Dataset Information

Genome wide association scan in psoriasis

ABSTRACT: To identify novel susceptibility loci for psoriasis, we undertook a genome-wide association scan of of 594,224 SNPs in 2,622 individuals with psoriasis and 5,667 controls.

PROVIDER: EGAS00000000108 | EGA |

REPOSITORIES: EGA

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Publications

A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1.

Strange Amy A Capon Francesca F Spencer Chris C A CC Knight Jo J Weale Michael E ME Allen Michael H MH Barton Anne A Band Gavin G Bellenguez Céline C Bergboer Judith G M JG Blackwell Jenefer M JM Bramon Elvira E Bumpstead Suzannah J SJ Casas Juan P JP Cork Michael J MJ Corvin Aiden A Deloukas Panos P Dilthey Alexander A Duncanson Audrey A Edkins Sarah S Estivill Xavier X Fitzgerald Oliver O Freeman Colin C Giardina Emiliano E Gray Emma E Hofer Angelika A Hüffmeier Ulrike U Hunt Sarah E SE Irvine Alan D AD Jankowski Janusz J Kirby Brian B Langford Cordelia C Lascorz Jesús J Leman Joyce J Leslie Stephen S Mallbris Lotus L Markus Hugh S HS Mathew Christopher G CG McLean W H Irwin WH McManus Ross R Mössner Rotraut R Moutsianas Loukas L Naluai Asa T AT Nestle Frank O FO Novelli Giuseppe G Onoufriadis Alexandros A Palmer Colin N A CN Perricone Carlo C Pirinen Matti M Plomin Robert R Potter Simon C SC Pujol Ramon M RM Rautanen Anna A Riveira-Munoz Eva E Ryan Anthony W AW Salmhofer Wolfgang W Samuelsson Lena L Sawcer Stephen J SJ Schalkwijk Joost J Smith Catherine H CH Ståhle Mona M Su Zhan Z Tazi-Ahnini Rachid R Traupe Heiko H Viswanathan Ananth C AC Warren Richard B RB Weger Wolfgang W Wolk Katarina K Wood Nicholas N Worthington Jane J Young Helen S HS Zeeuwen Patrick L J M PL Hayday Adrian A Burden A David AD Griffiths Christopher E M CE Kere Juha J Reis André A McVean Gilean G Evans David M DM Brown Matthew A MA Barker Jonathan N JN Peltonen Leena L Donnelly Peter P Trembath Richard C RC

Nature genetics 20101017 11

To identify new susceptibility loci for psoriasis, we undertook a genome-wide association study of 594,224 SNPs in 2,622 individuals with psoriasis and 5,667 controls. We identified associations at eight previously unreported genomic loci. Seven loci harbored genes with recognized immune functions (IL28RA, REL, IFIH1, ERAP1, TRAF3IP2, NFKBIA and TYK2). These associations were replicated in 9,079 European samples (six loci with a combined P < 5 × 10⁻⁸ and two loci with a combined P < 5 × 10⁻⁷). W ...[more]

PMID: 20953190

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Project description:Sole ulcers (SU) and white line disease (WLD) are noninfectious claw lesions that arise due to compromised horn production and are common causes of lameness in dairy cattle, imposing welfare and profitability concerns. The low to moderate heritability estimates of SU and WLD susceptibility indicate that genetic selection could reduce their prevalence. To identify loci associated with SU and WLD susceptibility, generalized linear mixed model (GLMM) regression and random forest (RF) genome-wide association studies (GWAS) were performed. Cows from five commercial dairies in California were classified as sound controls having no instances of lameness and above six years of age (n = 102) or cases having SU (n = 152), WLD (n = 117), SU and/or WLD (SU+WLD, n = 198), or any type of noninfectious claw lesion (n = 217). Top SNPs were defined as those passing Bonferroni-corrected suggestive and significance thresholds in the GLMM analysis or those that a validated RF model considered important. Effects of top SNPs were quantified using Bayesian estimation. Linkage disequilibrium (LD) blocks defined by top SNPs were explored for candidate genes and previously identified, functionally relevant quantitative trait loci. The GLMM GWAS revealed regions of association on BTA8 for SU and BTA13 common to WLD, SU+WLD, and noninfectious claw lesions. Bayesian estimation of effect sizes indicated that these SNPs had effects significantly different from zero, indicating their small but notable contribution to susceptibility. Promising candidate genes identified in these regions were involved in wound healing, skin lesions, bone growth and mineralization, adipose tissue, and keratinization. The LD block defined by the most significant SNP on BTA8 for SU included a SNP previously reported to be associated with SU. The RF models were overfitted, indicating that SNP effects were very small and thereby preventing meaningful interpretation of SNPs with the highest importance values and downstream analyses. These findings suggested that variants associated with a variety of physiological systems may contribute to susceptibility for noninfectious claw lesions, demonstrating the complexity of genetic predisposition.

Dataset Information

Genome wide association scan in psoriasis

Publications

A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1.

Similar Datasets

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