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Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease
TLDR
A meta-analysis of Crohn’s disease and ulcerative colitis genome-wide association scans is undertaken, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. Expand
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci
TLDR
A meta-analysis of six Crohn's disease genome-wide association studies and a series of in silico analyses highlighted particular genes within these loci implicated functionally interesting candidate genes including SMAD3, ERAP2, IL10, IL2RA, TYK2, FUT2, DNMT3A, DENND1B, BACH2 and TAGAP. Expand
Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations
TLDR
The first trans-ancestry association study of IBD is reported, with genome-wide or Immunochip genotype data from an extended cohort of 86,640 European individuals and immunochip data from 9,846 individuals of East Asian, Indian or Iranian descent, implicate 38 loci in IBD risk for the first time. Expand
A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
TLDR
Functional and evolutionary differences between LoF-tolerant and recessive disease genes and a method for using these differences to prioritize candidate genes found in clinical sequencing studies are described. Expand
Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression
TLDR
This work mapped interindividual variation in gene expression as a quantitative trait, defining expression quantitative trait loci (eQTLs) and found trans associations to the major histocompatibility complex are dependent on context, paralleling the expression of class II genes. Expand
Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci
TLDR
The COMorbidities among the five immune diseases were best explained by biological pleiotropy rather than heterogeneity (a subgroup of cases genetically identical to those with another disease, possibly owing to diagnostic misclassification, molecular subtypes or excessive comorbidity), and the strong comor bid between primary sclerosing cholangitis and inflammatory bowel disease is likely the result of a unique disease. Expand
Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease
TLDR
This work identified 25 new susceptibility loci, 3 of which contain integrin genes that encode proteins in pathways that have been identified as important therapeutic targets in inflammatory bowel disease and identified 3 associated variants that are correlated with expression changes in response to immune stimulus at two of these genes. Expand
Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study
TLDR
The largest genotype association study, to date, in widely used clinical subphenotypes of inflammatory bowel disease with the goal of further understanding the biological relations between diseases. Expand
Microindel detection in short-read sequence data
TLDR
This study provides insights into systematic errors in SNV detection that is based on ungapped short sequence read alignments and demonstrates that indel detection works well on short-read data. Expand
High density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis
TLDR
High-density SNP typing of the MHC in >32,000 individuals with IBD implicates multiple HLA alleles, with a primary role for HLA-DRB1*01:03 in both Crohn's disease and ulcerative colitis, suggesting an important role of the adaptive immune response in the colonic environment in the pathogenesis of IBD. Expand
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