IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes

David C. Wilson | Judy H. Cho | C. Gieger | M. Daly | M. Nöthen | H. Hakonarson | Kai Wang | Hongyu Zhao | J. Rioux | R. Xavier | C. Wijmenga | J. Barrett | M. Tremelling | M. Parkes | C. Lees | J. Satsangi | N. Prescott | J. Sanderson | C. Mathew | J. Mansfield | T. Ahmad | Bin Zhang | E. Schadt | M. Silverberg | T. Green | A. Griffiths | A. Bitton | S. Raychaudhuri | R. Baldassano | B. Charloteaux | S. Targan | M. Dubinsky | E. Vasiliauskas | T. Karlsen | S. Schreiber | M. Imieliński | Z. Zhao | G. Montgomery | N. Hayward | R. Duerr | S. Brant | A. Steinhart | C. Abraham | M. Regueiro | L. Schumm | M. Lathrop | O. Dewit | D. Laukens | M. Mni | D. Franchimont | J. Hugot | S. Vermeire | E. Louis | C. Anderson | M. Georges | D. Massey | M. Kubo | A. Ananthakrishnan | Zhi Wei | Aylwin Ng | A. Franke | D. McGovern | L. Jostins | C. Hawkey | S. Ripke | C. Edwards | James C. Lee | C. Mowat | W. Newman | R. Scott | A. Phillips | Y. Momozawa | Kaida Ning | T. Bayless | Y. Aulchenko | L. Ferguson | R. Weersma | Ken Y. Hui | Y. Sharma | J. Essers | M. Mitrovič | I. Cleynen | E. Théâtre | S. Spain | P. Goyette | J. Achkar | L. Amininejad | V. Andersen | J. Andrews | L. Baidoo | P. Bampton | G. Boucher | S. Brand | C. Büning | A. Cohain | M. D’Amato | Kathy L. Devaney | D. Ellinghaus | K. Fransén | R. Gearry | J. Glas | T. Haritunians | A. Hart | M. Hedl | Xinli Hu | L. Kupčinskas | S. Kugathasan | A. Latiano | I. Lawrance | G. Mahy | O. Palmieri | C. Ponsioen | U. Potočnik | R. Russell | M. Sans | L. Simms | Jurgita Šventoraitytė | H. Verspaget | M. De Vos | J. Winkelmann | Clarence K. Zhang | V. Annese | G. Radford-Smith | D. Whiteman | M. Visschedijk | Hailiang Huang | N. Kennedy | P. Henderson | Mark Seielstad | S. Guthery | M. Löwenberg | R. Roberts | S. Rahmouni | S. Nikolaus | A. Ippoliti | S. Danese | Eleonora A. M. Festen | Jimmy Z Liu | J. Halfvarson | Julia Dmitrieva | V. Deffontaine | François Crins | E. Docampo | Mahmoud Elansary | Ann-Stephan Gori | C. Lecut | R. Mariman | C. Oury | I. Altukhov | D. Alexeev | G. Bouma | F. Hoentjen | B. Oldenburg | M. Pierik | Andrea E. vander Meulen-de Jong | C. Janneke van der Woude | G. Aumais | M. Barclay | J. Bethge | B. Brandt | Angela C. Chew | A. Croft | D. Jong | G. Denapiene | L. Denson | R. D'Incà | P. Fleshner | T. Florin | K. Hanigan | L. Jonaitis | M. Khan | G. Kiudelis | K. Krishnaprasad | M. Leja | J. Limbergen | P. Lionetti | R. Milgrom | S. Ng | S. M. Ng | I. Oikonomou | D. Proctor | J. Rahier | F. Rieder | D. Schulte | J. Skieceviciene | J. Stempak | L. Stronati | K. Taylor | Anje ter Velde | L. Torkvist | S. Sommeren | T. Walters | Ming-Hsi Wang | Hu Zhang | Wei Zhang | D. Wilson | S. Schreiber | J. Liu | M. Löwenberg | J. V. Limbergen | C. Büning | A. Gori | S. V. Sommeren | M. Kubo | Judy H. Cho | Todd Green | R. Russell | J. Andrews | L. P. Schumm | Souad Rahmouni

[1]  Nicola J. Rinaldi,et al.  Genetic effects on gene expression across human tissues , 2017, Nature.

[2]  Hailiang Huang,et al.  Fine-mapping inflammatory bowel disease loci to single variant resolution , 2017, Nature.

[3]  Yang I Li,et al.  An Expanded View of Complex Traits: From Polygenic to Omnigenic , 2017, Cell.

[4]  Nikolaos A Patsopoulos,et al.  Limited statistical evidence for shared genetic effects of eQTLs and autoimmune disease-associated loci in three major immune cell types , 2017, Nature Genetics.

[5]  Helen E. Parkinson,et al.  The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) , 2016, Nucleic Acids Res..

[6]  Tom R. Gaunt,et al.  A pathway-centric approach to rare variant association analysis , 2016, European Journal of Human Genetics.

[7]  David C. Wilson,et al.  Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease , 2016, Nature Genetics.

[8]  Y. Kamatani,et al.  Low-frequency coding variants in CETP and CFB are associated with susceptibility of exudative age-related macular degeneration in the Japanese population. , 2016, Human molecular genetics.

[9]  D. Nicolae.  Association Tests for Rare Variants. , 2016, Annual review of genomics and human genetics.

[10]  Jian Yang,et al.  Predicting gene targets from integrative analyses of summary data from GWAS and eQTL studies for 28 human complex traits , 2016, Genome Medicine.

[11]  Stephen C. J. Parker,et al.  The genetic architecture of type 2 diabetes , 2016, Nature.

[12]  P. Visscher,et al.  Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets , 2016, Nature Genetics.

[13]  James Y. Zou.  Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[14]  Andre Altmann,et al.  Re-Annotator: Annotation Pipeline for Microarray Probe Sequences , 2015, PloS one.

[15]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[16]  Tom R. Gaunt,et al.  Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel , 2015, Nature Communications.

[17]  Manolis Kellis,et al.  FTO Obesity Variant Circuitry and Adipocyte Browning in Humans. , 2015, The New England journal of medicine.

[18]  Judy H. Cho,et al.  Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations , 2015, Nature Genetics.

[19]  Kaanan P. Shah,et al.  A gene-based association method for mapping traits using reference transcriptome data , 2015, Nature Genetics.

[20]  Jun S. Liu,et al.  The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.

[21]  A. Skol,et al.  Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci , 2015, BMC Genomics.

[22]  R. Andrews,et al.  Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression , 2014, Science.

[23]  David Haussler,et al.  Current status and new features of the Consensus Coding Sequence database , 2013, Nucleic Acids Res..

[24]  C. Wallace,et al.  Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics , 2013, PLoS genetics.

[25]  Tatsuhiko Tsunoda,et al.  A practical method to detect SNVs and indels from whole genome and exome sequencing data , 2013, Scientific Reports.

[26]  David C. Wilson,et al.  Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease , 2012, Nature.

[27]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[28]  Joshua M. Korn,et al.  Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease , 2011, Nature Genetics.

[29]  Xihong Lin,et al.  Rare-variant association testing for sequencing data with the sequence kernel association test. , 2011, American journal of human genetics.

[30]  R. Xavier,et al.  Genetics and pathogenesis of inflammatory bowel disease , 2011, Nature.

[31]  Tom Druet,et al.  Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature , 2011, Nature Genetics.

[32]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[33]  Isabelle Cleynen,et al.  Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease , 2011, Nature Genetics.

[34]  E. Dermitzakis,et al.  Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations , 2010, PLoS genetics.

[35]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[36]  Johan Van Limbergen,et al.  Common variants at five new loci associated with early-onset inflammatory bowel disease , 2009, Nature Genetics.

[37]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[38]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[39]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[40]  Judy H Cho,et al.  Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease , 2008, Nature Genetics.

[41]  Pan Du,et al.  lumi: a pipeline for processing Illumina microarray , 2008, Bioinform..

[42]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[43]  A. McGregor,et al.  Morphological evolution through multiple cis-regulatory mutations at a single gene , 2007, Nature.

[44]  Simon Heath,et al.  Novel Crohn Disease Locus Identified by Genome-Wide Association Maps to a Gene Desert on 5p13.1 and Modulates Expression of PTGER4 , 2007, PLoS genetics.

[45]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[46]  W. Thilly,et al.  A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). , 2007, Mutation research.

[47]  Cheng Li,et al.  Adjusting batch effects in microarray expression data using empirical Bayes methods. , 2007, Biostatistics.

[48]  Thomas Lengauer,et al.  A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1 , 2007, Nature Genetics.

[49]  Andrew P Morris,et al.  Genetic dissection of a behavioral quantitative trait locus shows that Rgs2 modulates anxiety in mice , 2004, Nature Genetics.

[50]  Bill Newman,et al.  Functional variants of OCTN cation transporter genes are associated with Crohn disease , 2004, Nature Genetics.

[51]  J. Pritchard,et al.  The allelic architecture of human disease genes: common disease-common variant...or not? , 2002, Human molecular genetics.

[52]  Daniel R. Richards,et al.  Dissecting the architecture of a quantitative trait locus in yeast , 2002, Nature.

[53]  Mourad Sahbatou,et al.  Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease , 2001, Nature.

[54]  Trudy F. C. Mackay,et al.  Quantitative trait loci in Drosophila , 2001, Nature Reviews Genetics.