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• Journal article
  Davies JC, Alton EWFW, 2010,

  Gene therapy for cystic fibrosis.

  , Proc Am Thorac Soc, Vol: 7, Pages: 408-414

  The report of the first patients with cystic fibrosis (CF) to receive cystic fibrosis transmembrane conductance regulator gene (CFTR) therapy appeared in 1993, and since then there have been more than 20 clinical trials of both viral and nonviral gene transfer agents. These have largely been single dose to either nose or lower airway and have been designed around molecular or bioelectrical outcome measures. Both transgene mRNA and partial correction of chloride secretion have been reported, although sodium hyperabsorption has not been improved. The U.K. Cystic Fibrosis Gene Therapy Consortium is focused on a clinical program to establish whether these proof-of-principle measures translate into clinical benefit. Here, we review the published literature, discuss the limitations to gene therapy in the CF airway, and consider issues influencing the design of clinical trial programs.

  • Abstract
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• Journal article
  Heid IM, Jackson AU, Randall JC, Winkler TW, Qi L, Steinthorsdottir V, Thorleifsson G, Zillikens MC, Speliotes EK, Maegi R, Workalemahu T, White CC, Bouatia-Naji N, Harris TB, Berndt SI, Ingelsson E, Willer CJ, Weedon MN, Luan J, Vedantam S, Esko T, Kilpelaeinen TO, Kutalik Z, Li S, Monda KL, Dixon AL, Holmes CC, Kaplan LM, Liang L, Min JL, Moffatt MF, Molony C, Nicholson G, Schadt EE, Zondervan KT, Feitosa MF, Ferreira T, Allen HL, Weyant RJ, Wheeler E, Wood AR, Estrada K, Goddard ME, Lettre G, Mangino M, Nyholt DR, Purcell S, Smith AV, Visscher PM, Yang J, McCarroll SA, Nemesh J, Voight BF, Absher D, Amin N, Aspelund T, Coin L, Glazer NL, Hayward C, Heard-Costa NL, Hottenga J-J, Johansson A, Johnson T, Kaakinen M, Kapur K, Ketkar S, Knowles JW, Kraft P, Kraja AT, Lamina C, Leitzmann MF, McKnight B, Morris AP, Ong KK, Perry JRB, Peters MJ, Polasek O, Prokopenko I, Rayner NW, Ripatti S, Rivadeneira F, Robertson NR, Sanna S, Sovio U, Surakka I, Teumer A, van Wingerden S, Vitart V, Zhao JH, Cavalcanti-Proenca C, Chines PS, Fisher E, Kulzer JR, Lecoeur C, Narisu N, Sandholt C, Scott LJ, Silander K, Stark K, Tammesoo M-L, Teslovich TM, Timpson NJ, Watanabe RM, Welch R, Chasman DI, Cooper MN, Jansson J-O, Kettunen J, Lawrence RW, Pellikka N, Perola M, Vandenput L, Alavere H, Almgren P, Atwood LD, Bennett AJ, Biffar R, Bonnycastle LL, Bornstein SR, Buchanan TA, Campbell H, Day INM, Dei M, Doerr M, Elliott P, Erdos MR, Eriksson JG, Freimer NB, Fu M, Gaget S, Geus EJC, Gjesing AP, Grallert H, Graessler J, Groves CJ, Guiducci C, Hartikainen A-L, Hassanali N, Havulinna AS, Herzig K-H, Hicks AA, Hui J, Igl W, Jousilahti P, Jula A, Kajantie E, Kinnunen L, Kolcic I, Koskinen S, Kovacs P, Kroemer HK, Krzelj V, Kuusisto J, Kvaloy K, Laitinen J, Lantieri O, Lathrop GM, Lokki M-L, Luben RN, Ludwig B, McArdle WL, McCarthy A, Morken MA, Nelis M, Neville MJ, Pare G, Parker AN, Peden JF, Pichler I, Pietilainen KH, Platou CGP, Pouta A, Ridderstrale M, Samani NJ, Saramies J, Sinisalo J Set al., 2010,

  Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution

  , NATURE GENETICS, Vol: 42, Pages: 949-U160, ISSN: 1061-4036
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  • Citations: 748
• Journal article
  Feary JR, Rodrigues LC, Smith CJ, Hubbard RB, Gibson JEet al., 2010,

  Prevalence of major comorbidities in subjects with COPD and incidence of myocardial infarction and stroke: a comprehensive analysis using data from primary care

  , THORAX, Vol: 65, Pages: 956-962, ISSN: 0040-6376
  • Author Web Link
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  • Citations: 338
• Journal article
  Menzel R, Tran MQ, Menner A, Kay CWM, Bismarck A, Shaffer MSPet al., 2010,

  A versatile, solvent-free methodology for the functionalisation of carbon nanotubes

  , CHEMICAL SCIENCE, Vol: 1, Pages: 603-608, ISSN: 2041-6520
  • Author Web Link
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  • Citations: 36
• Journal article
  Mortaz E, Adcock IM, Ito K, Kraneveld AD, Nijkamp FP, Folkerts Get al., 2010,

  Cigarette smoke induces CXCL8 production by human neutrophils <i>via</i> activation of TLR9 receptor

  , EUROPEAN RESPIRATORY JOURNAL, Vol: 36, Pages: 1143-1154, ISSN: 0903-1936
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  • Citations: 69
• Journal article
  Chotirmall SH, O'Donoghue E, Bennett K, Gunaratnam C, O'Neill SJ, McElvaney NGet al., 2010,

  Sputum <i>Candida albicans</i> Presages FEV₁ Decline and Hospital-Treated Exacerbations in Cystic Fibrosis

  , CHEST, Vol: 138, Pages: 1186-1195, ISSN: 0012-3692
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• Journal article
  Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Eichler EE, Altshuler DL, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Collins FS, De La Vega FM, Donnelly P, Egholm M, Flicek P, Gabriel SB, Gibbs RA, Knoppers BM, Lander ES, Lehrach H, Mardis ER, McVean GA, Nickerson DA, Peltonen L, Schafer AJ, Sherry ST, Wang J, Wilson RK, Deiros D, Metzker M, Muzny D, Reid J, Wheeler D, Li J, Jian M, Li G, Li R, Liang H, Tian G, Wang B, Wang W, Yang H, Zhang X, Zheng H, Ambrogio L, Bloom T, Cibulskis K, Fennell TJ, Jaffe DB, Shefler E, Sougnez CL, Gormley N, Humphray S, Kingsbury Z, Koko-Gonzales P, Stone J, McKernan KJ, Costa GL, Ichikawa JK, Lee CC, Sudbrak R, Borodina TA, Dahl A, Davydov AN, Marquardt P, Mertes F, Nietfeld W, Rosenstiel P, Schreiber S, Soldatov AV, Timmermann B, Tolzmann M, Affourtit J, Ashworth D, Attiya S, Bachorski M, Buglione E, Burke A, Caprio A, Celone C, Clark S, Conners D, Desany B, Gu L, Guccione L, Kao K, Kebbel A, Knowlton J, Labrecque M, McDade L, Mealmaker C, Minderman M, Nawrocki A, Niazi Fet al., 2010,

  Diversity of human copy number variation and multicopy genes

  , Science, Vol: 330, Pages: 641-646, ISSN: 0036-8075

  Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ∼1000 genes accessible to genetic studies of disease association.

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  • Citations: 566
• Journal article
  Altshuler D, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Collins FS, De la Vega FM, Donnelly P, Egholm M, Flicek P, Gabriel SB, Gibbs RA, Knoppers BM, Lander ES, Lehrach H, Mardis ER, McVean GA, Nickerson D, Peltonen L, Schafer AJ, Sherry ST, Wang J, Wilson RK, Gibbs RA, Deiros D, Metzker M, Muzny D, Reid J, Wheeler D, Wang J, Li J, Jian M, Li G, Li R, Liang H, Tian G, Wang B, Wang J, Wang W, Yang H, Zhang X, Zheng H, Lander ES, Altshuler DL, Ambrogio L, Bloom T, Cibulskis K, Fennell TJ, Gabriel SB, Jaffe DB, Shefler E, Sougnez CL, Bentley DR, Gormley N, Humphray S, Kingsbury Z, Koko-Gonzales P, Stone J, McKernan KJ, Costa GL, Ichikawa JK, Lee CC, Sudbrak R, Lehrach H, Borodina TA, Dahl A, Davydov AN, Marquardt P, Mertes F, Nietfeld W, Rosenstiel P, Schreiber S, Soldatov AV, Timmermann B, Tolzmann M, Egholm M, Affourtit J, Ashworth D, Attiya S, Bachorski M, Buglione E, Burke A, Caprio A, Celone C, Clark S, Conners D, Desany B, Gu L, Guccione L, Kao K, Kebbel A, Knowlton J, Labrecque M, McDade L, Mealmaker C, Minderman M, Nawrocki A, Niazi F, Pareja K, Ramenani R, Riches D, Song W, Turcotte C, Wang S, Mardis ER, Dooling D, Fulton L, Fulton R, Weinstock G, Durbin RM, Burton J, Carter DM, Churcher C, Coffey A, Cox A, Palotie A, Quail M, Skelly T, Stalker J, Swerdlow HP, Turner D, De Witte A, Giles S, Gibbs RA, Wheeler D, Bainbridge M, Challis D, Sabo A, Yu F, Yu J, Wang J, Fang X, Guo X, Li R, Li Y, Luo R, Tai S, Wu H, Zheng H, Zheng X, Zhou Y, Yang H, Marth GT, Garrison EP, Huang W, Indap A, Kural D, Lee W-P, Leong WF, Huang W, Indap A, Kural D, Lee W-P, Leong WF, Quinlan AR, Stewart C, Stromberg MP, Ward AN, Wu J, Lee C, Mills RE, Shi X, Daly MJ, DePristo MA, Altshuler DL, Ball AD, Banks E, Bloom T, Browning BL, Cibulskis K, Fennell TJ, Garimella KV, Grossman SR, Handsaker RE, Hanna M, Hartl C, Jaffe DB, Kernytsky AM, Korn JM, Li H, Maguire JR, McCarroll SA, McKenna A, Nemesh JC, Philippakis AA, Poplin RE, Price A, Rivas MA, Sabeti PC, Schaffner SFet al., 2010,

  A map of human genome variation from population-scale sequencing

  , NATURE, Vol: 467, Pages: 1061-1073, ISSN: 0028-0836
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  • Citations: 6045
• Journal article
  Binia A, Khorasani N, Bhavsar PK, Adcock I, Brightling CE, Chung KF, Cookson WOC, Moffatt MFet al., 2010,

  Chromosome 17q21 SNP and severe asthma

  , Journal of Human Genetics, Vol: 56, Pages: 97-98, ISSN: 1435-232X
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• Journal article
  Oberhaensli S, Parlange F, Buchmann JP, Jenny FH, Abbott JC, Burgis TA, Spanu PD, Keller B, Wicker Tet al., 2010,

  Comparative sequence analysis of wheat and barley powdery mildew fungi reveals gene colinearity, dates divergence and indicates host pathogen co-evolution

  , Fugal Genetics and Biology, Vol: 48, Pages: 327-334

  The two fungal pathogens Blumeria graminis f. sp. tritici (B.g. tritici) and hordei (B.g. hordei) cause powdery mildew specifically in wheat or barley. They have the same life cycle, but their growth is restricted to the respective host. Here, we compared the sequences of two loci in both cereal mildews to determine their divergence time and their relationship with the evolution of their hosts. We sequenced a total of 273.3 kb derived from B.g. tritici BAC sequences and compared them with the orthologous regions in the B.g. hordei genome. Protein-coding genes were colinear and well conserved. In contrast, the intergenic regions showed very low conservation mostly due to different integration patterns of transposable elements. To estimate the divergence time of B.g. tritici and B.g. hordei, we used conserved intergenic sequences including orthologous transposable elements. This revealed that B.g. tritici and B.g. hordei have diverged about 10 million years ago (MYA), two million years after wheat and barley (12 MYA). These data suggest that B.g. tritici and B.g. hordei have co-evolved with their hosts during most of their evolutionary history after host divergence, possibly after a short phase of host expansion when the same pathogen could still grow on the two diverged hosts.

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