Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease.

PubWeight™: 1.21‹?› | Rank: Top 10%

🔗 View Article (PMC 2850616)

Published in Hum Mol Genet on January 27, 2010

Authors

Natalie J Prescott1, Katherine M Dominy, Michiaki Kubo, Cathryn M Lewis, Sheila A Fisher, Richard Redon, Ni Huang, Barbara E Stranger, Katarzyna Blaszczyk, Barry Hudspith, Gareth Parkes, Naoya Hosono, Keiko Yamazaki, Clive M Onnie, Alastair Forbes, Emmanouil T Dermitzakis, Yusuke Nakamura, John C Mansfield, Jeremy Sanderson, Matthew E Hurles, Roland G Roberts, Christopher G Mathew

Author Affiliations

1: Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK. natalie.prescott@genetics.kcl.ac.uk

Articles citing this

A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease. Nat Genet (2011) 3.59

Autophagy in immunity: implications in etiology of autoimmune/autoinflammatory diseases. Autophagy (2012) 1.16

Host genetic susceptibility, dysbiosis, and viral triggers in inflammatory bowel disease. Curr Opin Gastroenterol (2011) 1.12

Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis. BMC Bioinformatics (2012) 1.04

IRGM variants and susceptibility to inflammatory bowel disease in the German population. PLoS One (2013) 0.98

Genetic studies of Crohn's disease: past, present and future. Best Pract Res Clin Gastroenterol (2014) 0.94

Functional anatomy of distant-acting mammalian enhancers. Philos Trans R Soc Lond B Biol Sci (2013) 0.91

The JAK2 variant rs10758669 in Crohn's disease: altering the intestinal barrier as one mechanism of action. Int J Colorectal Dis (2011) 0.90

Transcriptional control of the human glucocorticoid receptor: identification and analysis of alternative promoter regions. Hum Genet (2011) 0.89

Contribution of higher risk genes and European admixture to Crohn's disease in African Americans. Inflamm Bowel Dis (2012) 0.88

Human IRGM gene "to be or not to be". Semin Immunopathol (2010) 0.88

Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance. BMC Genomics (2014) 0.88

Biomarkers of inflammatory bowel disease. Dis Markers (2014) 0.86

Viruses, autophagy genes, and Crohn's disease. Viruses (2011) 0.86

Copy number variation prevalence in known asthma genes and their impact on asthma susceptibility. Clin Exp Allergy (2013) 0.84

Autophagy-related IRGM polymorphism is associated with mortality of patients with severe sepsis. PLoS One (2014) 0.83

Association between variants of the autophagy related gene--IRGM and susceptibility to Crohn's disease and ulcerative colitis: a meta-analysis. PLoS One (2013) 0.83

Genetic variants associated with Crohn's disease. Appl Clin Genet (2013) 0.81

Characteristics of Japanese inflammatory bowel disease susceptibility loci. J Gastroenterol (2013) 0.81

Comparative genomic analysis of eutherian interferon-γ-inducible GTPases. Funct Integr Genomics (2012) 0.81

Coordinating GWAS results with gene expression in a systems immunologic paradigm in autoimmunity. Curr Opin Immunol (2012) 0.80

Human complex trait genetics: lifting the lid of the genomics toolbox - from pathways to prediction. Curr Genomics (2012) 0.78

IRGM rs13361189 polymorphism may contribute to susceptibility to Crohn's disease: A meta-analysis. Exp Ther Med (2014) 0.78

Combining genetic mapping with genome-wide expression in experimental autoimmune encephalomyelitis highlights a gene network enriched for T cell functions and candidate genes regulating autoimmunity. Hum Mol Genet (2013) 0.77

Inflammatory bowel disease in pediatric and adolescent patients: a biomolecular and histopathological review. World J Gastroenterol (2014) 0.77

Association of IRGM gene mutations with inflammatory bowel disease in the Indian population. PLoS One (2014) 0.77

Genome-wide copy number variation association analyses for age at menarche. J Clin Endocrinol Metab (2012) 0.77

Is Whole Exome Sequencing Clinically Practical in the Management of Pediatric Crohn's Disease? Gut Liver (2015) 0.76

Genetic variation in IBD: progress, clues to pathogenesis and possible clinical utility. Expert Rev Clin Immunol (2016) 0.76

Clinical implications of copy number variations in autoimmune disorders. Korean J Intern Med (2015) 0.75

Efficient Software for Multi-marker, Region-Based Analysis of GWAS Data. G3 (Bethesda) (2016) 0.75

Evidence of expression variation and allelic imbalance in Crohn's disease susceptibility genes NOD2 and ATG16L1 in human dendritic cells. Gene (2013) 0.75

Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice. Am J Hum Genet (2017) 0.75

Articles cited by this

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature (2007) 144.95

Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics (2004) 125.23

Global variation in copy number in the human genome. Nature (2006) 57.50

Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet (2008) 30.94

Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet (2008) 30.20

Population genomics of human gene expression. Nat Genet (2007) 24.49

Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet (2007) 19.08

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet (2006) 15.14

Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat Genet (2007) 13.74

Cohort profile: 1958 British birth cohort (National Child Development Study). Int J Epidemiol (2005) 10.88

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet (2008) 9.52

Human IRGM induces autophagy to eliminate intracellular mycobacteria. Science (2006) 9.17

Pedigree disequilibrium tests for multilocus haplotypes. Genet Epidemiol (2003) 8.65

Single nucleotide polymorphisms in TNFSF15 confer susceptibility to Crohn's disease. Hum Mol Genet (2005) 5.35

Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility. Nat Genet (2008) 5.05

New links to the pathogenesis of Crohn disease provided by genome-wide association scans. Nat Rev Genet (2008) 4.35

The interferon-inducible p47 (IRG) GTPases in vertebrates: loss of the cell autonomous resistance mechanism in the human lineage. Genome Biol (2005) 4.21

Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases. Hum Mol Genet (2007) 4.07

A nonsynonymous SNP in ATG16L1 predisposes to ileal Crohn's disease and is independent of CARD15 and IBD5. Gastroenterology (2007) 3.37

Survey of allelic expression using EST mining. Genome Res (2005) 2.67

Autophagy gene variant IRGM -261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains. PLoS Pathog (2009) 2.35

Absence of mutation in the NOD2/CARD15 gene among 483 Japanese patients with Crohn's disease. J Hum Genet (2002) 1.88

Death and resurrection of the human IRGM gene. PLoS Genet (2009) 1.72

Haplotype structure and association to Crohn's disease of CARD15 mutations in two ethnically divergent populations. Eur J Hum Genet (2003) 1.60

ABINs: A20 binding inhibitors of NF-kappa B and apoptosis signaling. Biochem Pharmacol (2009) 1.48

Confirmation of association of IRGM and NCF4 with ileal Crohn's disease in a population-based cohort. Genes Immun (2008) 1.43

Confirmation of multiple Crohn's disease susceptibility loci in a large Dutch-Belgian cohort. Am J Gastroenterol (2009) 1.37

Positive association of genetic variants in the upstream region of NKX2-3 with Crohn's disease in Japanese patients. Gut (2008) 1.11

Association of ATG16L1 and IRGM genes polymorphisms with inflammatory bowel disease: a meta-analysis approach. Genes Immun (2009) 1.05

Identification and functional analysis of a novel human KRAB/C2H2 zinc finger gene ZNF300. Biochim Biophys Acta (2004) 0.88

Genotyping of IRGM tetranucleotide promoter oligorepeats by fluorescence resonance energy transfer. Biotechniques (2009) 0.86

Germline variants of IRGM in childhood-onset Crohn's disease. Gut (2009) 0.83

Identification of the DNA binding element of the human ZNF300 protein. Cell Mol Biol Lett (2008) 0.81

Articles by these authors

Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15

Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20

A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

Global variation in copy number in the human genome. Nature (2006) 57.50

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63

Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet (2008) 30.20

Population genomics of human gene expression. Nat Genet (2007) 24.49

Origins and functional impact of copy number variation in the human genome. Nature (2009) 23.63

Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science (2007) 23.38

International network of cancer genome projects. Nature (2010) 20.35

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet (2010) 17.38

Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27

Genome-wide associations of gene expression variation in humans. PLoS Genet (2005) 17.27

A high-resolution survey of deletion polymorphism in the human genome. Nat Genet (2005) 16.99

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature (2012) 16.13

Common variants near MC4R are associated with fat mass, weight and risk of obesity. Nat Genet (2008) 15.94

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet (2006) 15.14

Transcriptome genetics using second generation sequencing in a Caucasian population. Nature (2010) 14.85

Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat Genet (2007) 13.74

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature (2011) 13.23

Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. Nat Genet (2007) 12.62

Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature (2010) 12.27

A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25

Common regulatory variation impacts gene expression in a cell type-dependent manner. Science (2009) 11.28

High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet (2008) 9.68

Variants in KCNQ1 are associated with susceptibility to type 2 diabetes mellitus. Nat Genet (2008) 9.39

Cerebral organoids model human brain development and microcephaly. Nature (2013) 9.07

Transcriptome and genome sequencing uncovers functional variation in humans. Nature (2013) 8.89

Variation in genome-wide mutation rates within and between human families. Nat Genet (2011) 8.84

Copy number variation: new insights in genome diversity. Genome Res (2006) 8.66

Diet and the evolution of human amylase gene copy number variation. Nat Genet (2007) 8.64

SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. Nat Genet (2008) 8.63

Meta-analysis and imputation refines the association of 15q25 with smoking quantity. Nat Genet (2010) 8.55

A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat Genet (2010) 8.48

Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME. Bioinformatics (2011) 8.23

Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease. Nat Genet (2009) 8.11

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nat Genet (2013) 8.02

Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet (2003) 7.98

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet (2011) 7.98

Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet (2009) 7.64

Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat Genet (2013) 7.44

Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. Nat Genet (2003) 7.04

The DNA sequence of the human X chromosome. Nature (2005) 6.97

Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet (2012) 6.97

Genome assembly comparison identifies structural variants in the human genome. Nat Genet (2006) 6.93

Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nat Genet (2008) 6.75

Functional SNPs in the lymphotoxin-alpha gene that are associated with susceptibility to myocardial infarction. Nat Genet (2002) 6.46

Hypothetical LOC387715 is a second major susceptibility gene for age-related macular degeneration, contributing independently of complement factor H to disease risk. Hum Mol Genet (2005) 6.36

A mega-analysis of genome-wide association studies for major depressive disorder. Mol Psychiatry (2012) 6.34

Heterozygous TGFBR2 mutations in Marfan syndrome. Nat Genet (2004) 6.15

Challenges and standards in integrating surveys of structural variation. Nat Genet (2007) 6.05

Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res (2006) 5.97

The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet (2011) 5.95

Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility. Nat Genet (2011) 5.56

Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res (2006) 5.50

Germline mutations in breast and ovarian cancer pedigrees establish RAD51C as a human cancer susceptibility gene. Nat Genet (2010) 5.48

Single nucleotide polymorphisms in TNFSF15 confer susceptibility to Crohn's disease. Hum Mol Genet (2005) 5.35

A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians. Nat Genet (2009) 5.29