pattern, and long-range sequence comparisons of the human and murine SCL loci have identified additional candidate enhancers. To facilitate the characterization of regulatory elements, we have sequenced and analyzed 33 kb of the SCL genomic locus from the pufferfish Fugu rubripes , a species with a highly compact genome. Although the pattern of SCL expression is highly conserved from mammals to teleost fish, the genes flanking pufferfish SCL were unrelated to those known to flank both avian and mammalian SCL genes. These data suggest that SCL regulatory elements are confined to the region between the upstream and downstream flanking genes, a region of 65 kb in human and 8.5 kb in pufferfish. Consistent with this hypothesis, the entire 33-kb pufferfish SCL locus directed appropriate expression to hemopoietic and neural tissue in transgenic zebrafish embryos, as did a 10.4-kb fragment containing the SCL gene and extending to the 5′ and 3′ flanking genes. These results demonstrate the power of combining the compact genome of the pufferfish with the advantages that zebrafish provide for studies of gene regulation during development. Furthermore, the pufferfish SCL locus provides a powerful tool for the manipulation of hemopoiesis and vasculogenesis in vivo .

Published
2001

28. Long-Range Comparison of Human and Mouse SCL Loci: Localized Regions of Sensitivity to Restriction Endonucleases Correspond Precisely with Peaks of Conserved Noncoding Sequences

Author

Berthold Göttgens, David R. Bentley, Anthony R. Green, Jane Rogers, Darren Grafham, James G. R. Gilbert, and Linda M. Barton

Subjects
Genetic Markers, Letter, Sequence analysis, Molecular Sequence Data, Locus (genetics), Mice, Inbred Strains, Biology, DNA, Mitochondrial, Homology (biology), Conserved sequence, Mice, Proto-Oncogene Proteins, Sequence Homology, Nucleic Acid, Genetics, Basic Helix-Loop-Helix Transcription Factors, Animals, Deoxyribonuclease I, Humans, Leukemia-Lymphoma, Adult T-Cell, Gene, Genetics (clinical), Conserved Sequence, T-Cell Acute Lymphocytic Leukemia Protein 1, Base Composition, Base Sequence, Hydrolysis, Stem Cells, Genetic Variation, DNA Restriction Enzymes, Chromatin, DNA-Binding Proteins, Restriction enzyme, Regulatory sequence, Genes, Neoplasm, Transcription Factors
Abstract

Long-range comparative sequence analysis provides a powerful strategy for identifying conserved regulatory elements. The stem cell leukemia (SCL) gene encodes a bHLH transcription factor with a pivotal role in hemopoiesis and vasculogenesis, and it displays a highly conserved expression pattern. We present here a detailed sequence comparison of 193 kb of the human SCL locus to 234 kb of the mouse SCL locus. Four new genes have been identified together with an ancient mitochondrial insertion in the human locus. The SCL gene is flanked upstream by theSIL gene and downstream by the MAP17 gene in both species, but the gene order is not collinear downstream fromMAP17. To facilitate rapid identification of candidate regulatory elements, we have developed a new sequence analysis tool (SynPlot) that automates the graphical display of large-scale sequence alignments. Unlike existing programs, SynPlot can display the locus features of more than one sequence, thereby indicating the position of homology peaks relative to the structure of all sequences in the alignment. In addition, high-resolution analysis of the chromatin structure of the mouse SCL gene permitted the accurate positioning of localized zones accessible to restriction endonucleases. Zones known to be associated with functional regulatory regions were found to correspond precisely with peaks of human/mouse homology, thus demonstrating that long-range human/mouse sequence comparisons allow accurate prediction of the extent of accessible DNA associated with active regulatory regions.

Published
2001

29. Genome Project Standards in a New Era of Sequencing

Author

George M. Weinstock, D. C. Bruce, Dawn Field, Scott H. Harrison, Eugene Kolker, T. Metha, Patrick S. G. Chain, Jeremy Schmutz, Xiang Qin, Julian Parkhill, Tina GravesT. Graves, D. Lang, Karen E. Nelson, Robert L. Strausberg, Aye Wollam, Alla Lapidus, Victor Markowitz, Yan Ding, Michael Fitzgerald, Robert S. Fulton, Donna M. Muzny, Jessica B. Hostetler, Samuel Pitluck, S. A. Malfatti, Chinnappa D. Kodira, James R. Cole, Christian J. Buhay, Nicholas R. Thomson, Shanmuga Sozhamannan, George M. Garrity, Bruce W. Birren, James M. Tiedje, Darren Grafham, Shannon Dugan, Timothy D. Read, Richard A. Gibbs, Granger G. Sutton, Johar Ali, H. M. Khouri, Cliff S. Han, Peter Sterk, Nikos C. Kyrpides, Philip Hugenholtz, Sarah K. Highlander, and John C. Detter

Subjects
Genetics, Multidisciplinary, Contig, Test data generation, DNA sequencing theory, Pyrosequencing, Hybrid genome assembly, Genomics, Genome project, Biology, Data science, Genome
Abstract

For over a decade, genome sequences have adhered to only two standards that are relied on for purposes of sequence analysis by interested third parties (1, 2). However, ongoing developments in revolutionary sequencing technologies have resulted in a redefinition of traditional whole-genome sequencing that requires reevaluation of such standards. With commercially available 454 pyrosequencing (followed by Illumina, SOLiD, and now Helicos), there has been an explosion of genomes sequenced under the moniker “draft”; however, these can be very poor quality genomes (due to inherent errors in the sequencing technologies, and the inability of assembly programs to fully address these errors). Further, one can only infer that such draft genomes may be of poor quality by navigating through the databases to find the number and type of reads deposited in sequence trace repositories (and not all genomes have this available), or to identify the number of contigs or genome fragments deposited to the database. The difficulty in assessing the quality of such deposited genomes has created some havoc for genome analysis pipelines and has contributed to many wasted hours. Exponential leaps in raw sequencing capability and greatly reduced prices have further skewed the time- and cost-ratios of draft data generation versus the painstaking process of improving and finishing a genome. The result is an ever-widening gap between drafted and finished genomes that only promises to continue (see the figure, page 236); hence, there is an urgent need to distinguish good from poor data sets.

Published
2009
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30. The DNA sequence of human chromosome 22

Author

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

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

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

Published
1999

31. Tdr2, a new zebrafish transposon of the Tc1 family

Author

Anthony R. Green, Berthold Göttgens, Darren Grafham, Linda M. Barton, and Mark Vaudin

Subjects
Transposable element, Inverted repeat, Molecular Sequence Data, Transposases, Biology, Sequence Homology, Nucleic Acid, Simple transposon, Genetics, Animals, Amino Acid Sequence, Insertion sequence, Zebrafish, Transposase, Phylogeny, Repetitive Sequences, Nucleic Acid, Expressed sequence tag, Base Sequence, Sequence Homology, Amino Acid, General Medicine, DNA, Sequence Analysis, DNA, biology.organism_classification, Composite transposon, DNA Transposable Elements, Sequence Alignment
Abstract

We describe here Tdr2, a new class of Tc1-like transposons in zebrafish. Tdr2 was identified from the genomic sequence of a zebrafish PAC (P1 artificial chromosome) clone, and fragments of Tdr2 were found in several zebrafish EST (expressed sequence tag) sequences. Predicted translation of the Tdr2 transposase gene showed that it was most closely related to Caenorhabditis elegans Tc3A, suggesting an ancient origin of the Tdr2 transposon. Tdr2 spans 1.1 kb and is flanked by inverted repeats of approx. 100 bp. The 5′ repeat is itself composed of an inverted repeat, raising the possibility of the formation of a cruciform DNA structure. Tdr2 transposons may facilitate the development of novel transposon-based tools for the genetic analysis of zebrafish.

Published
1999

32. 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
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33. Correction: Initial sequencing and analysis of the human genome

Author

Paul Predki, John Sulston, William Morris, Sarah Wenning, Jun Gu, Danielle Thierry-Mieg, Roger A. Schultz, Michael J. Morgan, Michael Doyle, Joseph Szustakowki, Lorenzo Cerutti, A. Coulson, Alex Bateman, Patrick Wincker, Michael C. Zody, Mark T. Ross, Paul G. Richardson, Keri Devon, Yasushi Totoki, Karsten Hokamp, George M. Weinstock, John Howland, Arek Kaspryzk, James G. R. Gilbert, Cher Miranda, Aristides Patrinos, William Saurin, A. Pia Abola, Kazuhiko Kawasaki, John Bouck, Marvin Frazier, Wonhee Jang, Jan Fang Cheng, Stephanie L. Chissoe, Matthew C. Jones, Glen A. Evans, Huanming Yang, Daniel G. Brown, Richard Durbin, Jennifer Baldwin, Tracie L. Miner, Asif T. Chinwalla, Arian F.A. Smit, C M Clee, Elaine R. Mardis, Henning Hermjakob, Nicole Stange-Thomann, Maynard V. Olson, Jian Wang, Cyrus L. Harmon, Shiaw Pyng Yang, André Rosenthal, Catherine Robert, Masahira Hattori, Jane Peterson, Ratna Shownkeen, Maria Athanasiou, Christopher B. Burge, Erica Sodergren, Carrie Sougnez, Lynn Doucette-Stamm, Hidemi Watanabe, Ronald W. Davis, Tarjei S. Mikkelsen, Mark Rosetti, Christopher J. Elkin, Todd M. Lowe, LaDeana W. Hillier, Jane Grimwood, Kazutoyo Osoegawa, Richard R. Copley, Simon Kasif, Joseph J. Catanese, Keith Weinstock, Lee Rowen, Roel Funke, Paul Kitts, Lukas Wagner, Guy Slater, Anne S. Olsen, Edward Uberbacher, Lucinda Fulton, Andrew Dunham, Andrew Heaford, David Kulp, Elbert Branscomb, William Fitzhugh, Eugene V. Koonin, Leroy Hood, Anup Madan, Jean Thierry-Mieg, Richard Reinhardt, Kim C. Worley, Richard M. Myers, Dudley Wyman, Jean Weissenbach, David R. Bentley, Panos Deloukas, Philippe Brottier, H. Blöcker, Stephan Beck, Marc Rubenfield, Terrence S. Furey, Ken Dewar, Michael L. Metzker, Rajinder Kaul, Guyang Huang, Hsiu Chuan Chen, Ewan Birney, Warren Gish, John Douglas Mcpherson, Asao Fujiyama, Aoife McLysaght, Shinsei Minoshima, Sandra W. Clifton, Lisa Kann, R Ainscough, K. Hornischer, Simon G. Gregory, Lauren Linton, Kim D. Delehaunty, James C. Mullikin, Neilay Dedhia, Matthias Platzer, Gerald Nyakatura, John V. Moran, Andrew J. Mungall, Chiharu Kawagoe, François Artiguenave, Deanna M. Church, Elia Stupka, Jun Yu, Peer Bork, Evan E. Eichler, L. Aravind, James H. Gorrell, Bruce A. Roe, Raymond Wheeler, Norman A. Doggett, Douglas R. Smith, Yu Juin Chen, David Haussler, Todd D. Taylor, Stefan Taudien, Susan Lucas, Rebecca Deadman, Hans Lehrach, Hiroaki Shizuya, Doron Lancet, Greg Schuler, Nigel P. Carter, John Burton, Huaqin Pan, Eric S. Lander, Andreas Rump, Nikola Stojanovic, Victor J. Pollara, Alan Williams, Melissa De La Bastide, W. James Kent, Mark S. Guyer, Nicola Mulder, Sarah Milne, Bruce W. Birren, John W. Wallis, Joann Dubois, Tom Slezak, Lisa Cook, Raju Kucherlapati, Andrew Delehaunty, Lucy Matthews, Ian Dunham, L. Steven Johnson, Robert H. Waterston, Andrew Sheridan, Jörg Schultz, Nancy A. Federspiel, Jason B. Kramer, Tim Hubbard, Ru Fang Yeh, Steven E. Scherer, Francis S. Collins, David L. Nelson, Sean Humphray, Tobias Doerks, Chad Nusbaum, Darren Grafham, Mei Lee Hong, Michael Proctor, Christopher K. Raymond, Diane Gage, Kris A. Wetterstrand, Feng Chen, Simon Mercer, Thomas A. Jones, Trevor Hawkins, Aravind Subramanian, Jeffrey A. Bailey, Amanda McMurray, Serafim Batzoglou, Jeremy Schmutz, Jill P. Mesirov, Shizen Qin, Rosie Levine, Adam Felsenfeld, Thomas Brüls, Kevin McKernan, Michele E. Clamp, Christine Lloyd, Susan L. Naylor, Gabriele Nordsiek, Jessica A. Lehoczky, Adrienne Hunt, Marco A. Marra, David R. Cox, Mark Dickson, Michael C. Wendl, Yuri I. Wolf, Jane Rogers, Ian F Korf, Eric Pelletier, Takehiko Itoh, Juliane Ramser, Robert S. Fulton, Sarah Sims, Richard A. Gibbs, Lisa French, Katrina Harris, Richa Agarwala, Christina Raymond, James Meldrim, Sangdun Choi, Richard K. Wilson, Patrick Minx, Douglas L. Johnson, Yoshiyuki Sakaki, Scot Kennedy, Pieter J. de Jong, Yoshihide Hayashizaki, W. Richard McCombie, Sean R. Eddy, Donna M. Muzny, Jerome Naylor, Paul A. McEwan, Atsushi Toyoda, Tetsushi Yada, Nobuyoshi Shimizu, Robert W. Plumb, Catherine M. Rives, Chris P. Ponting, Ralph Santos, Kenneth H. Wolfe, Kymberlie H. Pepin, Roland Heilig, and James E. Galagan

Subjects
Multidisciplinary, Correction, Human genome, Computational biology, Biology
Published
2001
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34. Correction: Corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Author

Lindsay Robertson, Christian von Mering, David Torrents, Paul E. Boardman, Erik Axelsson, Pieter J. deJong, Darren K. Griffin, Ivan Ovcharenko, James K. Bonfield, Tina Graves, Hidetoshi Inoko, Cheryll Tickle, Tracie L. Miner, Kevin J. Beattie, Leo Goodstadt, David W. Burt, John W. Wallis, Richard P. M. A. Crooijmans, Marcia M. Miller, Zissimos Mourelatos, David Speed, Dan Layman, Robert L. Davies, Laura Elnitski, Michael N Romanov, Michael R. Brent, Francesca Chiaromonte, Svitlana Tyekucheva, Jun Wang, Susanne Kerje, Wesley C. Warren, J. J. Emerson, Sergi Castellano, Catrina Fronick, Mary E. Delany, Stuart McLaren, Eduardo Eyras, Kimberly D. Delehaunty, Takashi Shiina, Lucinda Fulton, Michael N. Nhan, Elaine R. Mardis, Mikael Brandström, Patrick Minx, LaDeana W. Hillier, Pavel A. Pevzner, John Douglas Mcpherson, Adam Siepel, David C. King, Lisa Stubbs, Ivica Letunic, Niclas Backström, Hiroshi Arakawa, Maxim Koriabine, Stephen M. J. Searle, Valerie Fillon, Gill Bejerano, Bob Paton, Glenn Tesler, Jessica Severin, Ze Cheng, Leif C. Andersson, Zhirong Bao, David Haussler, Roderic Guigó, Francisco Camara, Sandra W. Clifton, Robert Ivarie, Rick K. Wilson, James C. Kaufman, Mikhail Nefedov, Scott M. Smith, David Shteynberg, Anton Nekrutenko, Mikita Suyama, Jacqueline Smith, Susan Lucas, Arian F.A. Smit, Robert Castelo, Martien A. M. Groenen, Ewan Birney, William Brown, Shiaw-Pyng Yang, Karsten Skjoedt, Lina Jacobbson, Carol Scott, Paul Flicek, Webb Miller, Andrzej M. Kierzek, Yuri Bezzubov, Catherine M. Rondelli, David Morrice, Olivier Pourquié, Stylianos E. Antonarakis, Michael D. R. Croning, Catherine Ucla, Brian J. Raney, Jan Aerts, Jian Wang, Lachlan G. Oddy, Simon J. Hubbard, Peer Bork, Asif T. Chinwalla, Anusha Radakrishnan, Evgeny M. Zdobnov, Artemis G. Hatzigeorgiou, Hans Ellegren, Alain Vignal, Jean-Marie Buerstedde, Matthew T. Webster, Robert S. Harris, Lior Pachter, Henrik Kaessmann, Manyuan Long, Bin Liu, Colin Kremitzki, Pallavi Eswara, Jane Rogers, Evan E. Eichler, Darren Grafham, Jianbin He, D. Waddington, Laurie Gordon, Caleb Webber, W. James Kent, Sam Griffiths-Jones, Gane Ka-Shu Wong, Esther Betrán, Andrew H. Paterson, Sourav Chatterji, Jan J. van der Poel, Nicholas J. Dickens, Terrence S. Furey, Genís Parra, Ian M. Overton, Chris P. Ponting, Randolph B. Caldwell, Sofia Berlin, Isabelle Dupanloup, Rachel A. Harte, Eray Tuzun, Julio S. Masabanda, Matthew D. Francis, Elizabeth J. Huckle, Andy Law, Robert S. Fulton, Kateryna D. Makova, Jan Salomonsen, William E. Nash, Helen G. Tempest, Ross C. Hardison, Sean Humphray, Jerry B. Dodgson, James E. Taylor, Paul F. Cliften, Guillaume Bourque, Monique Rijnkels, Angie S. Hinrichs, Joanne O. Nelson, Josep F. Abril, Colin N. Dewey, Alexandre Reymond, Andrei Kouranov, Craig Pohl, Michael M. Hoffman, Jun Yu, Vincent Magrini, Jacqueline M. Bye, Huanming Yang, Abel Ureta-Vidal, Ruth Taylor, Laura M. Daniels, Shan Yang, Stuart A. Wilson, and Jennifer Randall-Maher

Subjects
Multidisciplinary, biology, Evolutionary biology, biology.animal, Perspective (graphical), Vertebrate, Erratum, Genome, Sequence (medicine)
Published
2005

Catalog

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