Dr Jeffrey Barrett

Jeffrey analyzes genomic variation in thousands of individuals to identify genetic risk factors for complex human diseases, especially those involving autoimmunity and infection.

Jeffrey Barrett became interested in human disease genetics during an undergraduate research project in Mark Daly's lab at the Whitehead Institute while he was a student at the Massachusetts Institute of Technology (MIT).

After he graduated in 2002 (BS, Physics) Jeff joined Mark's group full-time, where he developed software tools, including the widely used Haploview program, and analysed large scale human genetic variation datasets, including the HapMap project. In 2005 Jeff moved to Lon Cardon's group at the University of Oxford to undertake a DPhil in Statistics (jointly supervised by Peter Donnelly). While at Oxford Jeff worked on the design and subsequent analysis of the first generation of Genome Wide Association Studies (GWAS). He was a member of the analysis team for the Wellcome Trust Case Control Consortium (WTCCC), which comprised seven disease collections of 2000 cases each, with a shared set of 3000 controls. In addition to his work with the project as a whole, Jeff led the analysis of the replication effort in Crohn's disease (the most common type of inflammatory bowel disease [IBD]). In late 2007 Jeff moved to a post-doctoral position in David Clayton's group at the University of Cambridge, where he worked on meta-analyses and follow-up of GWAS in both Crohn's disease and type 1 diabetes, each of which resulted in the identification of twenty novel associations.

Jeff moved to the Wellcome Trust Sanger Institute in November 2008 to start a team in medical genomics, where he is continuing to work on both the general methodology for complex trait gene hunting and the specific follow-up projects of inflammatory diseases like IBD and infectious diseases like tuberculosis. Jeff is also excited to take advantage of the unique capabilities of the Sanger Institute, including genome-wide sequence and transcription datasets. He is involved in a number of international consortia, including the International IBD Genetics Consortium, the UK10K and Deciphering Developmental Disorders.

Selected Publications

• Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.

  Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA, Essers J, Mitrovic M, Ning K, Cleynen I, Theatre E, Spain SL, Raychaudhuri S, Goyette P, Wei Z, Abraham C, Achkar JP, Ahmad T, Amininejad L, Ananthakrishnan AN, Andersen V, Andrews JM, Baidoo L, Balschun T, Bampton PA, Bitton A, Boucher G, Brand S, Büning C, Cohain A, Cichon S, D'Amato M, De Jong D, Devaney KL, Dubinsky M, Edwards C, Ellinghaus D, Ferguson LR, Franchimont D, Fransen K, Gearry R, Georges M, Gieger C, Glas J, Haritunians T, Hart A, Hawkey C, Hedl M, Hu X, Karlsen TH, Kupcinskas L, Kugathasan S, Latiano A, Laukens D, Lawrance IC, Lees CW, Louis E, Mahy G, Mansfield J, Morgan AR, Mowat C, Newman W, Palmieri O, Ponsioen CY, Potocnik U, Prescott NJ, Regueiro M, Rotter JI, Russell RK, Sanderson JD, Sans M, Satsangi J, Schreiber S, Simms LA, Sventoraityte J, Targan SR, Taylor KD, Tremelling M, Verspaget HW, De Vos M, Wijmenga C, Wilson DC, Winkelmann J, Xavier RJ, Zeissig S, Zhang B, Zhang CK, Zhao H, International IBD Genetics Consortium (IIBDGC), Silverberg MS, Annese V, Hakonarson H, Brant SR, Radford-Smith G, Mathew CG, Rioux JD, Schadt EE, Daly MJ, Franke A, Parkes M, Vermeire S, Barrett JC and Cho JH

  Nature 2012;491;7422;119-24

  PUBMED: 23128233; PMC: 3491803; DOI: 10.1038/nature11582

• Misuse of hierarchical linear models overstates the significance of a reported association between OXTR and prosociality.

  Jostins L, Pickrell JK, MacArthur DG and Barrett JC

  Proceedings of the National Academy of Sciences of the United States of America 2012;109;18;E1048

  PUBMED: 22499788; PMC: 3344973; DOI: 10.1073/pnas.1202539109

• From HLA association to function.

  Barrett JC

  Nature genetics 2012;44;3;235-6

  PUBMED: 22366857; DOI: 10.1038/ng.2207

• A systematic survey of loss-of-function variants in human protein-coding genes.

  MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB and Tyler-Smith C

  Science (New York, N.Y.) 2012;335;6070;823-8

  PUBMED: 22344438; PMC: 3299548; DOI: 10.1126/science.1215040

• Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease.

  Trynka G, Hunt KA, Bockett NA, Romanos J, Mistry V, Szperl A, Bakker SF, Bardella MT, Bhaw-Rosun L, Castillejo G, de la Concha EG, de Almeida RC, Dias KR, van Diemen CC, Dubois PC, Duerr RH, Edkins S, Franke L, Fransen K, Gutierrez J, Heap GA, Hrdlickova B, Hunt S, Plaza Izurieta L, Izzo V, Joosten LA, Langford C, Mazzilli MC, Mein CA, Midah V, Mitrovic M, Mora B, Morelli M, Nutland S, Núñez C, Onengut-Gumuscu S, Pearce K, Platteel M, Polanco I, Potter S, Ribes-Koninckx C, Ricaño-Ponce I, Rich SS, Rybak A, Santiago JL, Senapati S, Sood A, Szajewska H, Troncone R, Varadé J, Wallace C, Wolters VM, Zhernakova A, Spanish Consortium on the Genetics of Coeliac Disease (CEGEC), PreventCD Study Group, Wellcome Trust Case Control Consortium (WTCCC), Thelma BK, Cukrowska B, Urcelay E, Bilbao JR, Mearin ML, Barisani D, Barrett JC, Plagnol V, Deloukas P, Wijmenga C and van Heel DA

  Nature genetics 2011;43;12;1193-201

  PUBMED: 22057235; PMC: 3242065; DOI: 10.1038/ng.998

• Genetic risk prediction in complex disease.

  Jostins L and Barrett JC

  Human molecular genetics 2011;20;R2;R182-8

  PUBMED: 21873261; PMC: 3179379; DOI: 10.1093/hmg/ddr378

• Imputation of low-frequency variants using the HapMap3 benefits from large, diverse reference sets.

  Jostins L, Morley KI and Barrett JC

  European journal of human genetics : EJHG 2011;19;6;662-6

  PUBMED: 21364697; PMC: 3110048; DOI: 10.1038/ejhg.2011.10

• Synthetic associations are unlikely to account for many common disease genome-wide association signals.

  Anderson CA, Soranzo N, Zeggini E and Barrett JC

  PLoS biology 2011;9;1;e1000580

  PUBMED: 21267062; PMC: 3022527; DOI: 10.1371/journal.pbio.1000580

• Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.

  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 and Parkes M

  Nature genetics 2010;42;12;1118-25

  PUBMED: 21102463; PMC: 3299551; DOI: 10.1038/ng.717

• Evoker: a visualization tool for genotype intensity data.

  Morris JA, Randall JC, Maller JB and Barrett JC

  Bioinformatics (Oxford, England) 2010;26;14;1786-7

  PUBMED: 20507892; PMC: 3073232; DOI: 10.1093/bioinformatics/btq280

• Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.

  UK IBD Genetics Consortium, Barrett JC, Lee JC, Lees CW, Prescott NJ, Anderson CA, Phillips A, Wesley E, Parnell K, Zhang H, Drummond H, Nimmo ER, Massey D, Blaszczyk K, Elliott T, Cotterill L, Dallal H, Lobo AJ, Mowat C, Sanderson JD, Jewell DP, Newman WG, Edwards C, Ahmad T, Mansfield JC, Satsangi J, Parkes M, Mathew CG, Wellcome Trust Case Control Consortium 2, Donnelly P, Peltonen L, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Craddock N, Deloukas P, Duncanson A, Jankowski J, Markus HS, Mathew CG, McCarthy MI, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Samani N, Trembath RC, Viswanathan AC, Wood N, Spencer CC, Barrett JC, Bellenguez C, Davison D, Freeman C, Strange A, Donnelly P, Langford C, Hunt SE, Edkins S, Gwilliam R, Blackburn H, Bumpstead SJ, Dronov S, Gillman M, Gray E, Hammond N, Jayakumar A, McCann OT, Liddle J, Perez ML, Potter SC, Ravindrarajah R, Ricketts M, Waller M, Weston P, Widaa S, Whittaker P, Deloukas P, Peltonen L, Mathew CG, Blackwell JM, Brown MA, Corvin A, McCarthy MI, Spencer CC, Attwood AP, Stephens J, Sambrook J, Ouwehand WH, McArdle WL, Ring SM and Strachan DP

  Nature genetics 2009;41;12;1330-4

  PUBMED: 19915572; PMC: 2812019; DOI: 10.1038/ng.483

• Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.

  Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS and Type 1 Diabetes Genetics Consortium

  Nature genetics 2009;41;6;703-7

  PUBMED: 19430480; PMC: 2889014; DOI: 10.1038/ng.381

• Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.

  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, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, 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 and Daly MJ

  Nature genetics 2008;40;8;955-62

  PUBMED: 18587394; PMC: 2574810; DOI: 10.1038/ng.175

• Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.

  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 and Mathew CG

  Nature genetics 2007;39;7;830-2

  PUBMED: 17554261; PMC: 2628541; DOI: 10.1038/ng2061

• Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.

  Wellcome Trust Case Control Consortium

  Nature 2007;447;7145;661-78

  PUBMED: 17554300; PMC: 2719288; DOI: 10.1038/nature05911

• Evaluating coverage of genome-wide association studies.

  Barrett JC and Cardon LR

  Nature genetics 2006;38;6;659-62

  PUBMED: 16715099; DOI: 10.1038/ng1801

• A haplotype map of the human genome.

  International HapMap Consortium

  Nature 2005;437;7063;1299-320

  PUBMED: 16255080; PMC: 1880871; DOI: 10.1038/nature04226

• Haploview: analysis and visualization of LD and haplotype maps.

  Barrett JC, Fry B, Maller J and Daly MJ

  Bioinformatics (Oxford, England) 2005;21;2;263-5

  PUBMED: 15297300; DOI: 10.1093/bioinformatics/bth457

Related links

• Helminth genomes
• Global health research
• Barrett Group homepage