Dr Jeffrey Barrett

Jeff analyzes genomic variation in thousands of individuals to identify genetic risk factors for a wide range of human diseases.

Jeff became interested in human disease genetics during a research project in Mark Daly's lab at the Whitehead Institute while he was a student at MIT. After graduating in 2002 he joined Mark's group full-time where he focused on the development of software tools, including the widely used Haploview program, and analysis of patterns of linkage disequilibrium in the HapMap project.

In 2005 Jeff moved to Lon Cardon's group in Oxford to undertake a D. Phil in Statistics (jointly supervised by Peter Donnelly). He helped design the first generation of genome-wide association studies (GWAS), was a lead analyst for the Wellcome Trust Case Control Consortium, and led the follow-up analysis for Crohn's disease (a common type of inflammatory bowel disease [IBD]). In late 2007 he moved to a post-doc in David Clayton's group in 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 Sanger Institute in November 2008 to start a team in medical genomics. He used GWAS as a tool to explore the overlapping genetic architecture of diseases of inflammation, immunity, and infection including celiac disease, ulcerative colitis, multiple sclerosis, tuberculosis and malaria. He then led the development of the Immunochip, a genotyping array used on nearly a million samples and in over 100 publications, with his own involvement culminating in a synthesis of IBD genetics identifying 163 distinct associations. More recently, Jeff has begun using sequencing in IBD and beyond to hunt for rarer genetic variation affecting complex disease. He has also expanded his work to include the interpretation of sequence analysis of Mendelian disorders as part of the Deciphering Developmental Disorders (DDD) study.

Jeff has been involved in a number of consortia, including all 3 phases of the WTCCC, the 1000 Genomes project and the Autism Sequencing Consortium. His leadership roles include editorships at Bioinformatics and Human Molecular Genetics, the management committees of the UK10K and DDD studies, and current co-chairmanship of the International IBD Genetics Consortium.

Selected Publications

  • Genome wide association study of fetal hemoglobin in sickle cell anemia in Tanzania.

    Mtatiro SN, Singh T, Rooks H, Mgaya J, Mariki H, Soka D, Mmbando B, Msaki E, Kolder I, Thein SL, Menzel S, Cox SE, Makani J and Barrett JC

    PloS one 2014;9;11;e111464

  • Imputation-based meta-analysis of severe malaria in three African populations.

    Band G, Le QS, Jostins L, Pirinen M, Kivinen K, Jallow M, Sisay-Joof F, Bojang K, Pinder M, Sirugo G, Conway DJ, Nyirongo V, Kachala D, Molyneux M, Taylor T, Ndila C, Peshu N, Marsh K, Williams TN, Alcock D, Andrews R, Edkins S, Gray E, Hubbart C, Jeffreys A, Rowlands K, Schuldt K, Clark TG, Small KS, Teo YY, Kwiatkowski DP, Rockett KA, Barrett JC, Spencer CC, Malaria Genomic Epidemiology Network and Malaria Genomic Epidemiological Network

    PLoS genetics 2013;9;5;e1003509

  • 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

  • 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

  • From HLA association to function.

    Barrett JC

    Nature genetics 2012;44;3;235-6

  • 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

  • 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

  • Genetic risk prediction in complex disease.

    Jostins L and Barrett JC

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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • Evaluating coverage of genome-wide association studies.

    Barrett JC and Cardon LR

    Nature genetics 2006;38;6;659-62

  • A haplotype map of the human genome.

    International HapMap Consortium

    Nature 2005;437;7063;1299-320

  • 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

[Wellcome Library, London]

Jeffrey's Project
Medical genomics
Research Area
Human Genetics
* quick link - http://q.sanger.ac.uk/nkkm5ybe