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1. The Precision Allergy Molecular Diagnosis (PAMD@) in Monitoring the Atopic March in a Child with a Primary Food Allergy: Case Report

Author

Knyziak-Mędrzycka I, Szychta M, Majsiak E, Fal AM, Doniec Z, and Cukrowska B

Subjects
atopic march, allergy, anaphylaxis, sige, pamd, multiplex molecular tests, Immunologic diseases. Allergy, RC581-607
Abstract

Izabela Knyziak-Mędrzycka,1,2 Monika Szychta,3 Emilia Majsiak,4 Andrzej M Fal,2,5,6 Zbigniew Doniec,7 Bożena Cukrowska8 1Allergy Clinic, Children’s Memorial Health Institute, Warsaw, Poland; 2The Department of Allergy, Pulmonary Diseases and Internal Medicine, Central Clinical Hospital of the Ministry of Interior and Administration in Warsaw, Warsaw, Poland; 3Department of Gastroenterology, Hepatology, Nutritional Disturbances and Pediatrics, Children’s Memorial Health Institute, Warsaw, Poland; 4Department of Health Promotion, Chair of Nursing Development, Faculty Health of Sciences, Medical University of Lublin, Lublin, Poland; 5Collegium Medicum, Faculty of Medicine, Cardinal Stefan Wyszyński University, Warsaw, Poland; 6Department of Public Health, Wroclaw Medical University, Wrocław, Poland; 7The Institute of Tuberculosis and Lung Diseases, Regional Branch in Rabka-Zdrój, Rabka-Zdrój, Poland; 8Department of Pathomorphology, Children’s Memorial Health Institute, Warsaw, PolandCorrespondence: Emilia Majsiak, Department of Health Promotion, Chair of Nursing Development, Faculty Health of Sciences, Medical University of Lublin, Staszica 4 m.6 (Collegium Maximum), Lublin, 20-081, Poland, Tel +48 81 448 6700, Fax +48 48 814 4867, Email emiliamajsiak@umlub.pl; wnoz@umlub.plAbstract: The case of a 9-month-old boy with an initial diagnosis of atopic dermatitis and confirmed allergy to hen’s egg, cow’s milk allergens with episodes of anaphylaxis who developed birch allergy whilst under observation with asthma symptoms was presented. The precision allergy molecular diagnosis (PAMD @) allowed for individualisation of dietary recommendations and observing the early progression of food sensitisation to the main birch molecule. The presented identification of major allergic molecules with PAMD@ in the preclinical phase of asthma contributes to the discussion related to early specific immunotherapy to suppress molecular spread and allergic march. However, more research is needed to verify this hypothesis.Graphical Abstract: Keywords: atopic march, allergy, anaphylaxis, sIgE, PAMD@, multiplex molecular tests

Published
2022

17. LIST OF CONTRIBUTORS

Author

Albini, B., primary, Adler, B., additional, Adler, H., additional, Ameratunga, R., additional, Anderson, A.O., additional, Andrews, A.E., additional, Arstila, T.P., additional, Bailey, M., additional, Barnes, H.J., additional, Bazin, H., additional, Bertoni, G., additional, Blacklaws, B., additional, Bos, N.A., additional, Brait, M., additional, Butler, J.E., additional, Cahill, R.N.P., additional, Carter, S.D., additional, Cesbron, J.-Y., additional, Charlemagne, J., additional, Charley, B., additional, Cunningham, C., additional, Cukrowska, B., additional, Daha, M.R., additional, Dammers, P.M., additional, Deenen, G.J., additional, Defresne, M.P., additional, Delhem, N., additional, Demaries, S.L., additional, Desmecht, D., additional, Dijkstra, C.D., additional, Ellis, A.E., additional, Fatzer, R., additional, Felsburg, P.J., additional, Fletcher, O.J., additional, Fluri, A., additional, Foss, D.L., additional, Gianello, P., additional, Giger, U., additional, Goddeeris, B., additional, Govaerts, A., additional, Grant, C.K., additional, Greiner, D.L., additional, Griebel, P.J., additional, Grimholt, U., additional, Groen, H., additional, Hague, B., additional, Haig, D., additional, Hala, K., additional, Hamers, R., additional, Hanken, R.J., additional, Hannant, D., additional, Harbour, D.A., additional, Harlan, J., additional, Hawken, R.J., additional, Hein, W.R., additional, Heinen, E., additional, Helfand, S.C., additional, Hermann, T., additional, Høgåsen, K., additional, Hogenesch, H., additional, Hordvik, I., additional, Horohov, D.W., additional, Howard, C., additional, Hünig, T., additional, Husband, A., additional, Hüttner, S.W., additional, Hylkema, M.N., additional, Ingram, G.A., additional, Ishiguro, N., additional, Jakowlew, S.B., additional, Jeurissen, S.H.M., additional, Joosten, E., additional, Jørgensen, T., additional, Jungi, T.W., additional, Kaplan, M.H., additional, Kaufman, J., additional, Kimpton, W.G., additional, Knight, K.L., additional, Koch, C., additional, Komatsu, M., additional, Koppenheffer, T.L., additional, Krakowka, G.S., additional, Kroese, F.G.M., additional, Landsverk, T., additional, Lanning, D., additional, Latinne, D., additional, Leblond, V., additional, Leutenegger, C., additional, Levy, J.K., additional, Lewin, H., additional, Lie, Ø., additional, Lillehoj, H.S., additional, Llanes, D., additional, Lumsden, J.S., additional, Lunn, D.P., additional, Lunney, J., additional, Lutz, H., additional, MacHugh, N., additional, Maddox, J.F., additional, Mage, R.G., additional, Martin, H.M., additional, McClure, S., additional, McConnell, T.J., additional, McCormack, W.T., additional, McCullagh, P.P., additional, McKeever, D., additional, Mertens, B., additional, Miller, N.W., additional, Modiano, J.F., additional, Morgan, B.P., additional, Morizot, D.C., additional, Moutschen, M.P., additional, Murtaugh, M.P., additional, Muyldermans, S., additional, Naessens, J., additional, Nash, A.D., additional, Nguyen, T.C., additional, Nieuwenhuis, P., additional, Obexer-Ruff, G., additional, Pabst, R., additional, Pastoret, P.P., additional, Pedersen, N.C., additional, Pertile, T.L., additional, Pescovitz, M.D., additional, Peterhans, E., additional, Pilstöm, L., additional, Plachy, J., additional, Press, C. McL., additional, Pu, R., additional, Ramamoorthy, C., additional, Ratcliffe, M.J.H., additional, Rautenschlein, S., additional, Reinacher, M., additional, Ritchey, J.W., additional, Robertsen, B., additional, Rodkey, L.S., additional, Rombout, J.H.W.M., additional, Roth, J., additional, Rothkötter, H.J., additional, Rozing, J., additional, Schat, K.A., additional, Seto, A., additional, Sharar, S., additional, Sharma, J.M., additional, Sinkora, J., additional, Sittisombut, N., additional, Soares, M., additional, Sopp, P., additional, Stokes, C.R., additional, Suter, M., additional, Tabel, H., additional, Tatner, M.F., additional, Tissot, R.G., additional, Tlaskalová-Hogenová, H., additional, Toivanen, P., additional, Tompkins, M.B., additional, Tompkins, W.A.F., additional, Torres-Nagel, N.E., additional, Tournefier, A., additional, Trebichavsky, I., additional, Tucker, E., additional, Urbain, J., additional, Vainio, O., additional, van den Berg, R.H., additional, van den Berg, T.K., additional, van den Broeke, A., additional, van der Meide, P., additional, Vandevelde, M., additional, van Rees, E.P., additional, Vögeli, P., additional, Wagner, J.L., additional, Wakenell, P.S., additional, Watson, D., additional, Weinstein, P.D., additional, Werner, E.R., additional, Westermann, J., additional, Whalen, B.J., additional, Willett, B.J., additional, Winkelstein, J.A., additional, Winn, R., additional, Yamamoto, J.K., additional, Young, A.J., additional, and Zurbriggen, A., additional

Published
1998
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25. Accuracy in Diagnosis of Celiac Disease Without Biopsies in Clinical Practice

Author

Werkstetter, K.J. Korponay-Szabó, I.R. Popp, A. Villanacci, V. Salemme, M. Heilig, G. Lillevang, S.T. Mearin, M.L. Ribes-Koninckx, C. Thomas, A. Troncone, R. Filipiak, B. Mäki, M. Gyimesi, J. Najafi, M. Dolinšek, J. Dydensborg Sander, S. Auricchio, R. Papadopoulou, A. Vécsei, A. Szitanyi, P. Donat, E. Nenna, R. Alliet, P. Penagini, F. Garnier-Lengliné, H. Castillejo, G. Kurppa, K. Shamir, R. Hauer, A.C. Smets, F. Corujeira, S. van Winckel, M. Buderus, S. Chong, S. Husby, S. Koletzko, S. Socha, P. Cukrowska, B. Szajewska, H. Wyhowski, J. Brown, N. Batra, G. Misak, Z. Seiwerth, S. Dmitrieva, Y. Abramov, D. Vandenplas, Y. Goossens, A. Schaart, M.W. Smit, V.T.H.B.M. Kalach, N. Gosset, P. Kovács, J.B. Nagy, A. Lellei, I. Kőbányai, R. Khatami, K. Monajemzadeh, M. Dimakou, K. Patereli, A. Hansen, T.P. Kavalar, R. Bolonio, M. Ramos, D. Kogler, H. Amann, G. Kosova, R. Maglio, M. Janssens, E. Achten, R. Frűhauf, P. Skálová, H. Kirchner, T. Petrarca, L. Magliocca, F.M. Martínez, F. Morente, V. Thanner-Lechner, S. Ratschek, M. Gasparetto, M. Hook, L. Canioni, D. Wanty, C. Mourin, A. Laurila, K. Vornane, M. Friedler, V.N. Morgenstern, S.L. Amil Dias, J. Carneiro, F. João, H.S. Van Biervliet, S. Velde, S.V. Banoub, H. Sampson, S. Müller, A.M. Ene, A. Rafeey, M. Eftekhar Sadat, A.T. ProCeDE study group ProCeDE study group

Abstract

Background & Aims The guidelines of the European Society of Pediatric Gastroenterology, Hepatology, and Nutrition allow for diagnosis of celiac disease without biopsies in children with symptoms and levels of immunoglobulin A against tissue-transglutaminase (TGA-IgA) 10-fold or more the upper limit of normal (ULN), confirmed by detection of endomysium antibodies (EMA) and positivity for HLA-DQ2/DQ8. We performed a large, international prospective study to validate this approach. Methods We collected data from consecutive pediatric patients (18 years or younger) on a gluten-containing diet who tested positive for TGA-IgA from November 2011 through May 2014, seen at 33 pediatric gastroenterology units in 21 countries. Local centers recorded symptoms; measurements of total IgA, TGA, and EMA; and histopathology findings from duodenal biopsies. Children were considered to have malabsorption if they had chronic diarrhea, weight loss (or insufficient gain), growth failure, or anemia. We directly compared central findings from 16 antibody tests (8 for TGA-IgA, 1 for TGA-IgG, 6 for IgG against deamidated gliadin peptides, and 1 for EMA, from 5 different manufacturers), 2 HLA-DQ2/DQ8 tests from 2 manufacturers, and histopathology findings from the reference pathologist. Final diagnoses were based on local and central results. If all local and central results were concordant for celiac disease, cases were classified as proven celiac disease. Patients with only a low level of TGA-IgA (threefold or less the ULN) but no other results indicating celiac disease were classified as no celiac disease. Central histo-morphometry analyses were performed on all other biopsies and cases were carefully reviewed in a blinded manner. Inconclusive cases were regarded as not having celiac disease for calculation of diagnostic accuracy. The primary aim was to determine whether the nonbiopsy approach identifies children with celiac disease with a positive predictive value (PPV) above 99% in clinical practice. Secondary aims included comparing performance of different serological tests and to determine whether the suggested criteria can be simplified. Results Of 803 children recruited for the study, 96 were excluded due to incomplete data, low level of IgA, or poor-quality biopsies. In the remaining 707 children (65.1% girls; median age, 6.2 years), 645 were diagnosed with celiac disease, 46 were found not to have celiac disease, and 16 had inconclusive results. Findings from local laboratories of TGA-IgA 10-fold or more the ULN, a positive result from the test for EMA, and any symptom identified children with celiac disease (n = 399) with a PPV of 99.75 (95% confidence interval [CI], 98.61–99.99); the PPV was 100.00 (95% CI, 98.68–100.00) when only malabsorption symptoms were used instead of any symptom (n = 278). Inclusion of HLA analyses did not increase accuracy. Findings from central laboratories differed greatly for patients with lower levels of antibodies, but when levels of TGA-IgA were 10-fold or more the ULN, PPVs ranged from 99.63 (95% CI, 98.67–99.96) to 100.00 (95% CI, 99.23–100.00). Conclusions Children can be accurately diagnosed with celiac disease without biopsy analysis. Diagnosis based on level of TGA-IgA 10-fold or more the ULN, a positive result from the EMA tests in a second blood sample, and the presence of at least 1 symptom could avoid risks and costs of endoscopy for more than half the children with celiac disease worldwide. HLA analysis is not required for accurate diagnosis. Clinical Trial Registration no: DRKS00003555. © 2017 AGA Institute

Published
2017

26. Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants

Author

Romanos, J., Rosén, A., Kumar, V., Trynka, G., Franke, L., Szperl, A., Gutierrez-Achury, J., van Diemen, C.C., Kanninga, R., Jankipersadsing, S.A., Steck, A., Eisenbarth, G., van Heel, D.A., Cukrowska, B., Bruno, V., Mazzilli, M.C., Núñez, C., Bilbao, J.R., Mearin, M.L., Barisani, D., Rewers, M., Norris, J.M., Ivarsson, A., Boezen. H.M., Liu, E., Wijmenga, C., Prevent, C.D., Kolaček, Sanja, Steck, A, Mearin, M, L, Barisani, D, Rewers, M, Boezen, H.M., Romanos, J, Rosen, A, Kumar, V, Trynka, G, Franke, L, Szperl, A, Gutierrez Achury, J, Van Diemen, Cc, Kanninga, R, Jankipersadsing, Sa, Steck, A, Eisenbarth, G, van Heel, Da, Cukrowska, B, Bruno, V, Mazzilli, Mc, Nunez, C, Bilbao, Jr, Mearin, Ml, Barisani, D, Rewers, M, Norris, Jm, Ivarsson, A, Boezen, Hm, Liu, E, Wijmenga, C, Auricchio, Renata, Prevent CD, G. r. o. u. p., Rosén, A, van Diemen, C, Jankipersadsing, S, van Heel, D, Mazzilli, M, Núñez, C, Bilbao, J, Mearin, M, Norris, J, Boezen, H, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Life Course Epidemiology (LCE), Groningen Research Institute for Asthma and COPD (GRIAC), and Stem Cell Aging Leukemia and Lymphoma (SALL)

Subjects
Male, INCREASING PREVALENCE, ACCURACY, AUTOIMMUNITY, Genome-wide association study, Human chromosome abnormalities -- Diagnosis, Celiac disease, Elméleti orvostudományok, Prospective Studies, MULTIPLE COMMON, education.field_of_study, medicine.diagnostic_test, Gastroenterology, Orvostudományok, 3. Good health, Hla, Female, Risk assessment, Genetic Markers, Population, Single-nucleotide polymorphism, Human leukocyte antigen, GENETIC RISK, Coeliac Disease, Polymorphism, Single Nucleotide, Risk Assessment, Decision Support Techniques, Molecular Genetics, Molecular Genetic, HLA-DQ Antigens, medicine, Genetics, LINKAGE, SNP, Humans, Genetic Predisposition to Disease, Genetic Testing, GENOME-WIDE ASSOCIATION, education, Genetic testing, Proportional Hazards Models, Models, Genetic, business.industry, Case-control study, BIO/13 - BIOLOGIA APPLICATA, ALLELES, Celiac Disease, Logistic Models, ROC Curve, Case-Control Studies, Immunology, business
Abstract

Background The majority of coeliac disease (CD) patients are not being properly diagnosed and therefore remain untreated, leading to a greater risk of developing CD-associated complications. The major genetic risk heterodimer, HLA-DQ2 and DQ8, is already used clinically to help exclude disease. However, approximately 40% of the population carry these alleles and the majority never develop CD. Objective We explored whether CD risk prediction can be improved by adding non-HLA-susceptible variants to common HLA testing. Design We developed an average weighted genetic risk score with 10, 26 and 57 single nucleotide polymorphisms (SNP) in 2675 cases and 2815 controls and assessed the improvement in risk prediction provided by the non-HLA SNP. Moreover, we assessed the transferability of the genetic risk model with 26 non-HLA variants to a nested case–control population (n=1709) and a prospective cohort (n=1245) and then tested how well this model predicted CD outcome for 985 independent individuals. Results Adding 57 non-HLA variants to HLA testing showed a statistically significant improvement compared to scores from models based on HLA only, HLA plus 10 SNP and HLA plus 26 SNP. With 57 non-HLA variants, the area under the receiver operator characteristic curve reached 0.854 compared to 0.823 for HLA only, and 11.1% of individuals were reclassified to a more accurate risk group. We show that the risk model with HLA plus 26 SNP is useful in independent populations. Conclusions Predicting risk with 57 additional non-HLA variants improved the identification of potential CD patients. This demonstrates a possible role for combined HLA and non-HLA genetic testing in diagnostic work for CD., peer-reviewed

Published
2013

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

Author

Trynka, G., Hunt, K.A., Bockett, N.A., Romanos, J., Mistry, V., Szperl, A., Bakker, S.F., Bardella, M.T., Bhaw-Rosun, L., Castillejo, G., Concha, E.G. de la, Almeida, R.C. de, Dias, K.R.M., Diemen, C.C. van, Dubois, P.C.A., Duerr, R.H., Edkins, S., Franke, L., Fransen, K., Gutierrez, J., Heap, G.A.R., Hrdlickova, B., Hunt, S., Izurieta, L.P., Izzo, V., Joosten, L.A.B., Langford, C., Mazzilli, M.C., Mein, C.A., Midah, V., Mitrovic, M., Mora, B., Morelli, M., Nutland, S., Nunez, C., Onengut-Gumuscu, S., Pearce, K., Platteel, M., Polanco, I., Potter, S., Ribes-Koninckx, C., Ricano-Ponce, I., Rich, S.S., Rybak, A., Santiago, J.L., Senapati, S., Sood, A., Szajewska, H., Troncone, R., Varade, J., Wallace, C., Wolters, V.M., Zhernakova, A., Thelma, B.K., Cukrowska, B., Urcelay, E., Bilbao, J.R., Mearin, M.L., Barisani, D., Barrett, J.C., Plagnol, V., Deloukas, P., Wijmenga, C., Heel, D.A. van, Spanish Consortium Genetics Coelia, PreventCD Study Grp, WTCCC, Trynka, G, Hunt, K, Bockett, N, Romanos, J, Mistry, V, Szperl, A, Bakker, S, Bardella, M, Bhaw Rosun, L, Castillejo, G, De la Concha, E, De Almeida, R, Dias, K, Van Diemen, C, Dubois, P, Duerr, R, Edkins, S, Franke, L, Fransen, K, Gutierrez, J, Heap, G, Hrdlickova, B, Hunt, S, Izurieta, L, Izzo, V, Joosten, L, Langford, C, Mazzilli, M, Mein, C, 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, S, Rybak, A, Santiago, J, Senapati, S, Sood, A, Szajewska, H, Troncone, R, Varadé, J, Wallace, C, Wolters, V, Zhernakova, A, Spanish Consortium on the Genetics of Coeliac, D, PreventCD Study, G, Wellcome Trust Case Control, C, Thelma, B, Cukrowska, B, Urcelay, E, Bilbao, J, Mearin, M, Barisani, D, Barrett, J, Plagnol, V, Deloukas, P, Wijmenga, C, Van Heel, D, Gastroenterology and hepatology, CCA - Disease profiling, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Stem Cell Aging Leukemia and Lymphoma (SALL), and Translational Immunology Groningen (TRIGR)

Subjects
EXPRESSION, Linkage disequilibrium, Population, LOCI, Genome-wide association study, Locus (genetics), Human leukocyte antigen, Biology, PHENOTYPE, Polymorphism, Single Nucleotide, Linkage Disequilibrium, REGION, 03 medical and health sciences, 0302 clinical medicine, Gene Frequency, Risk Factors, Genetics, RISK VARIANTS, Humans, 1000 Genomes Project, GENOME-WIDE ASSOCIATION, education, Genotyping, POPULATION, 030304 developmental biology, 0303 health sciences, education.field_of_study, celiac disease, GWAS, LARGE-SCALE, BIO/13 - BIOLOGIA APPLICATA, Chromosome Mapping, Pathogenesis and modulation of inflammation Infection and autoimmunity [N4i 1], GENE, Genetic architecture, Celiac Disease, Haplotypes, Genetic Loci, 030220 oncology & carcinogenesis, Case-Control Studies, MAP, Genome-Wide Association Study
Abstract

Using variants from the 1000 Genomes Project pilot European CEU dataset and data from additional resequencing studies, we densely genotyped 183 non-HLA risk loci previously associated with immune-mediated diseases in 12,041 individuals with celiac disease (cases) and 12,228 controls. We identified 13 new celiac disease risk loci reaching genome-wide significance, bringing the number of known loci (including the HLA locus) to 40. We found multiple independent association signals at over one-third of these loci, a finding that is attributable to a combination of common, low-frequency and rare genetic variants. Compared to previously available data such as those from HapMap3, our dense genotyping in a large sample collection provided a higher resolution of the pattern of linkage disequilibrium and suggested localization of many signals to finer scale regions. In particular, 29 of the 54 fine-mapped signals seemed to be localized to single genes and, in some instances, to gene regulatory elements. Altogether, we define the complex genetic architecture of the risk regions of and refine the risk signals for celiac disease, providing the next step toward uncovering the causal mechanisms of the disease. © 2011 Nature America, Inc. All rights reserved.

Published
2011
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28. Multiple common variants for celiac disease influencing immnune gene expression

Author

Dubois PC, Trynka G, Francke L, Hunt KA, Rpmanos J, Curtotti A, Zhernakova A, Heap GA, Adàny R, Aromaa A, Bardella MT, Van Den Berg LH, Bockett NA, De La Concha EG, DEma B, Fehrmann RS, Fernandez Aquero M, Fiatal S, Grandone E, Green PM, Groen HJ, Gwilliam R, Houwn RH, Hunt SE, Kaukinen K, Kelleher D, Korponay Szabo I, Kurppa K, Mac Mathuna P, Maki M, Mazzilli MC, McCann OT, Mearin ML, Mein CA, Mirza MM, Mistry V, Mora B, Morley KI, Mulder CJ, Murray JA, Nunez C, Oosterom E, Ophoff RA, Polanco I, Peltonen L, Platteel M, Rybak A, Salomaa V, Schweizer JJ, Sperandeo MP, Tack GJ, Turner G, Veldink JH, Verbeek WH, Weersma RK, Wolters WM, Urcelay E, Cukrowska B, Neuhausen SL, McManus R, Barisani D, Deloukas P, Barrett JC, Saavalainen P, Wijmenga C, Van Heel DA, GRECO, LUIGI, Dubois, Pc, Trynka, G, Francke, L, Hunt, Ka, Rpmanos, J, Curtotti, A, Zhernakova, A, Heap, Ga, Adàny, R, Aromaa, A, Bardella, Mt, Van Den Berg, Lh, Bockett, Na, De La Concha, Eg, Dema, B, Fehrmann, R, Fernandez Aquero, M, Fiatal, S, Grandone, E, Green, Pm, Groen, Hj, Gwilliam, R, Houwn, Rh, Hunt, Se, Kaukinen, K, Kelleher, D, Korponay Szabo, I, Kurppa, K, Mac Mathuna, P, Maki, M, Mazzilli, Mc, Mccann, Ot, Mearin, Ml, Mein, Ca, Mirza, Mm, Mistry, V, Mora, B, Morley, Ki, Mulder, Cj, Murray, Ja, Nunez, C, Oosterom, E, Ophoff, Ra, Polanco, I, Peltonen, L, Platteel, M, Rybak, A, Salomaa, V, Schweizer, Jj, Sperandeo, Mp, Tack, Gj, Turner, G, Veldink, Jh, Verbeek, Wh, Weersma, Rk, Wolters, Wm, Urcelay, E, Cukrowska, B, Greco, Luigi, Neuhausen, Sl, Mcmanus, R, Barisani, D, Deloukas, P, Barrett, Jc, Saavalainen, P, Wijmenga, C, and Van Heel, Da

Subjects
gene, celiac disease
Abstract

We performed a second-generation genome-wide association study of 4,533 individuals with celiac disease (cases) and 10,750 control subjects. We genotyped 113 selected SNPs with P(GWAS) < 10(-4) and 18 SNPs from 14 known loci in a further 4,918 cases and 5,684 controls. Variants from 13 new regions reached genome-wide significance (P(combined) < 5 x 10(-8)); most contain genes with immune functions (BACH2, CCR4, CD80, CIITA-SOCS1-CLEC16A, ICOSLG and ZMIZ1), with ETS1, RUNX3, THEMIS and TNFRSF14 having key roles in thymic T-cell selection. There was evidence to suggest associations for a further 13 regions. In an expression quantitative trait meta-analysis of 1,469 whole blood samples, 20 of 38 (52.6%) tested loci had celiac risk variants correlated (P < 0.0028, FDR 5%) with cis gene expression.

Published
2010

29. Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants

Author

Romanos, J., Rosen, A., Kumar, V., Trynka, G., Franke, L., Szperl, A., Gutierrez-Achury, J., Van, Diemen C.C., Kanninga, R., Jankipersadsing, S.A., Steck, A., Eisenbarth, G., Van, Heel D.A., Cukrowska, B., Bruno, V., Mazzilli, M.C., Nunez, C., Bilbao, J.R., Mearin, M.L., Barisani, D., Rewers, M., Norris, J.M., Ivarsson, A., Boezen, H.M., Liu, E., Wijmenga, C., Romanos, J., Rosen, A., Kumar, V., Trynka, G., Franke, L., Szperl, A., Gutierrez-Achury, J., Van, Diemen C.C., Kanninga, R., Jankipersadsing, S.A., Steck, A., Eisenbarth, G., Van, Heel D.A., Cukrowska, B., Bruno, V., Mazzilli, M.C., Nunez, C., Bilbao, J.R., Mearin, M.L., Barisani, D., Rewers, M., Norris, J.M., Ivarsson, A., Boezen, H.M., Liu, E., and Wijmenga, C.

Abstract

Background The majority of coeliac disease (CD) patients are not being properly diagnosed and therefore remain untreated, leading to a greater risk of developing CD-associated complications. The major genetic risk heterodimer, HLA-DQ2 and DQ8, is already used clinically to help exclude disease. However, approximately 40% of the population carry these alleles and the majority never develop CD. Objective We explored whether CD risk prediction can be improved by adding non-HLA-susceptible variants to common HLA testing. Design We developed an average weighted genetic risk score with 10, 26 and 57 single nucleotide polymorphisms (SNP) in 2675 cases and 2815 controls and assessed the improvement in risk prediction provided by the non-HLA SNP. Moreover, we assessed the transferability of the genetic risk model with 26 non-HLA variants to a nested case-control population (n=1709) and a prospective cohort (n=1245) and then tested how well this model predicted CD outcome for 985 independent individuals. Results Adding 57 non-HLA variants to HLA testing showed a statistically significant improvement compared to scores from models based on HLA only, HLA plus 10 SNP and HLA plus 26 SNP. With 57 non-HLA variants, the area under the receiver operator characteristic curve reached 0.854 compared to 0.823 for HLA only, and 11.1% of individuals were reclassified to a more accurate risk group. We show that the risk model with HLA plus 26 SNP is useful in independent populations. Conclusions Predicting risk with 57 additional non-HLA variants improved the identification of potential CD patients. This demonstrates a possible role for combined HLA and non-HLA genetic testing in diagnostic work for CD., Collaborators:PreventCD GroupHär ingår Lotta Högberg och Lars Stenhammar från Barn-och ungdomskliniken, VrinneviFunding Agencies|5R1DK084568-02, NIH, National Institutes of Health

Published
2014
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30. Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant

Author

Almeida, R, Ricanõ Ponce, I, Kumar, V, Deelen, P, Szperl, A, Trynka, G, Gutierrez Achury, J, Kanterakis, A, Westra, H, Franke, L, Swertz, M, Platteel, M, Bilbao, J, Barisani, D, Greco, L, Mearin, L, Wolters, V, Mulder, C, Mazzilli, M, Sood, A, Cukrowska, B, Núñez, C, Pratesi, R, Withoff, S, Wijmenga, C, Wijmenga, C., BARISANI, DONATELLA, Almeida, R, Ricanõ Ponce, I, Kumar, V, Deelen, P, Szperl, A, Trynka, G, Gutierrez Achury, J, Kanterakis, A, Westra, H, Franke, L, Swertz, M, Platteel, M, Bilbao, J, Barisani, D, Greco, L, Mearin, L, Wolters, V, Mulder, C, Mazzilli, M, Sood, A, Cukrowska, B, Núñez, C, Pratesi, R, Withoff, S, Wijmenga, C, Wijmenga, C., and BARISANI, DONATELLA

Abstract

Using theImmunochip for genotyping, weidentified 39non-human leukocyte antigen(non-HLA) loci associated to celiac disease (CeD), an immune-mediated disease with aworldwide frequency of ~1%. The most significant non-HLA signal mapped to the intronic region of 70 kb in the LPP gene. Our aim was to fine map and identify possible functional variants in the LPP locus. We performed a meta-analysis in a cohort of 25 169 individuals from six different populations previously genotyped using Immunochip. Imputation using data from the Genome of the Netherlands and 1000 Genomes projects, followed by meta-analysis, confirmed the strong association signal on the LPP locus (rs2030519, P = 1.79 × 10-49), without any novel associations. The conditional analysis on this top SNP-indicated association to a single common haplotype. By performing haplotype analyses in each population separately, as well as in a combined group of the four populations that reach the significant threshold after correction (P < 0.008), we narrowed down the CeD-associated region from 70 to 2.8 kb (P = 1.35×10-44). By intersecting regulatory data from the ENCODE project, we found a functional SNP, rs4686484 (P = 3.12×10-499), that maps to several B-cell enhancer elements and a highly conserved region. This SNP was also predicted to change the binding motif of the transcription factors IRF4, IRF11, Nkx2.7 and Nkx2.9, suggesting its role in transcriptional regulation. We later found significantly low levels of LPP mRNA in CeD biopsies compared with controls, thus our results suggest that rs4686484 is the functional variant in this locus, while LPP expression is decreased in CeD. © The Author 2013. Published by Oxford University Press. All rights reserved.

Published
2014

31. Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants

Author

Romanos, J, Rosén, A, Kumar, V, Trynka, G, Franke, L, Szperl, A, Gutierrez Achury, J, van Diemen, C, Kanninga, R, Jankipersadsing, S, Steck, A, Eisenbarth, G, van Heel, D, Cukrowska, B, Bruno, V, Mazzilli, M, Núñez, C, Bilbao, J, Mearin, M, Barisani, D, Rewers, M, Norris, J, Ivarsson, A, Boezen, H, Liu, E, Wijmenga, C, van Diemen, CC, Jankipersadsing, SA, van Heel, DA, Mazzilli, MC, Bilbao, JR, Mearin, ML, Norris, JM, Boezen, HM, Wijmenga, C., BARISANI, DONATELLA, Romanos, J, Rosén, A, Kumar, V, Trynka, G, Franke, L, Szperl, A, Gutierrez Achury, J, van Diemen, C, Kanninga, R, Jankipersadsing, S, Steck, A, Eisenbarth, G, van Heel, D, Cukrowska, B, Bruno, V, Mazzilli, M, Núñez, C, Bilbao, J, Mearin, M, Barisani, D, Rewers, M, Norris, J, Ivarsson, A, Boezen, H, Liu, E, Wijmenga, C, van Diemen, CC, Jankipersadsing, SA, van Heel, DA, Mazzilli, MC, Bilbao, JR, Mearin, ML, Norris, JM, Boezen, HM, Wijmenga, C., and BARISANI, DONATELLA

Abstract

BACKGROUND: The majority of coeliac disease (CD) patients are not being properly diagnosed and therefore remain untreated, leading to a greater risk of developing CD-associated complications. The major genetic risk heterodimer, HLA-DQ2 and DQ8, is already used clinically to help exclude disease. However, approximately 40% of the population carry these alleles and the majority never develop CD. OBJECTIVE: We explored whether CD risk prediction can be improved by adding non-HLA-susceptible variants to common HLA testing. DESIGN: We developed an average weighted genetic risk score with 10, 26 and 57 single nucleotide polymorphisms (SNP) in 2675 cases and 2815 controls and assessed the improvement in risk prediction provided by the non-HLA SNP. Moreover, we assessed the transferability of the genetic risk model with 26 non-HLA variants to a nested case-control population (n=1709) and a prospective cohort (n=1245) and then tested how well this model predicted CD outcome for 985 independent individuals. RESULTS: Adding 57 non-HLA variants to HLA testing showed a statistically significant improvement compared to scores from models based on HLA only, HLA plus 10 SNP and HLA plus 26 SNP. With 57 non-HLA variants, the area under the receiver operator characteristic curve reached 0.854 compared to 0.823 for HLA only, and 11.1% of individuals were reclassified to a more accurate risk group. We show that the risk model with HLA plus 26 SNP is useful in independent populations. CONCLUSIONS: Predicting risk with 57 additional non-HLA variants improved the identification of potential CD patients. This demonstrates a possible role for combined HLA and non-HLA genetic testing in diagnostic work for CD.

Published
2014

32. MEDULLOBLASTOMA

Author

Vaidyanathan, G., primary, Gururangan, S., additional, Bigner, D., additional, Zalutsky, M., additional, Morfouace, M., additional, Shelat, A., additional, Megan, J., additional, Freeman, B. B., additional, Robinson, S., additional, Throm, S., additional, Olson, J. M., additional, Li, X.-N., additional, Guy, K. R., additional, Robinson, G., additional, Stewart, C., additional, Gajjar, A., additional, Roussel, M., additional, Sirachainan, N., additional, Pakakasama, S., additional, Anurathapan, U., additional, Hansasuta, A., additional, Dhanachai, M., additional, Khongkhatithum, C., additional, Hongeng, S., additional, Feroze, A., additional, Lee, K.-S., additional, Gholamin, S., additional, Wu, Z., additional, Lu, B., additional, Mitra, S., additional, Cheshier, S., additional, Northcott, P., additional, Lee, C., additional, Zichner, T., additional, Lichter, P., additional, Korbel, J., additional, Wechsler-Reya, R., additional, Pfister, S., additional, Project, I. P. T., additional, Li, K. K.-W., additional, Xia, T., additional, Ma, F. M. T., additional, Zhang, R., additional, Zhou, L., additional, Lau, K.-M., additional, Ng, H.-K., additional, Lafay-Cousin, L., additional, Chi, S., additional, Madden, J., additional, Smith, A., additional, Wells, E., additional, Owens, E., additional, Strother, D., additional, Foreman, N., additional, Packer, R., additional, Bouffet, E., additional, Wataya, T., additional, Peacock, J., additional, Taylor, M. D., additional, Ivanov, D., additional, Garnett, M., additional, Parker, T., additional, Alexander, C., additional, Meijer, L., additional, Grundy, R., additional, Gellert, P., additional, Ashford, M., additional, Walker, D., additional, Brent, J., additional, Cader, F. Z., additional, Ford, D., additional, Kay, A., additional, Walsh, R., additional, Solanki, G., additional, Peet, A., additional, English, M., additional, Shalaby, T., additional, Fiaschetti, G., additional, Baulande, S., additional, Gerber, N., additional, Baumgartner, M., additional, Grotzer, M., additional, Hayase, T., additional, Kawahara, Y., additional, Yagi, M., additional, Minami, T., additional, Kanai, N., additional, Yamaguchi, T., additional, Gomi, A., additional, Morimoto, A., additional, Hill, R., additional, Kuijper, S., additional, Lindsey, J., additional, Schwalbe, E., additional, Barker, K., additional, Boult, J., additional, Williamson, D., additional, Ahmad, Z., additional, Hallsworth, A., additional, Ryan, S., additional, Poon, E., additional, Ruddle, R., additional, Raynaud, F., additional, Howell, L., additional, Kwok, C., additional, Joshi, A., additional, Nicholson, S. L., additional, Crosier, S., additional, Wharton, S., additional, Robson, K., additional, Michalski, A., additional, Hargrave, D., additional, Jacques, T., additional, Pizer, B., additional, Bailey, S., additional, Swartling, F., additional, Petrie, K., additional, Weiss, W., additional, Chesler, L., additional, Clifford, S., additional, Kitanovski, L., additional, Prelog, T., additional, Kotnik, B. F., additional, Debeljak, M., additional, Grotzer, M. A., additional, Gevorgian, A., additional, Morozova, E., additional, Kazantsev, I., additional, Iukhta, T., additional, Safonova, S., additional, Kumirova, E., additional, Punanov, Y., additional, Afanasyev, B., additional, Zheludkova, O., additional, Grajkowska, W., additional, Pronicki, M., additional, Cukrowska, B., additional, Dembowska-Baginska, B., additional, Lastowska, M., additional, Murase, A., additional, Nobusawa, S., additional, Gemma, Y., additional, Yamazaki, F., additional, Masuzawa, A., additional, Uno, T., additional, Osumi, T., additional, Shioda, Y., additional, Kiyotani, C., additional, Mori, T., additional, Matsumoto, K., additional, Ogiwara, H., additional, Morota, N., additional, Hirato, J., additional, Nakazawa, A., additional, Terashima, K., additional, Fay-McClymont, T., additional, Walsh, K., additional, Mabbott, D., additional, Sturm, D., additional, Northcott, P. A., additional, Jones, D. T. W., additional, Korshunov, A., additional, Pfister, S. M., additional, Kool, M., additional, Hooper, C., additional, Hawes, S., additional, Kees, U., additional, Gottardo, N., additional, Dallas, P., additional, Siegfried, A., additional, Bertozzi, A. I., additional, Sevely, A., additional, Loukh, N., additional, Munzer, C., additional, Miquel, C., additional, Bourdeaut, F., additional, Pietsch, T., additional, Dufour, C., additional, Delisle, M. B., additional, Kawauchi, D., additional, Rehg, J., additional, Finkelstein, D., additional, Zindy, F., additional, Phoenix, T., additional, Gilbertson, R., additional, Trubicka, J., additional, Borucka-Mankiewicz, M., additional, Ciara, E., additional, Chrzanowska, K., additional, Perek-Polnik, M., additional, Abramczuk-Piekutowska, D., additional, Jurkiewicz, D., additional, Luczak, S., additional, Kowalski, P., additional, Krajewska-Walasek, M., additional, Sheila, C., additional, Lee, S., additional, Foster, C., additional, Manoranjan, B., additional, Pambit, M., additional, Berns, R., additional, Fotovati, A., additional, Venugopal, C., additional, O'Halloran, K., additional, Narendran, A., additional, Hawkins, C., additional, Ramaswamy, V., additional, Taylor, M., additional, Singhal, A., additional, Hukin, J., additional, Rassekh, R., additional, Yip, S., additional, Singh, S., additional, Duhman, C., additional, Dunn, S., additional, Chen, T., additional, Rush, S., additional, Fuji, H., additional, Ishida, Y., additional, Onoe, T., additional, Kanda, T., additional, Kase, Y., additional, Yamashita, H., additional, Murayama, S., additional, Nakasu, Y., additional, Kurimoto, T., additional, Kondo, A., additional, Sakaguchi, S., additional, Fujimura, J., additional, Saito, M., additional, Arakawa, T., additional, Arai, H., additional, Shimizu, T., additional, Jurkiewicz, E., additional, Daszkiewicz, P., additional, Drogosiewicz, M., additional, Hovestadt, V., additional, Buchhalter, I., additional, Jager, N. N., additional, Stuetz, A., additional, Johann, P., additional, Schmidt, C., additional, Ryzhova, M., additional, Landgraf, P., additional, Hasselblatt, M., additional, Schuller, U., additional, Yaspo, M.-L., additional, von Deimling, A., additional, Eils, R., additional, Modi, A., additional, Patel, M., additional, Berk, M., additional, Wang, L.-x., additional, Plautz, G., additional, Camara-Costa, H., additional, Resch, A., additional, Lalande, C., additional, Kieffer, V., additional, Poggi, G., additional, Kennedy, C., additional, Bull, K., additional, Calaminus, G., additional, Grill, J., additional, Doz, F., additional, Rutkowski, S., additional, Massimino, M., additional, Kortmann, R.-D., additional, Lannering, B., additional, Dellatolas, G., additional, Chevignard, M., additional, Solecki, D., additional, McKinnon, P., additional, Olson, J., additional, Hayden, J., additional, Ellison, D., additional, Buss, M., additional, Remke, M., additional, Lee, J., additional, Caspary, T., additional, Castellino, R., additional, Sabel, M., additional, Gustafsson, G., additional, Fleischhack, G., additional, Benesch, M., additional, Navajas, A., additional, Reddingius, R., additional, Delisle, M.-B., additional, Lafon, D., additional, Sevenet, N., additional, Pierron, G., additional, Delattre, O., additional, Ecker, J., additional, Oehme, I., additional, Mazitschek, R., additional, Lodrini, M., additional, Deubzer, H. E., additional, Kulozik, A. E., additional, Witt, O., additional, Milde, T., additional, Patmore, D., additional, Boulos, N., additional, Wright, K., additional, Boop, S., additional, Janicki, T., additional, Burzynski, S., additional, Burzynski, G., additional, Marszalek, A., additional, Triscott, J., additional, Green, M., additional, Rassekh, S. R., additional, Toyota, B., additional, Dunham, C., additional, Dunn, S. E., additional, Liu, K.-W., additional, Pei, Y., additional, Genovesi, L., additional, Ji, P., additional, Davis, M., additional, Ng, C. G., additional, Cho, Y.-J., additional, Jenkins, N., additional, Copeland, N., additional, Wainwright, B., additional, Tang, Y., additional, Schubert, S., additional, Nguyen, B., additional, Masoud, S., additional, Lee, A., additional, Willardson, M., additional, Bandopadhayay, P., additional, Bergthold, G., additional, Atwood, S., additional, Whitson, R., additional, Qi, J., additional, Beroukhim, R., additional, Tang, J., additional, Oro, A., additional, Link, B., additional, Bradner, J., additional, Vallero, S. G., additional, Bertin, D., additional, Basso, M. E., additional, Milanaccio, C., additional, Peretta, P., additional, Cama, A., additional, Mussano, A., additional, Barra, S., additional, Morana, G., additional, Morra, I., additional, Nozza, P., additional, Fagioli, F., additional, Garre, M. L., additional, Darabi, A., additional, Sanden, E., additional, Visse, E., additional, Stahl, N., additional, Siesjo, P., additional, Vaka, D., additional, Vasquez, F., additional, Weir, B., additional, Cowley, G., additional, Keller, C., additional, Hahn, W., additional, Gibbs, I. C., additional, Partap, S., additional, Yeom, K., additional, Martinez, M., additional, Vogel, H., additional, Donaldson, S. S., additional, Fisher, P., additional, Perreault, S., additional, Guerrini-Rousseau, L., additional, Pujet, S., additional, Kieffer-Renaux, V., additional, Raquin, M. A., additional, Varlet, P., additional, Longaud, A., additional, Sainte-Rose, C., additional, Valteau-Couanet, D., additional, Staal, J., additional, Lau, L. S., additional, Zhang, H., additional, Ingram, W. J., additional, Cho, Y. J., additional, Hathout, Y., additional, Brown, K., additional, Rood, B. R., additional, Handler, M., additional, Hankinson, T., additional, Kleinschmidt-Demasters, B. K., additional, Hutter, S., additional, Jones, D. T., additional, Kagawa, N., additional, Hirayama, R., additional, Kijima, N., additional, Chiba, Y., additional, Kinoshita, M., additional, Takano, K., additional, Eino, D., additional, Fukuya, S., additional, Yamamoto, F., additional, Nakanishi, K., additional, Hashimoto, N., additional, Hashii, Y., additional, Hara, J., additional, Yoshimine, T., additional, Wang, J., additional, Guo, C., additional, Yang, Q., additional, Chen, Z., additional, Filipek, I., additional, Swieszkowska, E., additional, Tarasinska, M., additional, Perek, D., additional, Kebudi, R., additional, Koc, B., additional, Gorgun, O., additional, Agaoglu, F. Y., additional, Wolff, J., additional, Darendeliler, E., additional, Kerl, K., additional, Gronych, J., additional, McGlade, J., additional, Endersby, R., additional, Hii, H., additional, Johns, T., additional, Sastry, J., additional, Murphy, D., additional, Ronghe, M., additional, Cunningham, C., additional, Cowie, F., additional, Jones, R., additional, Calisto, A., additional, Sangra, M., additional, Mathieson, C., additional, Brown, J., additional, Phuakpet, K., additional, Larouche, V., additional, Bartels, U., additional, Ishida, T., additional, Hasegawa, D., additional, Miyata, K., additional, Ochi, S., additional, Saito, A., additional, Kozaki, A., additional, Yanai, T., additional, Kawasaki, K., additional, Yamamoto, K., additional, Kawamura, A., additional, Nagashima, T., additional, Akasaka, Y., additional, Soejima, T., additional, Yoshida, M., additional, Kosaka, Y., additional, von Bueren, A., additional, Goschzik, T., additional, Kortmann, R., additional, von Hoff, K., additional, Friedrich, C., additional, Muehlen, A. z., additional, Warmuth-Metz, M., additional, Soerensen, N., additional, Deinlein, F., additional, Zwiener, I., additional, Faldum, A., additional, Kuehl, J., additional, KRAMER, K., additional, -Taskar, N. P., additional, Zanzonico, P., additional, Humm, J. L., additional, Wolden, S. L., additional, Cheung, N.-K. V., additional, Venkataraman, S., additional, Alimova, I., additional, Harris, P., additional, Birks, D., additional, Balakrishnan, I., additional, Griesinger, A., additional, Foreman, N. K., additional, Vibhakar, R., additional, Margol, A., additional, Robison, N., additional, Gnanachandran, J., additional, Hung, L., additional, Kennedy, R., additional, Vali, M., additional, Dhall, G., additional, Finlay, J., additional, Erdrich-Epstein, A., additional, Krieger, M., additional, Drissi, R., additional, Fouladi, M., additional, Gilles, F., additional, Judkins, A., additional, Sposto, R., additional, Asgharzadeh, S., additional, Peyrl, A., additional, Chocholous, M., additional, Holm, S., additional, Grillner, P., additional, Blomgren, K., additional, Azizi, A., additional, Czech, T., additional, Gustafsson, B., additional, Dieckmann, K., additional, Leiss, U., additional, Slavc, I., additional, Babelyan, S., additional, Dolgopolov, I., additional, Pimenov, R., additional, Mentkevich, G., additional, Gorelishev, S., additional, Laskov, M., additional, von Bueren, A. O., additional, Nowak, J., additional, Kortmann, R. D., additional, Mynarek, M., additional, Muller, K., additional, Gerber, N. U., additional, Ottensmeier, H., additional, Kwiecien, R., additional, Yankelevich, M., additional, Boyarshinov, V., additional, Glekov, I., additional, Ozerov, S., additional, Gorelyshev, S., additional, Popa, A., additional, Subbotina, N., additional, Martin, A. M., additional, Nirschl, C., additional, Polanczyk, M., additional, Bell, R., additional, Martinez, D., additional, Sullivan, L. M., additional, Santi, M., additional, Burger, P. C., additional, Taube, J. M., additional, Drake, C. G., additional, Pardoll, D. M., additional, Lim, M., additional, Li, L., additional, Wang, W.-G., additional, Pu, J.-X., additional, Sun, H.-D., additional, Ruggieri, R., additional, Symons, M. H., additional, Vanan, M. I., additional, Bolin, S., additional, Schumacher, S., additional, Zeid, R., additional, Yu, F., additional, Vue, N., additional, Gibson, W., additional, Paolella, B., additional, Swartling, F. J., additional, Kieran, M. W., additional, Bradner, J. E., additional, Maher, O., additional, Khatua, S., additional, Tarek, N., additional, Zaky, W., additional, Gupta, T., additional, Mohanty, S., additional, Kannan, S., additional, Jalali, R., additional, Kapitza, E., additional, Denkhaus, D., additional, Muhlen, A. z., additional, van Vuurden, D. G., additional, Garami, M., additional, Fangusaro, J., additional, Davidson, T. B., additional, da Costa, M. J. G., additional, Sterba, J., additional, Clifford, S. C., additional, Finlay, J. L., additional, Schmidt, R., additional, Felsberg, J., additional, Skladny, H., additional, Cremer, F., additional, Reifenberger, G., additional, Kunder, R., additional, Sridhar, E., additional, Moiyadi, A. A., additional, Goel, A., additional, Goel, N., additional, Shirsat, N., additional, Othman, R., additional, Storer, L., additional, Kerr, I., additional, Coyle, B., additional, Law, N., additional, Smith, M. L., additional, Greenberg, M., additional, Laughlin, S., additional, Malkin, D., additional, Liu, F., additional, Moxon-Emre, I., additional, Scantlebury, N., additional, Nasir, A., additional, Onion, D., additional, Lourdusamy, A., additional, Grabowska, A., additional, Cai, Y., additional, Bradshaw, T., additional, de Medeiros, R. S. S., additional, Beaugrand, A., additional, Soares, S., additional, Epelman, S., additional, Wang, W., additional, Sultan, M., additional, Wechsler-Reya, R. J., additional, Zapatka, M., additional, Radlwimmer, B., additional, Alderete, D., additional, Baroni, L., additional, Lubinieki, F., additional, Auad, F., additional, Gonzalez, M. L., additional, Puya, W., additional, Pacheco, P., additional, Aurtenetxe, O., additional, Gaffar, A., additional, Gros, L., additional, Cruz, O., additional, Calvo, C., additional, Shinojima, N., additional, Nakamura, H., additional, Kuratsu, J.-i., additional, Hanaford, A., additional, Eberhart, C., additional, Archer, T., additional, Tamayo, P., additional, Pomeroy, S., additional, Raabe, E., additional, De Braganca, K., additional, Gilheeney, S., additional, Khakoo, Y., additional, Kramer, K., additional, Wolden, S., additional, Dunkel, I., additional, Lulla, R. R., additional, Laskowski, J., additional, Goldman, S., additional, Gopalakrishnan, V., additional, Shih, D., additional, Wang, X., additional, Faria, C., additional, Raybaud, C., additional, Tabori, U., additional, Rutka, J., additional, Jacobs, S., additional, De Vathaire, F., additional, Diallo, I., additional, Llanas, D., additional, Verez, C., additional, Diop, F., additional, Kahlouche, A., additional, Puget, S., additional, Thompson, E., additional, Prince, E., additional, Amani, V., additional, Sin-Chan, P., additional, Lu, M., additional, Kleinman, C., additional, Spence, T., additional, Picard, D., additional, Ho, K. C., additional, Chan, J., additional, Majewski, J., additional, Jabado, N., additional, Dirks, P., additional, Huang, A., additional, Madden, J. R., additional, Donson, A. M., additional, Mirsky, D. M., additional, Dubuc, A., additional, Mack, S., additional, Gendoo, D., additional, Luu, B., additional, MacDonald, T., additional, Van Meter, T., additional, Croul, S., additional, Laureano, A., additional, Brugmann, W., additional, Denman, C., additional, Singh, H., additional, Huls, H., additional, Moyes, J., additional, Sandberg, D., additional, Silla, L., additional, Cooper, L., additional, and Lee, D., additional

Published
2014
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33. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci

Author

Zhernakova, A., Stahl, E.A., Trynka, G., Raychaudhuri, S., Festen, E.A., Franke, L., Westra, H.J., Fehrmann, R.S., Kurreeman, F.A., Thomson, B., Gupta, N., Romanos, J., McManus, R., Ryan, A.W., Turner, G., Brouwer, E., Posthumus, M.D., Remmers, E.F., Tucci, F., Toes, R., Grandone, E., Mazzilli, M.C., Rybak, A., Cukrowska, B., Coenen, M.J.H., Radstake, T.R.D.J., Riel, P.L. van, Li, Y., Bakker, P.I. de, Gregersen, P.K., Worthington, J., Siminovitch, K.A., Klareskog, L., Huizinga, T.W.J., Wijmenga, C., Plenge, R.M., Zhernakova, A., Stahl, E.A., Trynka, G., Raychaudhuri, S., Festen, E.A., Franke, L., Westra, H.J., Fehrmann, R.S., Kurreeman, F.A., Thomson, B., Gupta, N., Romanos, J., McManus, R., Ryan, A.W., Turner, G., Brouwer, E., Posthumus, M.D., Remmers, E.F., Tucci, F., Toes, R., Grandone, E., Mazzilli, M.C., Rybak, A., Cukrowska, B., Coenen, M.J.H., Radstake, T.R.D.J., Riel, P.L. van, Li, Y., Bakker, P.I. de, Gregersen, P.K., Worthington, J., Siminovitch, K.A., Klareskog, L., Huizinga, T.W.J., Wijmenga, C., and Plenge, R.M.

Abstract

Contains fulltext : 96095.pdf (publisher's version ) (Open Access), Epidemiology and candidate gene studies indicate a shared genetic basis for celiac disease (CD) and rheumatoid arthritis (RA), but the extent of this sharing has not been systematically explored. Previous studies demonstrate that 6 of the established non-HLA CD and RA risk loci (out of 26 loci for each disease) are shared between both diseases. We hypothesized that there are additional shared risk alleles and that combining genome-wide association study (GWAS) data from each disease would increase power to identify these shared risk alleles. We performed a meta-analysis of two published GWAS on CD (4,533 cases and 10,750 controls) and RA (5,539 cases and 17,231 controls). After genotyping the top associated SNPs in 2,169 CD cases and 2,255 controls, and 2,845 RA cases and 4,944 controls, 8 additional SNPs demonstrated P<5 x 10(-8) in a combined analysis of all 50,266 samples, including four SNPs that have not been previously confirmed in either disease: rs10892279 near the DDX6 gene (P(combined) = 1.2 x 10(-12)), rs864537 near CD247 (P(combined) = 2.2 x 10(-11)), rs2298428 near UBE2L3 (P(combined) = 2.5 x 10(-10)), and rs11203203 near UBASH3A (P(combined) = 1.1 x 10(-8)). We also confirmed that 4 gene loci previously established in either CD or RA are associated with the other autoimmune disease at combined P<5 x 10(-8) (SH2B3, 8q24, STAT4, and TRAF1-C5). From the 14 shared gene loci, 7 SNPs showed a genome-wide significant effect on expression of one or more transcripts in the linkage disequilibrium (LD) block around the SNP. These associations implicate antigen presentation and T-cell activation as a shared mechanism of disease pathogenesis and underscore the utility of cross-disease meta-analysis for identification of genetic risk factors with pleiotropic effects between two clinically distinct diseases.

Published
2011

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

Author

Trynka, G, Hunt, K, Bockett, N, Romanos, J, Mistry, V, Szperl, A, Bakker, S, Bardella, M, Bhaw Rosun, L, Castillejo, G, De la Concha, E, De Almeida, R, Dias, K, Van Diemen, C, Dubois, P, Duerr, R, Edkins, S, Franke, L, Fransen, K, Gutierrez, J, Heap, G, Hrdlickova, B, Hunt, S, Izurieta, L, Izzo, V, Joosten, L, Langford, C, Mazzilli, M, Mein, C, 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, S, Rybak, A, Santiago, J, Senapati, S, Sood, A, Szajewska, H, Troncone, R, Varadé, J, Wallace, C, Wolters, V, Zhernakova, A, Spanish Consortium on the Genetics of Coeliac, D, PreventCD Study, G, Wellcome Trust Case Control, C, Thelma, B, Cukrowska, B, Urcelay, E, Bilbao, J, Mearin, M, Barisani, D, Barrett, J, Plagnol, V, Deloukas, P, Wijmenga, C, Van Heel, D, Hunt, KA, Bockett, NA, Bakker, SF, Bardella, MT, De la Concha, EG, De Almeida, RC, Dias, KR, Van Diemen, CC, Dubois, PC, Duerr, RH, Heap, GA, Izurieta, LP, Joosten, LA, Mazzilli, MC, Mein, CA, Rich, SS, Santiago, JL, Wolters, VM, Spanish Consortium on the Genetics of Coeliac Disease, PreventCD Study Group, Wellcome Trust Case Control Consortium, Thelma, BK, Bilbao, JR, Mearin, ML, Barrett, JC, Van Heel,DA, BARISANI, DONATELLA, Trynka, G, Hunt, K, Bockett, N, Romanos, J, Mistry, V, Szperl, A, Bakker, S, Bardella, M, Bhaw Rosun, L, Castillejo, G, De la Concha, E, De Almeida, R, Dias, K, Van Diemen, C, Dubois, P, Duerr, R, Edkins, S, Franke, L, Fransen, K, Gutierrez, J, Heap, G, Hrdlickova, B, Hunt, S, Izurieta, L, Izzo, V, Joosten, L, Langford, C, Mazzilli, M, Mein, C, 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, S, Rybak, A, Santiago, J, Senapati, S, Sood, A, Szajewska, H, Troncone, R, Varadé, J, Wallace, C, Wolters, V, Zhernakova, A, Spanish Consortium on the Genetics of Coeliac, D, PreventCD Study, G, Wellcome Trust Case Control, C, Thelma, B, Cukrowska, B, Urcelay, E, Bilbao, J, Mearin, M, Barisani, D, Barrett, J, Plagnol, V, Deloukas, P, Wijmenga, C, Van Heel, D, Hunt, KA, Bockett, NA, Bakker, SF, Bardella, MT, De la Concha, EG, De Almeida, RC, Dias, KR, Van Diemen, CC, Dubois, PC, Duerr, RH, Heap, GA, Izurieta, LP, Joosten, LA, Mazzilli, MC, Mein, CA, Rich, SS, Santiago, JL, Wolters, VM, Spanish Consortium on the Genetics of Coeliac Disease, PreventCD Study Group, Wellcome Trust Case Control Consortium, Thelma, BK, Bilbao, JR, Mearin, ML, Barrett, JC, Van Heel,DA, and BARISANI, DONATELLA

Abstract

Using variants from the 1000 Genomes Project pilot European CEU dataset and data from additional resequencing studies, we densely genotyped 183 non-HLA risk loci previously associated with immune-mediated diseases in 12,041 individuals with celiac disease (cases) and 12,228 controls. We identified 13 new celiac disease risk loci reaching genome-wide significance, bringing the number of known loci (including the HLA locus) to 40. We found multiple independent association signals at over one-third of these loci, a finding that is attributable to a combination of common, low-frequency and rare genetic variants. Compared to previously available data such as those from HapMap3, our dense genotyping in a large sample collection provided a higher resolution of the pattern of linkage disequilibrium and suggested localization of many signals to finer scale regions. In particular, 29 of the 54 fine-mapped signals seemed to be localized to single genes and, in some instances, to gene regulatory elements. Altogether, we define the complex genetic architecture of the risk regions of and refine the risk signals for celiac disease, providing the next step toward uncovering the causal mechanisms of the disease. © 2011 Nature America, Inc. All rights reserved.

Published
2011

35. Multiple common variants for celiac disease influencing immune gene expression

Author

Dubois, PCA, Trynka, G, Franke, L, Hunt, KA, Romanos, J, Curtotti, A, Zhernakova, A, Heap, GAR, Adany, R, Aromaa, A, Bardella, MT, van den Berg, LH, Bockett, NA, de la Concha, EG, Dema, B, Fehrmann, RSN, Fernandez-Arquero, M, Fiatal, S, Grandone, E, Green, PM, Groen, HJM, Gwilliam, R, Houwen, RHJ, Hunt, SE, Kaukinen, K, Kelleher, D, Korponay-Szabo, I, Kurppa, K, MacMathuna, P, Maki, M, Mazzilli, MC, McCann, OT, Mearin, ML, Mein, CA, Mirza, MM, Mistry, V, Mora, B, Morley, KI, Mulder, CJ, Murray, JA, Nunez, C, Oosterom, E, Ophoff, RA, Polanco, I, Peltonen, L, Platteel, M, Rybak, A, Salomaa, V, Schweizer, JJ, Sperandeo, MP, Tack, GJ, Turner, G, Veldink, JH, Verbeek, WHM, Weersma, RK, Wolters, VM, Urcelay, E, Cukrowska, B, Greco, L, Neuhausen, SL, McManus, R, Barisani, D, Deloukas, P, Barrett, JC, Saavalainen, P, Wijmenga, C, van Heel, DA, Dubois, PCA, Trynka, G, Franke, L, Hunt, KA, Romanos, J, Curtotti, A, Zhernakova, A, Heap, GAR, Adany, R, Aromaa, A, Bardella, MT, van den Berg, LH, Bockett, NA, de la Concha, EG, Dema, B, Fehrmann, RSN, Fernandez-Arquero, M, Fiatal, S, Grandone, E, Green, PM, Groen, HJM, Gwilliam, R, Houwen, RHJ, Hunt, SE, Kaukinen, K, Kelleher, D, Korponay-Szabo, I, Kurppa, K, MacMathuna, P, Maki, M, Mazzilli, MC, McCann, OT, Mearin, ML, Mein, CA, Mirza, MM, Mistry, V, Mora, B, Morley, KI, Mulder, CJ, Murray, JA, Nunez, C, Oosterom, E, Ophoff, RA, Polanco, I, Peltonen, L, Platteel, M, Rybak, A, Salomaa, V, Schweizer, JJ, Sperandeo, MP, Tack, GJ, Turner, G, Veldink, JH, Verbeek, WHM, Weersma, RK, Wolters, VM, Urcelay, E, Cukrowska, B, Greco, L, Neuhausen, SL, McManus, R, Barisani, D, Deloukas, P, Barrett, JC, Saavalainen, P, Wijmenga, C, and van Heel, DA

Abstract

We performed a second-generation genome-wide association study of 4,533 individuals with celiac disease (cases) and 10,750 control subjects. We genotyped 113 selected SNPs with P(GWAS) < 10(-4) and 18 SNPs from 14 known loci in a further 4,918 cases and 5,684 controls. Variants from 13 new regions reached genome-wide significance (P(combined) < 5 x 10(-8)); most contain genes with immune functions (BACH2, CCR4, CD80, CIITA-SOCS1-CLEC16A, ICOSLG and ZMIZ1), with ETS1, RUNX3, THEMIS and TNFRSF14 having key roles in thymic T-cell selection. There was evidence to suggest associations for a further 13 regions. In an expression quantitative trait meta-analysis of 1,469 whole blood samples, 20 of 38 (52.6%) tested loci had celiac risk variants correlated (P < 0.0028, FDR 5%) with cis gene expression.

Published
2010

36. Multiple common variants for celiac disease influencing immune gene expression

Author

Dubois, P, Trynka, G, Franke, L, Hunt, K, Romanos, J, Curtotti, A, Zhernakova, A, Heap, G, Adány, R, Aromaa, A, Bardella, M, van den Berg, L, Bockett, N, de la Concha, E, Dema, B, Fehrmann, R, Fernández Arquero, M, Fiatal, S, Grandone, E, Green, P, Groen, H, Gwilliam, R, Houwen, R, Hunt, S, Kaukinen, K, Kelleher, D, Korponay Szabo, I, Kurppa, K, Macmathuna, P, Mäki, M, Mazzilli, M, Mccann, O, Mearin, M, Mein, C, Mirza, M, Mistry, V, Mora, B, Morley, K, Mulder, C, Murray, J, Núñez, C, Oosterom, E, Ophoff, R, Polanco, I, Peltonen, L, Platteel, M, Rybak, A, Salomaa, V, Schweizer, J, Sperandeo, M, Tack, G, Turner, G, Veldink, J, Verbeek, W, Weersma, R, Wolters, V, Urcelay, E, Cukrowska, B, Greco, L, Neuhausen, S, Mcmanus, R, Barisani, D, Deloukas, P, Barrett, J, Saavalainen, P, Wijmenga, C, van Heel, D, Dubois, PCA, Hunt, KA, Heap, GAR, Bardella, MT, van den Berg, LH, Bockett, NA, de la Concha, EG, Fehrmann, RSN, Green, PM, Groen, HJM, Houwen, RHJ, Hunt, SE, MacMathuna, P, Mazzilli, MC, McCann, OT, Mearin, ML, Mein, CA, Mirza, MM, Morley, KI, Mulder, CJ, Murray, JA, Ophoff, RA, Schweizer, JJ, Sperandeo, MP, Tack, GJ, Veldink, JH, Verbeek, WHM, Weersma, RK, Wolters, VM, Neuhausen, SL, McManus, R, Barrett, JC, van Heel, DA, BARISANI, DONATELLA, Dubois, P, Trynka, G, Franke, L, Hunt, K, Romanos, J, Curtotti, A, Zhernakova, A, Heap, G, Adány, R, Aromaa, A, Bardella, M, van den Berg, L, Bockett, N, de la Concha, E, Dema, B, Fehrmann, R, Fernández Arquero, M, Fiatal, S, Grandone, E, Green, P, Groen, H, Gwilliam, R, Houwen, R, Hunt, S, Kaukinen, K, Kelleher, D, Korponay Szabo, I, Kurppa, K, Macmathuna, P, Mäki, M, Mazzilli, M, Mccann, O, Mearin, M, Mein, C, Mirza, M, Mistry, V, Mora, B, Morley, K, Mulder, C, Murray, J, Núñez, C, Oosterom, E, Ophoff, R, Polanco, I, Peltonen, L, Platteel, M, Rybak, A, Salomaa, V, Schweizer, J, Sperandeo, M, Tack, G, Turner, G, Veldink, J, Verbeek, W, Weersma, R, Wolters, V, Urcelay, E, Cukrowska, B, Greco, L, Neuhausen, S, Mcmanus, R, Barisani, D, Deloukas, P, Barrett, J, Saavalainen, P, Wijmenga, C, van Heel, D, Dubois, PCA, Hunt, KA, Heap, GAR, Bardella, MT, van den Berg, LH, Bockett, NA, de la Concha, EG, Fehrmann, RSN, Green, PM, Groen, HJM, Houwen, RHJ, Hunt, SE, MacMathuna, P, Mazzilli, MC, McCann, OT, Mearin, ML, Mein, CA, Mirza, MM, Morley, KI, Mulder, CJ, Murray, JA, Ophoff, RA, Schweizer, JJ, Sperandeo, MP, Tack, GJ, Veldink, JH, Verbeek, WHM, Weersma, RK, Wolters, VM, Neuhausen, SL, McManus, R, Barrett, JC, van Heel, DA, and BARISANI, DONATELLA

Abstract

We performed a second-generation genome-wide association study of 4,533 individuals with celiac disease (cases) and 10,750 control subjects. We genotyped 113 selected SNPs with P(GWAS) < 10(-4) and 18 SNPs from 14 known loci in a further 4,918 cases and 5,684 controls. Variants from 13 new regions reached genome-wide significance (P(combined) < 5 x 10(-8)); most contain genes with immune functions (BACH2, CCR4, CD80, CIITA-SOCS1-CLEC16A, ICOSLG and ZMIZ1), with ETS1, RUNX3, THEMIS and TNFRSF14 having key roles in thymic T-cell selection. There was evidence to suggest associations for a further 13 regions. In an expression quantitative trait meta-analysis of 1,469 whole blood samples, 20 of 38 (52.6%) tested loci had celiac risk variants correlated (P < 0.0028, FDR 5%) with cis gene expression.

Published
2010

37. Early ontogeny of immune cells and their functions in the fetal pig

Author

Tlaskalova, B., Cukrowska, B., Splichal, I., Sinkora, J., Rehakova, Z., Sinkora, M., Pospisil, R., Kovaru, F., Charley, Bernard, Binns, R., Whyte, A., ProdInra, Migration, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), and Station de virologie et d'immunologie

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
1995

38. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci

Author

Zhernakova, A., primary, Stahl, E. A., additional, Trynka, G., additional, Raychaudhuri, S., additional, Festen, E., additional, Franke, L., additional, Fehrmann, R. S. N., additional, Kurreeman, F. A. S., additional, Thomson, B., additional, Gupta, N., additional, Romanos, J., additional, McManus, R., additional, Ryan, A. W., additional, Turner, G., additional, Remmers, E. F., additional, Greco, L., additional, Toes, R., additional, Grandone, E., additional, Mazzilli, M. C., additional, Rybak, A., additional, Cukrowska, B., additional, Li, Y., additional, de Bakker, P. I. W., additional, Gregersen, P. K., additional, Worthington, J., additional, Siminovitch, K. A., additional, Klareskog, L., additional, Huizinga, T. W. J., additional, Wijmenga, C., additional, and Plenge, R. M., additional

Published
2011
Full Text
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50. Autoimmune Reactions Induced by Gliadin Feeding in Germ-free AVN Rats and Athymic Nude Mice Animal Models for Celiac Disease

Author

TLASKALOVÁ-HOGENOVÁ, H., primary, ŠTĚPÁNKOVÁ, R., additional, FARRÉ, M., additional, FUNDA, D. P., additional, ŘEHÁKOVÁ, Z., additional, ŠINKORA, J., additional, TUČKOVÁ, L., additional, HORAK, I., additional, HORÁKOVÁ, D., additional, CUKROWSKA, B., additional, KOZÁKOVÁ, H., additional, and KOLÍNSKÁ, J., additional

Published
1997
Full Text
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