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1.  Rare and low-frequency coding variants in CXCR2 and other genes are associated with hematological traits 
Nature genetics  2014;46(6):629-634.
Hematological traits are important clinical parameters. To test the role of rare and low-frequency coding variants on hematological traits, we analyzed hemoglobin, hematocrit, white blood cell (WBC) and platelet count in 31,340 individuals genotyped on an exome array. We identified several missense variants of CXCR2 associated with reduced WBC count (gene-based P=2.6×10−13). In a separate family-based re-sequencing study, we identified a novel loss-of-function CXCR2 frameshift mutation in a pedigree with congenital neutropenia that abolished ligand-induced CXCR2 signal transduction and chemotaxis. We also identified novel missense or splice site variants in key hematopoiesis regulators (EPO, TRF2, HBB, TUBB1, SH2B3) associated with blood cell traits. Finally, we were able to detect associations between the rare somatic JAK2 p.Val617Phe mutation and platelet count (P=3.9×10−22) as well as hemoglobin (P=0.002), hematocrit (P=9.5×10−7) and WBC (P=3.1×10−5). In conclusion, exome arrays complement GWAS in identifying new variants that contribute to complex human traits.
doi:10.1038/ng.2962
PMCID: PMC4050975  PMID: 24777453
2.  Relationship between proximal Crohn’s disease location and disease behavior and surgery: A cross-sectional study of the IBD Genetics Consortium 
Objectives
In classifying Crohn’s disease (CD) location, proximal (L4) disease includes esophagogastroduodenal (EGD) and jejunal disease. Our aim was to determine the influence of proximal disease on outcomes of behavior and need for surgery and to determine if there was significant clinical heterogeneity between EGD and jejunal disease.
Methods
We performed a cross-sectional query of the NIDDK IBD Genetics Consortium (IBDGC) database of patients with a confirmed diagnosis of CD and phenotyped per the IBDGC manual. Presence of any L4, L4-EGD, L4-jejunal and non-L4 disease (L1-ileal, L2-colonic, and L3-ileocolonic) was compared with demographic features including age, race, ethnicity, smoking and IBD family history, diagnosis age, disease duration, clinical outcomes of inflammatory, stricturing or penetrating behavior, and CD abdominal surgeries. Univariate and multivariable analyses were performed with R.
Results
Among 2105 patients with complete disease location data, 346 had L4 disease (175 L4-EGD, 115 L4-jejunal, and 56 EGD and jejunal) with 321 having concurrent L1-L3 disease. 1759 had only L1-L3 disease. L4 vs. non-L4 patients were more likely (p<0.001) to be younger at diagnosis, non-smokers, have co-existing ileal involvement and have stricturing disease. L4- jejunal vs. L4-EGD patients were at least twice as likely (p<0.001) to have had ileal disease, stricturing behavior, and any or multiple abdominal surgeries. Remarkably, L4-jejunal patients had more (p<0.001) stricturing behavior and multiple abdominal surgeries than non-L4 ileal disease patients. Logistic regression showed stricturing risks were ileal (without proximal) site (OR 3.18; 95% CI 2.23-4.64), longer disease duration (OR 1.33/decade; 1.19-1.49), jejunal site (OR 2.90; 1.89-4.45), and older age at diagnosis (OR 1.21/decade; 1.10-1.34). Multiple surgeries risks were disease duration (OR 3.74/decade; 3.05-4.64), penetrating disease (OR 2.60; 1.64-4.21), and jejunal site (OR 2.39; 1.36-4.20), with short duration from diagnosis to first surgery protective (OR 0.87/decade to 1st surgery; 0.84-0.90).
Conclusion
Jejunal disease is a significantly greater risk factor for stricturing disease and multiple abdominal surgeries than either EGD or ileal (without proximal) disease. The Montreal site classification should be revised to include separate designations for jejunal and EGD disease.
doi:10.1038/ajg.2012.389
PMCID: PMC4059598  PMID: 23229423
3.  Identification of heart rate–associated loci and their effects on cardiac conduction and rhythm disorders 
den Hoed, Marcel | Eijgelsheim, Mark | Esko, Tõnu | Brundel, Bianca J J M | Peal, David S | Evans, David M | Nolte, Ilja M | Segrè, Ayellet V | Holm, Hilma | Handsaker, Robert E | Westra, Harm-Jan | Johnson, Toby | Isaacs, Aaron | Yang, Jian | Lundby, Alicia | Zhao, Jing Hua | Kim, Young Jin | Go, Min Jin | Almgren, Peter | Bochud, Murielle | Boucher, Gabrielle | Cornelis, Marilyn C | Gudbjartsson, Daniel | Hadley, David | Van Der Harst, Pim | Hayward, Caroline | Heijer, Martin Den | Igl, Wilmar | Jackson, Anne U | Kutalik, Zoltán | Luan, Jian’an | Kemp, John P | Kristiansson, Kati | Ladenvall, Claes | Lorentzon, Mattias | Montasser, May E | Njajou, Omer T | O’Reilly, Paul F | Padmanabhan, Sandosh | Pourcain, Beate St. | Rankinen, Tuomo | Salo, Perttu | Tanaka, Toshiko | Timpson, Nicholas J | Vitart, Veronique | Waite, Lindsay | Wheeler, William | Zhang, Weihua | Draisma, Harmen H M | Feitosa, Mary F | Kerr, Kathleen F | Lind, Penelope A | Mihailov, Evelin | Onland-Moret, N Charlotte | Song, Ci | Weedon, Michael N | Xie, Weijia | Yengo, Loic | Absher, Devin | Albert, Christine M | Alonso, Alvaro | Arking, Dan E | de Bakker, Paul I W | Balkau, Beverley | Barlassina, Cristina | Benaglio, Paola | Bis, Joshua C | Bouatia-Naji, Nabila | Brage, Søren | Chanock, Stephen J | Chines, Peter S | Chung, Mina | Darbar, Dawood | Dina, Christian | Dörr, Marcus | Elliott, Paul | Felix, Stephan B | Fischer, Krista | Fuchsberger, Christian | de Geus, Eco J C | Goyette, Philippe | Gudnason, Vilmundur | Harris, Tamara B | Hartikainen, Anna-liisa | Havulinna, Aki S | Heckbert, Susan R | Hicks, Andrew A | Hofman, Albert | Holewijn, Suzanne | Hoogstra-Berends, Femke | Hottenga, Jouke-Jan | Jensen, Majken K | Johansson, Åsa | Junttila, Juhani | Kääb, Stefan | Kanon, Bart | Ketkar, Shamika | Khaw, Kay-Tee | Knowles, Joshua W | Kooner, Angrad S | Kors, Jan A | Kumari, Meena | Milani, Lili | Laiho, Päivi | Lakatta, Edward G | Langenberg, Claudia | Leusink, Maarten | Liu, Yongmei | Luben, Robert N | Lunetta, Kathryn L | Lynch, Stacey N | Markus, Marcello R P | Marques-Vidal, Pedro | Leach, Irene Mateo | McArdle, Wendy L | McCarroll, Steven A | Medland, Sarah E | Miller, Kathryn A | Montgomery, Grant W | Morrison, Alanna C | Müller-Nurasyid, Martina | Navarro, Pau | Nelis, Mari | O’Connell, Jeffrey R | O’Donnell, Christopher J | Ong, Ken K | Newman, Anne B | Peters, Annette | Polasek, Ozren | Pouta, Anneli | Pramstaller, Peter P | Psaty, Bruce M | Rao, Dabeeru C | Ring, Susan M | Rossin, Elizabeth J | Rudan, Diana | Sanna, Serena | Scott, Robert A | Sehmi, Jaban S | Sharp, Stephen | Shin, Jordan T | Singleton, Andrew B | Smith, Albert V | Soranzo, Nicole | Spector, Tim D | Stewart, Chip | Stringham, Heather M | Tarasov, Kirill V | Uitterlinden, André G | Vandenput, Liesbeth | Hwang, Shih-Jen | Whitfield, John B | Wijmenga, Cisca | Wild, Sarah H | Willemsen, Gonneke | Wilson, James F | Witteman, Jacqueline C M | Wong, Andrew | Wong, Quenna | Jamshidi, Yalda | Zitting, Paavo | Boer, Jolanda M A | Boomsma, Dorret I | Borecki, Ingrid B | Van Duijn, Cornelia M | Ekelund, Ulf | Forouhi, Nita G | Froguel, Philippe | Hingorani, Aroon | Ingelsson, Erik | Kivimaki, Mika | Kronmal, Richard A | Kuh, Diana | Lind, Lars | Martin, Nicholas G | Oostra, Ben A | Pedersen, Nancy L | Quertermous, Thomas | Rotter, Jerome I | van der Schouw, Yvonne T | Verschuren, W M Monique | Walker, Mark | Albanes, Demetrius | Arnar, David O | Assimes, Themistocles L | Bandinelli, Stefania | Boehnke, Michael | de Boer, Rudolf A | Bouchard, Claude | Caulfield, W L Mark | Chambers, John C | Curhan, Gary | Cusi, Daniele | Eriksson, Johan | Ferrucci, Luigi | van Gilst, Wiek H | Glorioso, Nicola | de Graaf, Jacqueline | Groop, Leif | Gyllensten, Ulf | Hsueh, Wen-Chi | Hu, Frank B | Huikuri, Heikki V | Hunter, David J | Iribarren, Carlos | Isomaa, Bo | Jarvelin, Marjo-Riitta | Jula, Antti | Kähönen, Mika | Kiemeney, Lambertus A | van der Klauw, Melanie M | Kooner, Jaspal S | Kraft, Peter | Iacoviello, Licia | Lehtimäki, Terho | Lokki, Marja-Liisa L | Mitchell, Braxton D | Navis, Gerjan | Nieminen, Markku S | Ohlsson, Claes | Poulter, Neil R | Qi, Lu | Raitakari, Olli T | Rimm, Eric B | Rioux, John D | Rizzi, Federica | Rudan, Igor | Salomaa, Veikko | Sever, Peter S | Shields, Denis C | Shuldiner, Alan R | Sinisalo, Juha | Stanton, Alice V | Stolk, Ronald P | Strachan, David P | Tardif, Jean-Claude | Thorsteinsdottir, Unnur | Tuomilehto, Jaako | van Veldhuisen, Dirk J | Virtamo, Jarmo | Viikari, Jorma | Vollenweider, Peter | Waeber, Gérard | Widen, Elisabeth | Cho, Yoon Shin | Olsen, Jesper V | Visscher, Peter M | Willer, Cristen | Franke, Lude | Erdmann, Jeanette | Thompson, John R | Pfeufer, Arne | Sotoodehnia, Nona | Newton-Cheh, Christopher | Ellinor, Patrick T | Stricker, Bruno H Ch | Metspalu, Andres | Perola, Markus | Beckmann, Jacques S | Smith, George Davey | Stefansson, Kari | Wareham, Nicholas J | Munroe, Patricia B | Sibon, Ody C M | Milan, David J | Snieder, Harold | Samani, Nilesh J | Loos, Ruth J F
Nature genetics  2013;45(6):621-631.
Elevated resting heart rate is associated with greater risk of cardiovascular disease and mortality. In a 2-stage meta-analysis of genome-wide association studies in up to 181,171 individuals, we identified 14 new loci associated with heart rate and confirmed associations with all 7 previously established loci. Experimental downregulation of gene expression in Drosophila melanogaster and Danio rerio identified 20 genes at 11 loci that are relevant for heart rate regulation and highlight a role for genes involved in signal transmission, embryonic cardiac development and the pathophysiology of dilated cardiomyopathy, congenital heart failure and/or sudden cardiac death. In addition, genetic susceptibility to increased heart rate is associated with altered cardiac conduction and reduced risk of sick sinus syndrome, and both heart rate–increasing and heart rate–decreasing variants associate with risk of atrial fibrillation. Our findings provide fresh insights into the mechanisms regulating heart rate and identify new therapeutic targets.
doi:10.1038/ng.2610
PMCID: PMC3696959  PMID: 23583979
4.  Genome-wide analysis of immune system genes by EST profiling 
Profiling studies of mRNA and miRNA, particularly microarray-based studies, have been extensively used to create compendia of genes that are preferentially expressed in the immune system. In some instances, functional studies have been subsequently pursued. Recent efforts such as ENCODE have demonstrated the benefit of coupling RNA-Seq analysis with information from expressed sequence tags (ESTs) for transcriptomic analysis. However, the full characterization and identification of transcripts that function as modulators of human immune responses remains incomplete. In this study, we demonstrate that an integrated analysis of human ESTs provides a robust platform to identify the immune transcriptome. Beyond recovering a reference set of immune-enriched genes and providing large-scale cross-validation of previous microarray studies, we discovered hundreds of novel genes preferentially expressed in the immune system, including non-coding RNAs. As a result, we have established the Immunogene database, representing an integrated EST “road map” of gene expression in human immune cells, which can be used to further investigate the function of coding and non-coding genes in the immune system. Using this approach, we have uncovered a unique metabolic gene signature of human macrophages and identified PRDM15 as a novel overexpressed gene in human lymphomas. Thus we demonstrate the utility of EST profiling as a basis for further deconstruction of physiologic and pathologic immune processes.
doi:10.4049/jimmunol.1203471
PMCID: PMC3703829  PMID: 23616578
5.  The Dichotomous Pattern of IL-12R and IL-23R Expression Elucidates the Role of IL-12 and IL-23 in Inflammation 
PLoS ONE  2014;9(2):e89092.
IL-12 and IL-23 cytokines respectively drive Th1 and Th17 type responses. Yet, little is known regarding the biology of these receptors. As the IL-12 and IL-23 receptors share a common subunit, it has been assumed that these receptors are co-expressed. Surprisingly, we find that the expression of each of these receptors is restricted to specific cell types, in both mouse and human. Indeed, although IL-12Rβ2 is expressed by NK cells and a subset of γδ T cells, the expression of IL-23R is restricted to specific T cell subsets, a small number of B cells and innate lymphoid cells. By exploiting an IL-12- and IL-23-dependent mouse model of innate inflammation, we demonstrate an intricate interplay between IL-12Rβ2 NK cells and IL-23R innate lymphoid cells with respectively dominant roles in the regulation of systemic versus local inflammatory responses. Together, these findings support an unforeseen lineage-specific dichotomy in the in vivo role of both the IL-12 and IL-23 pathways in pathological inflammatory states, which may allow more accurate dissection of the roles of these receptors in chronic inflammatory diseases in humans.
doi:10.1371/journal.pone.0089092
PMCID: PMC3931659  PMID: 24586521
6.  Genome-wide Expression Profiling Implicates a MAST3-Regulated Gene Set in Colonic Mucosal Inflammation of Ulcerative Colitis Patients 
Inflammatory Bowel Diseases  2011;18(6):1072-1080.
Crohn’s disease (CD) and ulcerative colitis (UC) are inflammatory bowel diseases (IBD) presumably caused by dysregulated immune responses to the gut microbiota. Genetic association studies have implicated dozens of chromosomal regions or loci in IBD susceptibility. The next challenge is to explain the individual role of each of these modest effect loci in disease state. We have previously identified MAST3 as an IBD susceptibility gene through genetic fine-mapping of the 19p linkage region. Testing MAST3 in a reporter assay provided preliminary evidence that MAST3 modulates the activity of inflammation-related transcription factor nuclear factor kappa B (NF-κB). Here, we further characterized the function of MAST3 through an examination of the influence of the modulation of MAST3 expression on endogenous genome-wide expression patterns. More specifically, we looked at differential gene expression resulting from overexpression and knockdown of the MAST3 gene in epithelial and macrophage cell lines. We highlight a group of genes whose expression is modulated by MAST3 and correlate their expression with NF-κB activity. Their expression was found to be enriched in inflamed mucosal tissue of UC patients, confirming the importance of these genes in IBD. These MAST3-regulated genes are central to mucosal immune responses. Among them are pro-inflammatory cytokines (e.g. CCL20, IL8), regulators of NF-κB (e.g. TNFAIP3, LY96, NFKBIA), genes involved in interferon-induced defense against pathogen invasion (e.g. IFIT1, ISG15) and genes involved in cell adhesion and/or migration (e.g. CD44, TMOD1). Taken together, these results confirm MAST3 as a modulator of the inflammatory response through regulation of immune gene expression in the gut of IBD patients.
doi:10.1002/ibd.21887
PMCID: PMC3269563  PMID: 21994190
MAST3; Inflammatory Bowel Disease; NF-κB
7.  Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis 
Liu, Jimmy Z. | Hov, Johannes Roksund | Folseraas, Trine | Ellinghaus, Eva | Rushbrook, Simon M. | Doncheva, Nadezhda T. | Andreassen, Ole A. | Weersma, Rinse K. | Weismüller, Tobias J. | Eksteen, Bertus | Invernizzi, Pietro | Hirschfield, Gideon M. | Gotthardt, Daniel Nils | Pares, Albert | Ellinghaus, David | Shah, Tejas | Juran, Brian D. | Milkiewicz, Piotr | Rust, Christian | Schramm, Christoph | Müller, Tobias | Srivastava, Brijesh | Dalekos, Georgios | Nöthen, Markus M. | Herms, Stefan | Winkelmann, Juliane | Mitrovic, Mitja | Braun, Felix | Ponsioen, Cyriel Y. | Croucher, Peter J. P. | Sterneck, Martina | Teufel, Andreas | Mason, Andrew L. | Saarela, Janna | Leppa, Virpi | Dorfman, Ruslan | Alvaro, Domenico | Floreani, Annarosa | Onengut-Gumuscu, Suna | Rich, Stephen S. | Thompson, Wesley K. | Schork, Andrew J. | Næss, Sigrid | Thomsen, Ingo | Mayr, Gabriele | König, Inke R. | Hveem, Kristian | Cleynen, Isabelle | Gutierrez-Achury, Javier | Ricaño-Ponce, Isis | van Heel, David | Björnsson, Einar | Sandford, Richard N. | Durie, Peter R. | Melum, Espen | Vatn, Morten H | Silverberg, Mark S. | Duerr, Richard H. | Padyukov, Leonid | Brand, Stephan | Sans, Miquel | Annese, Vito | Achkar, Jean-Paul | Boberg, Kirsten Muri | Marschall, Hanns-Ulrich | Chazouillères, Olivier | Bowlus, Christopher L. | Wijmenga, Cisca | Schrumpf, Erik | Vermeire, Severine | Albrecht, Mario | Rioux, John D. | Alexander, Graeme | Bergquist, Annika | Cho, Judy | Schreiber, Stefan | Manns, Michael P. | Färkkilä, Martti | Dale, Anders M. | Chapman, Roger W. | Lazaridis, Konstantinos N. | Franke, Andre | Anderson, Carl A. | Karlsen, Tom H.
Nature genetics  2013;45(6):670-675.
doi:10.1038/ng.2616
PMCID: PMC3667736  PMID: 23603763
genetic association study; disease genetics; immunogenetics; liver
8.  Contribution of higher risk genes and European admixture to Crohn's disease in African Americans 
Inflammatory bowel diseases  2012;18(12):10.1002/ibd.22931.
Background & Aims
African Americans (AA) are an admixed population of West African (WA) and European ancestry (EA). Crohn's disease (CD) susceptibility genes have not been established. We therefore evaluated the contribution of European admixture and major established risk genes to AA CD.
Methods
Ninety-seven admixture informative markers were genotyped for ancestry estimates using STRUCTURE. 354 AA CD cases and 354 ethnicity-matched controls were genotyped for total 21 SNPs in ATG16L1, NOD2, IBD5, IL23R and IRGM by TaqMan or direct sequencing. Association was evaluated by logistic regression, adjusted for ancestry.
Results
Mean EA was similar among the CD cases and controls (20.9% and 20.4, respectively, p=0.58). No significant admixture differences were observed among cases (211 to 227) stratified by phenotypic sub-classifications including onset, surgery, site, and behavior. CD was associated with NOD2 carrier (6.93% CD, 2.15% Controls, p = 0.007), ATG16L1 Thr300Ala (36.1% CD, 29.3% Controls, p=0.003), SLC22A4 and SLC22A5 (IBD5 locus) functional SNPs (L503F [10.6% CD, 7.6% Controls, p=0.05] and g-207c [41.3% CD, 35.7% Controls, p=0.03], respectively) and IL23R rs2201841 (18.2% CD, 13.8% Controls, p=0.03), but not IRGM variants nor three African ancestral NOD2 nonsynonymous variants. IBD5 risk was recessive. An all-minor allele IBD5 haplotype from EA was associated (p=0.05), whereas a more common haplotype isolating g-207c was not.
Conclusions
Specific functional gene variations significantly contribute to AA CD risk. Established NOD2, SLC22A4-A5, and ATG16L1 variants show increased CD risk, with IBD5 in recessive. Although CD is more common in whites, European admixture is similar among AA cases and controls.
doi:10.1002/ibd.22931
PMCID: PMC3810419  PMID: 22411504
genetics; epidemiology; Crohn's disease
9.  Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis 
PLoS Genetics  2013;9(9):e1003723.
Genome-wide association studies and follow-up meta-analyses in Crohn's disease (CD) and ulcerative colitis (UC) have recently identified 163 disease-associated loci that meet genome-wide significance for these two inflammatory bowel diseases (IBD). These discoveries have already had a tremendous impact on our understanding of the genetic architecture of these diseases and have directed functional studies that have revealed some of the biological functions that are important to IBD (e.g. autophagy). Nonetheless, these loci can only explain a small proportion of disease variance (∼14% in CD and 7.5% in UC), suggesting that not only are additional loci to be found but that the known loci may contain high effect rare risk variants that have gone undetected by GWAS. To test this, we have used a targeted sequencing approach in 200 UC cases and 150 healthy controls (HC), all of French Canadian descent, to study 55 genes in regions associated with UC. We performed follow-up genotyping of 42 rare non-synonymous variants in independent case-control cohorts (totaling 14,435 UC cases and 20,204 HC). Our results confirmed significant association to rare non-synonymous coding variants in both IL23R and CARD9, previously identified from sequencing of CD loci, as well as identified a novel association in RNF186. With the exception of CARD9 (OR = 0.39), the rare non-synonymous variants identified were of moderate effect (OR = 1.49 for RNF186 and OR = 0.79 for IL23R). RNF186 encodes a protein with a RING domain having predicted E3 ubiquitin-protein ligase activity and two transmembrane domains. Importantly, the disease-coding variant is located in the ubiquitin ligase domain. Finally, our results suggest that rare variants in genes identified by genome-wide association in UC are unlikely to contribute significantly to the overall variance for the disease. Rather, these are expected to help focus functional studies of the corresponding disease loci.
Author Summary
Genetic studies of common diseases have seen tremendous progress in the last half-decade primarily due to recent technologies that enable a systematic examination of genetic markers across the entire genome in large numbers of patients and healthy controls. The studies, while identifying genomic regions that influence a person's risk for developing disease, often do not pinpoint the actual gene or gene variants that account for this risk (called a causal gene/variant). A prime example of this can be seen with the 163 genetic risk factors that have recently been associated with the chronic inflammatory bowel diseases known as Crohn's disease and ulcerative colitis. For less than a handful of these 163 is the causative change in the genetic code known. The current study used an approach to directly look at the genetic code for a subset of these and identified a causative change in the genetic code for eight risk factors for ulcerative colitis. This finding is particularly important because it directs biological studies to understand the mechanisms that lead to this chronic life-long inflammatory disease.
doi:10.1371/journal.pgen.1003723
PMCID: PMC3772057  PMID: 24068945
10.  Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci 
Nature genetics  2008;40(2):204-210.
Systemic lupus erythematosus (SLE) is a common systemic autoimmune disease with complex etiology but strong clustering in families (λS = ~30). We performed a genome-wide association scan using 317,501 SNPs in 720 women of European ancestry with SLE and in 2,337 controls, and we genotyped consistently associated SNPs in two additional independent sample sets totaling 1,846 affected women and 1,825 controls. Aside from the expected strong association between SLE and the HLA region on chromosome 6p21 and the previously confirmed non-HLA locus IRF5 on chromosome 7q32, we found evidence of association with replication (1.1 × 10−7 < Poverall < 1.6 × 10−23; odds ratio 0.82–1.62)in four regions: 16p11.2 (ITGAM), 11p15.5 (KIAA1542), 3p14.3 (PXK) and 1q25.1 (rs10798269). We also found evidence for association (P < 1 × 10−5) at FCGR2A, PTPN22 and STAT4, regions previously associated with SLE and other autoimmune diseases, as well as at ≥9 other loci (P < 2 × 10−7). Our results show that numerous genes, some with known immune-related functions, predispose to SLE.
doi:10.1038/ng.81
PMCID: PMC3712260  PMID: 18204446
11.  Polymorphism at the TNF superfamily gene TNFSF4 confers susceptibility to systemic lupus erythematosus 
Nature genetics  2007;40(1):83-89.
Systemic lupus erythematosus (SLE) is a multisystem complex autoimmune disease of uncertain etiology (OMIM 152700). Over recent years a genetic component to SLE susceptibility has been established1–3. Recent successes with association studies in SLE have identified genes including IRF5 (refs. 4,5) and FCGR3B6. Two tumor necrosis factor (TNF) superfamily members located within intervals showing genetic linkage with SLE are TNFSF4 (also known as OX40L; 1q25), which is expressed on activated antigen-presenting cells (APCs)7,8 and vascular endothelial cells9, and also its unique receptor, TNFRSF4 (also known as OX40; 1p36), which is primarily expressed on activated CD4+ T cells10. TNFSF4 produces a potent co-stimulatory signal for activated CD4+ T cells after engagement of TNFRSF4 (ref. 11). Using both a family-based and a case-control study design, we show that the upstream region of TNFSF4 contains a single risk haplotype for SLE, which is correlated with increased expression of both cell-surface TNFSF4 and the TNFSF4 transcript. We hypothesize that increased expression of TNFSF4 predisposes to SLE either by quantitatively augmenting T cell–APC interaction or by influencing the functional consequences of T cell activation via TNFRSF4.
doi:10.1038/ng.2007.47
PMCID: PMC3705866  PMID: 18059267
12.  Crohn disease 
Autophagy  2011;7(4):355-374.
Crohn disease (CD) is a chronic and debilitating inflammatory condition of the gastrointestinal tract.1 Prevalence in western populations is 100–150/100,000 and somewhat higher in Ashkenazi Jews. Peak incidence is in early adult life, although any age can be affected and a majority of affected individuals progress to relapsing and chronic disease. Medical treatments rely significantly on empirical corticosteroid therapy and immunosuppression, and intestinal resectional surgery is frequently required. Thus, 80% of patients with CD come to surgery for refractory disease or complications. It is hoped that an improved understanding of pathogenic mechanisms, for example by studying the genetic basis of CD and other forms of inflammatory bowel diseases (IBD), will lead to improved therapies and possibly preventative strategies in individuals identified as being at risk.
doi:10.4161/auto.7.4.13074
PMCID: PMC3842289  PMID: 20729636
Atg16L1; dendritic cells; gastrointestinal; genome-wide association; gut microbiota; inflammatory bowel diseases; IRGM; Paneth cell; ulcerative colitis
13.  Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease 
Jostins, Luke | Ripke, Stephan | Weersma, Rinse K | Duerr, Richard H | McGovern, Dermot P | Hui, Ken Y | Lee, James C | Schumm, L Philip | Sharma, Yashoda | Anderson, Carl A | Essers, Jonah | Mitrovic, Mitja | Ning, Kaida | Cleynen, Isabelle | Theatre, Emilie | Spain, Sarah L | Raychaudhuri, Soumya | Goyette, Philippe | Wei, Zhi | Abraham, Clara | Achkar, Jean-Paul | Ahmad, Tariq | Amininejad, Leila | Ananthakrishnan, Ashwin N | Andersen, Vibeke | Andrews, Jane M | Baidoo, Leonard | Balschun, Tobias | Bampton, Peter A | Bitton, Alain | Boucher, Gabrielle | Brand, Stephan | Büning, Carsten | Cohain, Ariella | Cichon, Sven | D’Amato, Mauro | De Jong, Dirk | Devaney, Kathy L | Dubinsky, Marla | Edwards, Cathryn | Ellinghaus, David | Ferguson, Lynnette R | Franchimont, Denis | Fransen, Karin | Gearry, Richard | Georges, Michel | Gieger, Christian | Glas, Jürgen | Haritunians, Talin | Hart, Ailsa | Hawkey, Chris | Hedl, Matija | Hu, Xinli | Karlsen, Tom H | Kupcinskas, Limas | Kugathasan, Subra | Latiano, Anna | Laukens, Debby | Lawrance, Ian C | Lees, Charlie W | Louis, Edouard | Mahy, Gillian | Mansfield, John | Morgan, Angharad R | Mowat, Craig | Newman, William | Palmieri, Orazio | Ponsioen, Cyriel Y | Potocnik, Uros | Prescott, Natalie J | Regueiro, Miguel | Rotter, Jerome I | Russell, Richard K | Sanderson, Jeremy D | Sans, Miquel | Satsangi, Jack | Schreiber, Stefan | Simms, Lisa A | Sventoraityte, Jurgita | Targan, Stephan R | Taylor, Kent D | Tremelling, Mark | Verspaget, Hein W | De Vos, Martine | Wijmenga, Cisca | Wilson, David C | Winkelmann, Juliane | Xavier, Ramnik J | Zeissig, Sebastian | Zhang, Bin | Zhang, Clarence K | Zhao, Hongyu | Silverberg, Mark S | Annese, Vito | Hakonarson, Hakon | Brant, Steven R | Radford-Smith, Graham | Mathew, Christopher G | Rioux, John D | Schadt, Eric E | Daly, Mark J | Franke, Andre | Parkes, Miles | Vermeire, Severine | Barrett, Jeffrey C | Cho, Judy H
Nature  2012;491(7422):119-124.
Crohn’s disease (CD) and ulcerative colitis (UC), the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry with rising prevalence in other populations1. Genome-wide association studies (GWAS) and subsequent meta-analyses of CD and UC2,3 as separate phenotypes implicated previously unsuspected mechanisms, such as autophagy4, in pathogenesis and showed that some IBD loci are shared with other inflammatory diseases5. Here we expand knowledge of relevant pathways by undertaking a meta-analysis of CD and UC genome-wide association scans, with validation of significant findings in more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional and balancing selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe striking overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.
doi:10.1038/nature11582
PMCID: PMC3491803  PMID: 23128233
14.  Assessment of Complement C4 Gene Copy Number Using the Paralog Ratio Test 
Human mutation  2010;31(7):866-874.
The complement C4 locus is in the class III region of the MHC, and exhibits copy number variation. Complement C4 null alleles have shown association with a number of diseases including systemic lupus erythematosus (SLE). However, most studies to date have used protein immunophenotyping and not direct interrogation of the genome to determine C4 null allele status. Moreover, a lack of accurate C4 gene copy number (GCN) estimation and tight linkage disequilibrium across the disease-associated MHC haplotypes has confounded attempts to establish whether or not these associations are causal. We have therefore developed a high through-put paralog ratio test (PRT) in association with two restriction enzyme digest variant ratio tests (REDVRs) to determine total C4 GCN, C4A GCN, and C4B GCN. In the densely genotyped CEU cohort we show that this method is accurate and reproducible when compared to gold standard Southern blot copy number estimation with a discrepancy rate of 9%. We find a broad range of C4 GCNs in the CEU and the 1958 British Birth Cohort populations under study. In addition, SNP-C4 CNV analyses show only moderate levels of correlation and therefore do not support the use of SNP genotypes as proxies for complement C4 GCN.
doi:10.1002/humu.21259
PMCID: PMC3567757  PMID: 20506482
complement C4; CNV; lupus; paralog ratio test
15.  MHC region and risk of systemic lupus erythematosus in African-American women 
Human genetics  2011;130(6):807-815.
The major histocompatibility complex (MHC) on chromosome 6p21 is a key contributor to the genetic basis of systemic lupus erythemathosus (SLE). Although SLE affects African Americans disproportionately compared to European Americans, there has been no comprehensive analysis of the MHC region in relationship to SLE in African Americans. We conducted a screening of the MHC region for 1,536 single nucleotide polymorphisms (SNPs) and the deletion of the C4A gene in a SLE case-control study (380 cases, 765 age-matched controls) nested within the prospective Black Women’s Health Study. We also genotyped 1,509 ancestral informative markers throughout the genome to estimate European ancestry in order to control for population stratification due to population admixture. The most strongly associated SNP with SLE was the rs9271366 (odds ratio, OR = 1.70, p = 5.6×10−5) near the HLA-DRB1 gene. Conditional haplotype analysis revealed three other SNPs, rs204890 (OR = 1.86, p = 1.2×10−4), rs2071349 (OR = 1.53, p = 1.0×10−3), and rs2844580 (OR = 1.43, p = 1.3×10−3) to be associated with SLE independent of the rs9271366 SNP. In univariate analysis, the OR for the C4A deletion was 1.38, p = 0.075, but after simultaneous adjustment for the other four SNPs the odds ratio was 1.01, p = 0.98. A genotype score combining the four newly identified SNPs showed an additive risk according to the number of high-risk alleles (OR = 1.67 per high-risk allele, p< 0.0001). Our strongest signal, the rs9271366 SNP, was also associated with higher risk of SLE in a previous Chinese genome-wide association study (GWAS). In addition, two SNPs found in a GWAS of European ancestry women were confirmed in our study, indicating that African Americans share some genetic risk factors for SLE with European and Chinese subjects. In summary, we found four independent signals in the MHC region associated with risk of SLE in African American women.
doi:10.1007/s00439-011-1045-2
PMCID: PMC3215804  PMID: 21695597
systemic lupus erythemathosus; African Americans; major histocompatibility complex; single nucleotide polymorphisms
16.  Genetic Variants in the Region Harbouring IL2/IL21 Associated to Ulcerative Colitis 
Gut  2009;58(6):799-804.
Objectives
Genetic susceptibility is known to play a large part in the predisposition to the inflammatory bowel diseases (IBD) known as Crohn’s disease (CD) and ulcerative colitis (UC). The IL2/IL21 locus on 4q27 is known to be a common risk locus for inflammatory disease (shown in celiac disease, type 1 diabetes, rheumatoid arthritis, systemic lupus erythematosus and psoriasis), while the roles that IL2 and IL21 play in the immune response also make them attractive candidates for inflammatory bowel disease. Our objective was to test for association between the IL2/IL21 locus and the inflammatory bowel diseases.
Methods
The four single nucleotide polymorphisms (SNPs) in the IL2/IL21 locus most associated to celiac disease were genotyped in 1590 IBD cases and 929 controls from the Netherlands, and then replicated in a North American cohort (2387 cases and 1266 controls) and an Italian cohort (805 cases and 421 controls), yielding a total of 4782 cases (3194 UC, 1588 CD) and 2616 controls. Allelic association testing and a pooled analysis using a Cochran-Mantel-Haenszel test were performed.
Results
All four SNPs were strongly associated with UC in all three cohorts and reached genome-wide significance in the pooled analysis (rs13151961 p= 1.35×10−10, rs13119723 p= 8.60×10−8, rs6840978 p= 3.07×10−8, rs6822844 p= 2.77×10−9). We also found a moderate association with CD in the pooled analysis (p value range 0.0016–9.86×10−5).
Conclusions
We found a strong association for the IL2/IL21 locus with UC, which also confirms it as a general susceptibility locus for inflammatory disease.
doi:10.1136/gut.2008.166918
PMCID: PMC2757103  PMID: 19201773
Inflammatory bowel disease; ulcerative colitis; Crohn’s disease; IL2; IL21
17.  Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci 
Human Molecular Genetics  2009;19(5):953-962.
Genome-wide association studies (GWASs) have proven highly effective, identifying hundreds of associations across numerous complex diseases. These studies typically test hundreds of thousands of variations and identify hundreds of potential associations. However, to date, follow-up attempts have generally only concentrated on just the few most significant initial associations, leaving the majority of true associations in any GWAS study without replication. Here, we present a substantially more comprehensive follow-up of the first genome-wide association screen performed in multiple sclerosis (MS), a complex genetic disease with central nervous system inflammation. We genotyped approximately 30 000 single-nucleotide polymorphisms (SNPs) that demonstrated mild-to-moderate levels of significance (P ≤ 0.10) in the initial GWAS in an independent set of 1343 MS cases and 1379 controls. We further replicated several of the most significant findings in another independent data set of 2164 MS cases and 2016 controls. We find considerable evidence for a number of novel susceptibility loci including KIF21B [rs12122721, combined P = 6.56 × 10−10, odds ratio (OR) = 1.22] and TMEM39A (rs1132200, P = 3.09 × 10−8, OR = 1.24), both of which meet genome-wide significance. Both of these loci were overlooked in the initial replication, despite being among the top 3000 (∼1%) SNP hits in the original screen.
doi:10.1093/hmg/ddp542
PMCID: PMC2816610  PMID: 20007504
18.  Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease 
Nature Genetics  2011;43(11):1066-1073.
More than a thousand disease susceptibility loci have been identified via genome-wide association studies (GWAS) of common variants; however, the specific genes and full allelic spectrum of causal variants underlying these findings generally remain to be defined. We utilize pooled next-generation sequencing to study 56 genes in regions associated to Crohn’s Disease in 350 cases and 350 controls. Follow up genotyping of 70 rare and low-frequency protein-altering variants (MAF ~ .001-.05) in nine independent case-control series (16054 CD patients, 12153 UC patients, 17575 healthy controls) identifies four additional independent risk factors in NOD2, two additional protective variants in IL23R, a highly significant association to a novel, protective splice variant in CARD9 (p < 1e-16, OR ~ 0.29), as well as additional associations to coding variants in IL18RAP, CUL2, C1orf106, PTPN22 and MUC19. We extend the results of successful GWAS by providing novel, rare, and likely functional variants that will empower functional experiments and predictive models.
doi:10.1038/ng.952
PMCID: PMC3378381  PMID: 21983784
19.  Genome-wide association study identifies five novel susceptibility loci for Crohn's disease and implicates a role for autophagy in disease pathogenesis. 
Nature genetics  2007;39(5):596-604.
We present a genome-wide association study of ileal Crohn's disease (CD) and two independent replication studies that identify five novel regions of association to CD. Specifically, in addition to the previously established CARD15 and IL23R associations, we report strong associations with independent replication to variation in the genomic regions encoding the PHOX2B, NCF4 and ATG16L1 genes, as well as a predicted gene on 16q24.1 (FAM92B) and an intergenic region on 10q21.1. We further demonstrate that the ATG16L1 gene is expressed in intestinal epithelial cell lines and that functional knock down of this gene abrogates autophagy of Salmonella typhimurium. Together these findings suggest that autophagy and host cell responses to intra-cellular microbes are involved in the pathogenesis of CD.
doi:10.1038/ng2032
PMCID: PMC2757939  PMID: 17435756
20.  A high resolution HLA and SNP haplotype map for disease association studies in the extended human MHC 
Nature genetics  2006;38(10):1166-1172.
The proteins encoded by the classical HLA class I and class II genes in the major histocompatibility complex (MHC) are highly polymorphic and play an essential role in self/non-self immune recognition. HLA variation is a crucial determinant of transplant rejection and susceptibility to a large number of infectious and autoimmune disease1. Yet identification of causal variants is problematic due to linkage disequilibrium (LD) that extends across multiple HLA and non-HLA genes in the MHC2,3. We therefore set out to characterize the LD patterns between the highly polymorphic HLA genes and background variation by typing the classical HLA genes and >7,500 common single nucleotide polymorphisms (SNPs) and deletion/insertion polymorphisms (DIPs) across four population samples. The analysis provides informative tag SNPs that capture some of the variation in the MHC region and that could be used in initial disease association studies, and provides new insight into the evolutionary dynamics and ancestral origins of the HLA loci and their haplotypes.
doi:10.1038/ng1885
PMCID: PMC2670196  PMID: 16998491
21.  MAST3: a Novel IBD Risk Factor that Modulates TLR4 Signaling 
Genes and immunity  2008;9(7):602-612.
Inflammatory bowel disease (IBD) is a chronic disorder caused by multiple factors in a genetically susceptible host. Significant advances in the study of genetic susceptibility have highlighted the importance of the innate immune system in this disease. We previously completed a genomewide linkage study and found a significant locus (IBD6) on chromosome 19p. We were interested in identifying the causal variant in IBD6. We performed a two-stage association mapping study. In stage one, 1530 SNPs were selected from the HapMap database and genotyped in 761 patients with IBD. Among the SNPs that passed the threshold for replication, 26 were successfully genotyped in 754 additional patients (stage two). One intronic variant, rs273506 located in the MAST3 gene was found to be associated in both stages (pooled P=2×10−4). We identified four MAST3 coding variants, including a non-synonymous SNP rs8108738, correlated to rs273506 and associated to IBD. To test whether MAST3 was expressed in cells of interest, we performed expression assays which showed abundant expression of MAST3 in antigen presenting cells and in lymphocytes. The knockdown of MAST3 specifically decreased TLR4 dependent NF-κB activity. Our findings are additional proof of the pivotal role played by modulators of NF-κB activity in IBD pathogenesis.
doi:10.1038/gene.2008.57
PMCID: PMC2574831  PMID: 18650832
MAST3; Inflammatory Bowel Disease; TLR4; NF-κB
22.  Meta-Analysis Increases to 71 the Tally of Confirmed Crohn’s Disease Susceptibility Loci 
Franke, Andre | McGovern, Dermot P.B. | Barrett, Jeffrey C. | Wang, Kai | Radford-Smith, Graham L. | Ahmad, Tariq | Lees, Charlie W. | Balschun, Tobias | Lee, James | Roberts, Rebecca | Anderson, Carl A. | Bis, Joshua C. | Bumpstead, Suzanne | Ellinghaus, David | Festen, Eleonora M. | Georges, Michel | Haritunians, Talin | Jostins, Luke | Latiano, Anna | Mathew, Christopher G. | Montgomery, Grant W. | Prescott, Natalie J. | Rotter, Jerome I. | Schumm, Philip | Sharma, Yashoda | Simms, Lisa A. | Taylor, Kent D. | Whiteman, David | Wijmenga, Cisca | Baldassano, Robert N. | Barclay, Murray | Bayless, Theodore M. | Brand, Stephan | Buning, Carsten | Cohen, Albert | Colombel, Jean-Frederick | Cottone, Mario | Stronati, Laura | Denson, Ted | De Vos, Martine | D’Inca, Renata | Dubinsky, Marla | Edwards, Cathryn | Florin, Tim | Franchimont, Denis | Gearry, Richard | Glas, Jürgen | Van Gossum, Andre | Guthery, Stephen L. | Halfvarson, Jonas | Hommes, Daan | Hugot, Jean-Pierre | Laukens, Debby | Lawrance, Ian | Lemann, Marc | Levine, Arie | Libioulle, Cecile | Louis, Edouard | Mowat, Craig | Newman, William | Panés, Julián | Phillips, Anne | Proctor, Deborah D. | Regueiro, Miguel | Rutgeerts, Paul | Sanderson, Jeremy | Sans, Miquel | Seibold, Frank | Steinhart, A. Hillary | Stokkers, Pieter C.F. | Torkvist, Leif | Ublick, Gerd Kullak | Raychaudhuri, Soumya | Green, Todd | Walters, Thomas | Targan, Stephan R. | Brant, Steven R. | Rioux, John D. | D’Amato, Mauro | Weersma, Rinse | Kugathasan, Subra | Griffiths, Anne M. | Mansfield, John C. | Vermeire, Severine | Duerr, Richard H. | Silverberg, Mark S. | Satsangi, Jack | Schreiber, Stefan | Cho, Judy H. | Annese, Vito | Hakonarson, Hakon | Daly, Mark J. | Parkes, Miles
Nature genetics  2010;42(12):1118-1125.
doi:10.1038/ng.717
PMCID: PMC3299551  PMID: 21102463
23.  Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis 
Sawcer, Stephen | Hellenthal, Garrett | Pirinen, Matti | Spencer, Chris C.A. | Patsopoulos, Nikolaos A. | Moutsianas, Loukas | Dilthey, Alexander | Su, Zhan | Freeman, Colin | Hunt, Sarah E. | Edkins, Sarah | Gray, Emma | Booth, David R. | Potter, Simon C. | Goris, An | Band, Gavin | Oturai, Annette Bang | Strange, Amy | Saarela, Janna | Bellenguez, Céline | Fontaine, Bertrand | Gillman, Matthew | Hemmer, Bernhard | Gwilliam, Rhian | Zipp, Frauke | Jayakumar, Alagurevathi | Martin, Roland | Leslie, Stephen | Hawkins, Stanley | Giannoulatou, Eleni | D’alfonso, Sandra | Blackburn, Hannah | Boneschi, Filippo Martinelli | Liddle, Jennifer | Harbo, Hanne F. | Perez, Marc L. | Spurkland, Anne | Waller, Matthew J | Mycko, Marcin P. | Ricketts, Michelle | Comabella, Manuel | Hammond, Naomi | Kockum, Ingrid | McCann, Owen T. | Ban, Maria | Whittaker, Pamela | Kemppinen, Anu | Weston, Paul | Hawkins, Clive | Widaa, Sara | Zajicek, John | Dronov, Serge | Robertson, Neil | Bumpstead, Suzannah J. | Barcellos, Lisa F. | Ravindrarajah, Rathi | Abraham, Roby | Alfredsson, Lars | Ardlie, Kristin | Aubin, Cristin | Baker, Amie | Baker, Katharine | Baranzini, Sergio E. | Bergamaschi, Laura | Bergamaschi, Roberto | Bernstein, Allan | Berthele, Achim | Boggild, Mike | Bradfield, Jonathan P. | Brassat, David | Broadley, Simon A. | Buck, Dorothea | Butzkueven, Helmut | Capra, Ruggero | Carroll, William M. | Cavalla, Paola | Celius, Elisabeth G. | Cepok, Sabine | Chiavacci, Rosetta | Clerget-Darpoux, Françoise | Clysters, Katleen | Comi, Giancarlo | Cossburn, Mark | Cournu-Rebeix, Isabelle | Cox, Mathew B. | Cozen, Wendy | Cree, Bruce A.C. | Cross, Anne H. | Cusi, Daniele | Daly, Mark J. | Davis, Emma | de Bakker, Paul I.W. | Debouverie, Marc | D’hooghe, Marie Beatrice | Dixon, Katherine | Dobosi, Rita | Dubois, Bénédicte | Ellinghaus, David | Elovaara, Irina | Esposito, Federica | Fontenille, Claire | Foote, Simon | Franke, Andre | Galimberti, Daniela | Ghezzi, Angelo | Glessner, Joseph | Gomez, Refujia | Gout, Olivier | Graham, Colin | Grant, Struan F.A. | Guerini, Franca Rosa | Hakonarson, Hakon | Hall, Per | Hamsten, Anders | Hartung, Hans-Peter | Heard, Rob N. | Heath, Simon | Hobart, Jeremy | Hoshi, Muna | Infante-Duarte, Carmen | Ingram, Gillian | Ingram, Wendy | Islam, Talat | Jagodic, Maja | Kabesch, Michael | Kermode, Allan G. | Kilpatrick, Trevor J. | Kim, Cecilia | Klopp, Norman | Koivisto, Keijo | Larsson, Malin | Lathrop, Mark | Lechner-Scott, Jeannette S. | Leone, Maurizio A. | Leppä, Virpi | Liljedahl, Ulrika | Bomfim, Izaura Lima | Lincoln, Robin R. | Link, Jenny | Liu, Jianjun | Lorentzen, Åslaug R. | Lupoli, Sara | Macciardi, Fabio | Mack, Thomas | Marriott, Mark | Martinelli, Vittorio | Mason, Deborah | McCauley, Jacob L. | Mentch, Frank | Mero, Inger-Lise | Mihalova, Tania | Montalban, Xavier | Mottershead, John | Myhr, Kjell-Morten | Naldi, Paola | Ollier, William | Page, Alison | Palotie, Aarno | Pelletier, Jean | Piccio, Laura | Pickersgill, Trevor | Piehl, Fredrik | Pobywajlo, Susan | Quach, Hong L. | Ramsay, Patricia P. | Reunanen, Mauri | Reynolds, Richard | Rioux, John D. | Rodegher, Mariaemma | Roesner, Sabine | Rubio, Justin P. | Rückert, Ina-Maria | Salvetti, Marco | Salvi, Erika | Santaniello, Adam | Schaefer, Catherine A. | Schreiber, Stefan | Schulze, Christian | Scott, Rodney J. | Sellebjerg, Finn | Selmaj, Krzysztof W. | Sexton, David | Shen, Ling | Simms-Acuna, Brigid | Skidmore, Sheila | Sleiman, Patrick M.A. | Smestad, Cathrine | Sørensen, Per Soelberg | Søndergaard, Helle Bach | Stankovich, Jim | Strange, Richard C. | Sulonen, Anna-Maija | Sundqvist, Emilie | Syvänen, Ann-Christine | Taddeo, Francesca | Taylor, Bruce | Blackwell, Jenefer M. | Tienari, Pentti | Bramon, Elvira | Tourbah, Ayman | Brown, Matthew A. | Tronczynska, Ewa | Casas, Juan P. | Tubridy, Niall | Corvin, Aiden | Vickery, Jane | Jankowski, Janusz | Villoslada, Pablo | Markus, Hugh S. | Wang, Kai | Mathew, Christopher G. | Wason, James | Palmer, Colin N.A. | Wichmann, H-Erich | Plomin, Robert | Willoughby, Ernest | Rautanen, Anna | Winkelmann, Juliane | Wittig, Michael | Trembath, Richard C. | Yaouanq, Jacqueline | Viswanathan, Ananth C. | Zhang, Haitao | Wood, Nicholas W. | Zuvich, Rebecca | Deloukas, Panos | Langford, Cordelia | Duncanson, Audrey | Oksenberg, Jorge R. | Pericak-Vance, Margaret A. | Haines, Jonathan L. | Olsson, Tomas | Hillert, Jan | Ivinson, Adrian J. | De Jager, Philip L. | Peltonen, Leena | Stewart, Graeme J. | Hafler, David A. | Hauser, Stephen L. | McVean, Gil | Donnelly, Peter | Compston, Alastair
Nature  2011;476(7359):214-219.
Multiple sclerosis (OMIM 126200) is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability.1 Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals;2,3 and systematic attempts to identify linkage in multiplex families have confirmed that variation within the Major Histocompatibility Complex (MHC) exerts the greatest individual effect on risk.4 Modestly powered Genome-Wide Association Studies (GWAS)5-10 have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects play a key role in disease susceptibility.11 Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the Class I region. Immunologically relevant genes are significantly over-represented amongst those mapping close to the identified loci and particularly implicate T helper cell differentiation in the pathogenesis of multiple sclerosis.
doi:10.1038/nature10251
PMCID: PMC3182531  PMID: 21833088
multiple sclerosis; GWAS; genetics
24.  Evidence for CRHR1 in multiple sclerosis using supervised machine learning and meta-analysis in 12 566 individuals 
Human Molecular Genetics  2010;19(21):4286-4295.
The primary genetic risk factor in multiple sclerosis (MS) is the HLA-DRB1*1501 allele; however, much of the remaining genetic contribution to MS has yet to be elucidated. Several lines of evidence support a role for neuroendocrine system involvement in autoimmunity which may, in part, be genetically determined. Here, we comprehensively investigated variation within eight candidate hypothalamic–pituitary–adrenal (HPA) axis genes and susceptibility to MS. A total of 326 SNPs were investigated in a discovery dataset of 1343 MS cases and 1379 healthy controls of European ancestry using a multi-analytical strategy. Random Forests, a supervised machine-learning algorithm, identified eight intronic SNPs within the corticotrophin-releasing hormone receptor 1 or CRHR1 locus on 17q21.31 as important predictors of MS. On the basis of univariate analyses, six CRHR1 variants were associated with decreased risk for disease following a conservative correction for multiple tests. Independent replication was observed for CRHR1 in a large meta-analysis comprising 2624 MS cases and 7220 healthy controls of European ancestry. Results from a combined meta-analysis of all 3967 MS cases and 8599 controls provide strong evidence for the involvement of CRHR1 in MS. The strongest association was observed for rs242936 (OR = 0.82, 95% CI = 0.74–0.90, P = 9.7 × 10−5). Replicated CRHR1 variants appear to exist on a single associated haplotype. Further investigation of mechanisms involved in HPA axis regulation and response to stress in MS pathogenesis is warranted.
doi:10.1093/hmg/ddq328
PMCID: PMC2951862  PMID: 20699326
25.  Occupational and environmental exposures and risk of systemic lupus erythematosus: silica, sunlight, solvents 
Rheumatology (Oxford, England)  2010;49(11):2172-2180.
Objectives. We examined occupational and non-occupational exposures in relation to risk of SLE in a case–control study conducted through the Canadian Network for Improved Outcomes in SLE (CaNIOS).
Methods. SLE cases (n = 258) were recruited from 11 rheumatology centres across Canada. Controls (without SLE, n = 263) were randomly selected from phone number listings and matched to cases by age, sex and area of residence. Data were collected using a structured telephone interview.
Results. An association was seen with outdoor work in the 12 months preceding diagnosis [odds ratio (OR) 2.0; 95% CI 1.1, 3.8]; effect modification by sun reaction was suggested, with the strongest effect among people who reported reacting to midday sun with a blistering sunburn or a rash (OR 7.9; 95% CI 0.97, 64.7). Relatively strong but imprecise associations were seen with work as an artist working with paints, dyes or developing film (OR 3.9; 95% CI 1.3, 12.3) and work that included applying nail polish or nail applications (OR 10.2; 95% CI 1.3, 81.5). Patients were more likely than controls to report participation in pottery or ceramics work as a leisure activity, with an increased risk among individuals with a total frequency of at least 26 days (OR 2.1; 95% CI 1.1, 3.9). Analyses of potential respirable silica exposures suggested an exposure–response gradient (OR 1.0, 1.4. and 2.1 for zero, one and two or more sources of exposure, respectively; trend test P < 0.01).
Conclusions. This study supports the role of specific occupational and non-occupational exposures in the development of SLE.
doi:10.1093/rheumatology/keq214
PMCID: PMC2954367  PMID: 20675707
Systemic lupus erythematosus; Risk factors; Silica; Ultraviolet radiation; Solvents; Occupation; Environment

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