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Dr Miles Parkes

Dr Miles Parkes

Miles Parkes is accepting applications for PhD students.

Miles Parkes is available for consultancy.


Research Interests

My interest is the molecular genetics of Crohn’s disease and ulcerative colitis. Our local IBD repository consists of >3000 DNA samples recruited from patients across Eastern England, intestinal biopsies from >400 IBD cases plus serum and stool samples. Current interests include fine mapping of the >160 confirmed IBD genetic susceptibility loci identified to date - using sequencing and array-based technologies together with expression and functional studies; functional interrogation of IBD-associated variants in primary human cells; investigation of differential methylation in colonoscopic biopsies and peripheral blood leukocyte subsets from IBD cases and controls; identification of microbial triggers of IBD, using metagenomic techniques; development of prognostic biomarkers in IBD; and participation in both investigator-led and commercial trials of new therapies in IBD.
 
We have close working relationships with colleagues at the Wellcome Trust Sanger Institute, with members of the UK IBD genetics research consortium (chaired by MP) and international IBD genetics research consortium (formerly chaired by MP), and with the Wellcome Trust Case Control Consortium.
 

Keywords

genomics ; genetics ; biostatistics ; methylation ; mucosal immunology ; prognosis ; bioinformatics ; colitis

Topics

  • inflammatory bowel disease
  • Crohn's disease

Key Publications

Lee  JC, EspéliM, AndersonCA, LintermanMA, PocockJM, WilliamsNJ, RobertsR, ViatteS, FuB,   PeshuN, Tran TH, Nguyen HP, WesleyE, EdwardsC, AhmadT, MansfieldJC, GearryR, DunstanS,   Williams TS, BartonA, VinuesaCG, UK IBD Genetics Consortium, ParkesM, LyonsPA, SmithKGC.  Human SNP links differential outcomes in inflammatory and infectious disease to a FOXO3-regulated pathway.  Cell 2013: in press.

Luke Jostins, Stephan Ripke, Rinse K Weersma, Richard H Duerr, Dermot P McGovern, Ken Y Hui, James C Lee, L Philip Schumm, Yashoda Sharma, Carl A Anderson, Jonah Essers, Mitja Mitrovic, Kaida Ning, Isabelle Cleynen, Emilie Theatre, Sarah L Spain, Soumya Raychaudhuri, Philippe Goyette, Zhi Wei, Clara Abraham, Jean-Paul Achkar, Tariq Ahmad, Leila Amininejad, Ashwin N Ananthakrishnan, Vibeke Andersen, Jane M Andrews, Leonard Baidoo, Tobias Balschun, Peter A Bampton, Alain Bitton, Gabrielle Boucher, Stephan Brand, Carsten Büning, Ariella Cohain, Sven Cichon, Mauro D’Amato, Dirk De Jong, Kathy L Devaney, Marla Dubinsky, Cathryn Edwards, David Ellinghaus, Lynnette R Ferguson, Denis Franchimont, Karin Fransen, Richard Gearry, Michel Georges, Christian Gieger, Jürgen Glas, Talin Haritunians, Ailsa Hart, Chris Hawkey, Matija Hedl, Xinli Hu,Tom H Karlsen, Limas Kupcinskas, Subra Kugathasan, Anna Latiano, Debby Laukens, Ian C Lawrance, Charlie W Lees, Edouard Louis, Gillian Mahy, John Mansfield, Angharad R Morgan, Craig Mowat, William Newman, Orazio Palmieri, Cyriel Y Ponsioen, Uros Potocnik, Natalie J Prescott, Miguel Regueiro, Jerome I Rotter, Richard K Russell, Jeremy D Sanderson, Miquel Sans, Jack Satsangi, Stefan Schreiber, Lisa A Simms, Jurgita Sventoraityte, Stephan R Targan, Kent D Taylor, Mark Tremelling, Hein W Verspaget, Martine De Vos, Cisca Wijmenga, David C Wilson, Juliane Winkelmann, Ramnik J Xavier, Sebastian Zeissig, Bin Zhang, Clarence K Zhang, Hongyu Zhao, The International IBD Genetics Consortium, Mark S Silverberg, Vito Annese, Hakon Hakonarson, Steven R Brant, Graham Radford-Smith, Christopher G Mathew, John D Rioux, Eric E Schadt, Mark J Daly, Andre Franke, Miles Parkes, Severine Vermeire, Jeffrey C Barrett, Judy H Cho. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012;491(7422):119-24
 
Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith GL, Ahmad T, Lees CW, Balschun T, Lee J, Roberts R, Anderson CA, Bis JC, Bumpstead S, Ellinghaus D, Festen EM, Georges M, Green T, Haritunians T, Jostins L, Latiano A, Mathew CG, Montgomery GW, Prescott NJ, Raychaudhuri S,Rotter JI, Schumm P, Sharma Y, Simms LA, Taylor KD, Whiteman D, Wijmenga C, Baldassano RN, Barclay M, Bayless TM, Brand S, Büning C, Cohen A, Colombel JF, Cottone M, Stronati L, Denson T, De Vos M, D'Inca R, Dubinsky M, Edwards C, Florin T, Franchimont D, Gearry R, Glas J, Van Gossum A, Guthery SL, Halfvarson J, Verspaget HW, Hugot JP, Karban A, Laukens D, Lawrance I, Lemann M, Levine A,Libioulle C, Louis E, Mowat C, Newman W, Panés J, Phillips A, Proctor DD, Regueiro M, Russell R, Rutgeerts P, Sanderson J, Sans M, Seibold F, Steinhart AH, Stokkers PC, Torkvist L, Kullak-Ublick G, Wilson D, Walters T, Targan SR, Brant SR, Rioux JD, D'Amato M, Weersma RK, Kugathasan S, Griffiths AM, Mansfield JC, Vermeire S, Duerr RH, Silverberg MS, Satsangi J, Schreiber S, Cho JH, Annese V, Hakonarson H, Daly MJ, Parkes M, Genome-Wide Meta-Analysis Increases to 71 the Number of Confirmed Crohn's Disease Susceptibility Loci. Nature Genetics 2010 Dec;42(12):1118–25.
The UK IBD Genetics Consortium and the Wellcome Trust Case Control Consortium 2, Genome-wide association study of ulcerative colitis identifies three susceptibility loci, including HNF4A. Nature Genetics 2009 Dec;41(12):1330 4,
Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ; NIDDK IBD Genetics Consortium, Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Hugot JP, de Vos M, Vermeire S, Louis E; Belgian-French IBD Consortium; Wellcome Trust Case Control Consortium, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwilliam R, Tremelling M, Deloukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nature Genetics. 2008 Aug;40(8):955–62.
Wellcome Trust Case Control Consortium [247 authors. Primary Investigators: Bentley D, Brown MA, Cardon LR, Caulfield M, Clayton DG, Compston A, Craddock N, Deloukas P, Donnelly P, Farrall M, Gough SCL, Hall AS, Hattersley AT, Hill AVS, Kwiatkowski DP, Mathew CG, McCarthy MI, Ouwehand WH, Parkes M, Pembrey M, Rahman N, Samani NJ, Stratton MR, Todd JA, Worthington J]. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007; 447, 661–678
Parkes M, Barrett JC, Prescott NJ, Tremelling M, Anderson CA, Fisher SA, Roberts RG, Nimmo ER, Cummings FR, Soars D, Drummond H, Lees CW, Khawaja SA, Bagnall R, Burke DA, Todhunter CE, Ahmad T, Onnie CM, McArdle W, Strachan D, Bethel G, Bryan C, Lewis CM, Deloukas P, Forbes A, Sanderson J, Jewell DP, Satsangi J, Mansfield JC; Wellcome Trust Case Control Consortium, Cardon L, Mathew CG. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nature Genetics. 2007 Jul;39(7):830–2