Multiple common variants for celiac disease influencing immune gene expression
By P. Dubois, G. Trynka, Lude Franke, K. Hunt, J. Romanos, Alessandra Curtotti, A. Zhernakova, Graham A. R. Heap, R. Ádány, A. Aromaa and 57 more. Nature Genetics, 2010
1,085 citations recorded by the source corpus.
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 PGWAS < 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 (Pcombined < 5 × 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.
Subfields: Gastroenterology, Immunology, Surgery
View Paper: https://www.semanticscholar.org/paper/3a1311d1bfaee397913dcccd232d462580d0e8d7
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Gastroenterology
In Immunology
In Surgery
Citations in the corpus
- Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease (2011, neutral): “11 120,601,187–120,605,968 (4; 5) Intron 10 of ARHGAP31”
- Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr (2018, methodology): “For detecting long-range LD regions during the computation of PCA, we tested the function snp_autoSVD on both the celiac and POPRES datasets.”
- Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells (2016, background): “We focused on seven autoimmune diseases (celiac disease [CEL] [Dubois et al., 2010], inflammatory bowel disease [IBD] [Liu et al.”
- Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics (2013, neutral): “, [5,8]).”
- Bayesian weighted Mendelian randomization for causal inference based on summary statistics (2018, background): “, 2015) Immune system disorder Celiac disease 15,283 (Dubois et al., 2010) Immune system disorder Eczema 40,835 (Paternoster et al.”
- Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47 (2011, methodology): “We attempted to identify plausible candidate genes by: (i) using a literature-mining tool (GRAIL) to identify non-random, evidence-based links between genes, (ii) searching an existing expression quantitative trait loci (eQTL) databas”
- New IBD genetics: common pathways with other diseases (2011, background): “114 Together with the HLA risk, these loci account for an estimated 40% of the genetic variance in coeliac disease risk.(113) Of the confirmed coeliac disease genes, PTPN2, ICOSLG, REL and KIF21B are associated with IBD,(28) 32 35 70 BACH2, TAGAP, IL18RAP, ZMIZ1, and ZFP36L1 with Crohn’s disease,(32”
- Global Testing and Large-Scale Multiple Testing for High-Dimensional Covariance Structures (2017, methodology): “…analysis (Shedden and Taylor (2005); de la Fuente (2010); Ideker and Krogan (2012); Fukushima (2013)), and correlation analysis of factors that interact to shape children’s language development and reading ability (Dubois et al. 2010; Hirai et al. 2007; Raizada et al. 2008; Zhu et al. 2005).”