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Epistasis within the MHC contributes to the genetic architecture of celiac disease

https://doi.org/10.1101/002485
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1 of the 70 references listed on this page is in the Retraction Watch database as retracted (export 2026-11-04): 10.1038/nature13005 (notice 2021-08-11).

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/eji.201141811openalex-snapshot
Epistasis: The key to understanding immunological disease?
inferredcites →https://doi.org/10.1002/gepi.1370090506openalex-snapshot
Two‐Locus models of disease
inferredcites →https://doi.org/10.1002/gepi.20473openalex-snapshot
Machine learning in genome‐wide association studies
inferredcites →https://doi.org/10.1002/gepi.20541openalex-snapshot
A simple and fast two‐locus quality control test to detect false positives due to batch effects in genome‐wide association studies
inferredcites →https://doi.org/10.1002/gepi.21698openalex-snapshot
Performance and Robustness of Penalized and Unpenalized Methods for Genetic Prediction of Complex Human Disease
inferredcites →https://doi.org/10.1007/978-0-387-98141-3openalex-snapshot
ggplot2: Elegant Graphics for Data Analysis
inferredcites →https://doi.org/10.1016/0040-5809(75)90028-3openalex-snapshot
Linkage disequilibrium among multiple neutral alleles produced by mutation in finite population
inferredcites →https://doi.org/10.1016/j.ajhg.2009.08.006openalex-snapshot
Epistasis and Its Implications for Personal Genetics
inferredcites →https://doi.org/10.1016/j.ajhg.2010.07.021openalex-snapshot
BOOST: A Fast Approach to Detecting Gene-Gene Interactions in Genome-wide Case-Control Studies
inferredcites →https://doi.org/10.1016/j.bpg.2005.01.001openalex-snapshot
Genetics in coeliac disease
inferredcites →https://doi.org/10.1016/j.jtbi.2005.11.036openalex-snapshot
A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility
inferredcites →https://doi.org/10.1038/cr.2010.68openalex-snapshot
SHEsisEpi, a GPU-enhanced genome-wide SNP-SNP interaction scanning algorithm, efficiently reveals the risk genetic epistasis in bipolar disorder
inferredcites →https://doi.org/10.1038/nature07331openalex-snapshot
Genes mirror geography within Europe
inferredcites →https://doi.org/10.1038/nature08494openalex-snapshot
Finding the missing heritability of complex diseases
inferredcites →https://doi.org/10.1038/nature11283openalex-snapshot
A mutation in APP protects against Alzheimer’s disease and age-related cognitive decline
inferredcites →https://doi.org/10.1038/nature11510openalex-snapshot
Epistasis as the primary factor in molecular evolution
inferredcites →https://doi.org/10.1038/nature12124openalex-snapshot
Nonsense mutation in the LGR4 gene is associated with several human diseases and other traits
inferredcites →https://doi.org/10.1038/nature12170openalex-snapshot
Negligible impact of rare autoimmune-locus coding-region variants on missing heritability
inferredcites →https://doi.org/10.1038/nature12678openalex-snapshot
Genetic incompatibilities are widespread within species
inferredcites →https://doi.org/10.1038/nature13005openalex-snapshot
RETRACTED ARTICLE: Detection and replication of epistasis influencing transcription in humans
inferredcites →https://doi.org/10.1038/nature13691openalex-snapshot
Another explanation for apparent epistasis
inferredcites →https://doi.org/10.1038/ng.102openalex-snapshot
Newly identified genetic risk variants for celiac disease related to the immune response
inferredcites →https://doi.org/10.1038/ng.1051openalex-snapshot
Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways
inferredcites →https://doi.org/10.1038/ng.2507openalex-snapshot
Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion
inferredcites →https://doi.org/10.1038/ng.2520openalex-snapshot
Genome-wide association analysis identifies new susceptibility loci for Behçet's disease and epistasis between HLA-B*51 and ERAP1
inferredcites →https://doi.org/10.1038/ng.381openalex-snapshot
Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
inferredcites →https://doi.org/10.1038/ng.543openalex-snapshot
Multiple common variants for celiac disease influencing immune gene expression
inferredcites →https://doi.org/10.1038/ng.694openalex-snapshot
A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1
inferredcites →https://doi.org/10.1038/ng.873openalex-snapshot
Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility
inferredcites →https://doi.org/10.1038/ng.998openalex-snapshot
Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease
inferredcites →https://doi.org/10.1038/ng1537openalex-snapshot
Genome-wide strategies for detecting multiple loci that influence complex diseases
inferredcites →https://doi.org/10.1038/ng1885openalex-snapshot
A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC
inferredcites →https://doi.org/10.1038/ng2058openalex-snapshot
A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21
inferredcites →https://doi.org/10.1038/ng2110openalex-snapshot
Bayesian inference of epistatic interactions in case-control studies
inferredcites →https://doi.org/10.1038/nmeth.1785openalex-snapshot
A linear complexity phasing method for thousands of genomes
inferredcites →https://doi.org/10.1038/nrd4051openalex-snapshot
Validating therapeutic targets through human genetics
inferredcites →https://doi.org/10.1038/nrg1407openalex-snapshot
Epistasis: too often neglected in complex trait studies?
inferredcites →https://doi.org/10.1038/nrg2452openalex-snapshot
Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems
inferredcites →https://doi.org/10.1038/nrg2579openalex-snapshot
Detecting gene–gene interactions that underlie human diseases
inferredcites →https://doi.org/10.1038/nrg2809openalex-snapshot
Missing heritability and strategies for finding the underlying causes of complex disease
inferredcites →https://doi.org/10.1038/nrg3627openalex-snapshot
Epistasis and quantitative traits: using model organisms to study gene–gene interactions
inferredcites →https://doi.org/10.1038/tpj.2013.18openalex-snapshot
HIBAG—HLA genotype imputation with attribute bagging
inferredcites →https://doi.org/10.1056/nejmoa0807917openalex-snapshot
Shared and Distinct Genetic Variants in Type 1 Diabetes and Celiac Disease
inferredcites →https://doi.org/10.1073/pnas.0812664106openalex-snapshot
Epistasis among HLA-DRB1, HLA-DQA1, and HLA-DQB1 loci determines multiple sclerosis susceptibility
inferredcites →https://doi.org/10.1073/pnas.1119675109openalex-snapshot
The mystery of missing heritability: Genetic interactions create phantom heritability
inferredcites →https://doi.org/10.1086/321276openalex-snapshot
Multifactor-Dimensionality Reduction Reveals High-Order Interactions among Estrogen-Metabolism Genes in Sporadic Breast Cancer
inferredcites →https://doi.org/10.1093/bioinformatics/bti623openalex-snapshot
ROCR: visualizing classifier performance in R
inferredcites →https://doi.org/10.1093/bioinformatics/btr172openalex-snapshot
EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards
inferredcites →https://doi.org/10.1093/hmg/11.20.2463openalex-snapshot
Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans
inferredcites →https://doi.org/10.1093/hmg/ddu227openalex-snapshot
Abundant local interactions in the 4p16.1 region suggest functional mechanisms underlying SLC2A9 associations with human serum uric acid
inferredcites →https://doi.org/10.1101/gr.137885.112openalex-snapshot
Ultrafast genome-wide scan for SNP–SNP interactions in common complex disease
inferredcites →https://doi.org/10.1111/j.1651-2227.1996.tb14258.xopenalex-snapshot
Female fertility, obstetric and gynaecological history in coeliac disease: a case control study
inferredcites →https://doi.org/10.1136/gutjnl-2012-304110openalex-snapshot
Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants
inferredcites →https://doi.org/10.1159/000022939openalex-snapshot
A Complete Enumeration and Classification of Two-Locus Disease Models
inferredcites →https://doi.org/10.1159/000201155openalex-snapshot
Female Fertility, Obstetric and Gynaecological History in Coeliac Disease
inferredcites →https://doi.org/10.1182/blood-2012-05-427989openalex-snapshot
PRRC2A and BCL2L11 gene variants influence risk of non-Hodgkin lymphoma: results from the InterLymph consortium
inferredcites →https://doi.org/10.1186/1471-2105-12-77openalex-snapshot
pROC: an open-source package for R and S+ to analyze and compare ROC curves
inferredcites →https://doi.org/10.1186/1471-2105-13-88openalex-snapshot
SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction
inferredcites →https://doi.org/10.1186/1471-2164-14-s3-s10openalex-snapshot
GWIS - model-free, fast and exhaustive search for epistatic interactions in case-control GWAS
inferredcites →https://doi.org/10.1371/journal.pgen.1000008openalex-snapshot
Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits
inferredcites →https://doi.org/10.1371/journal.pgen.1000529openalex-snapshot
A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies
inferredcites →https://doi.org/10.1371/journal.pgen.1000864openalex-snapshot
The Genetic Interpretation of Area under the ROC Curve in Genomic Profiling
inferredcites →https://doi.org/10.1371/journal.pgen.1001338openalex-snapshot
Genome-Wide Interaction-Based Association Analysis Identified Multiple New Susceptibility Loci for Common Diseases
inferredcites →https://doi.org/10.1371/journal.pgen.1002254openalex-snapshot
Pervasive Sharing of Genetic Effects in Autoimmune Disease
inferredcites →https://doi.org/10.1371/journal.pgen.1003295openalex-snapshot
An Evolutionary Perspective on Epistasis and the Missing Heritability
inferredcites →https://doi.org/10.1371/journal.pgen.1004137openalex-snapshot
Accurate and Robust Genomic Prediction of Celiac Disease Using Statistical Learning
inferredcites →https://doi.org/10.1371/journal.pone.0002270openalex-snapshot
Effective Detection of Human Leukocyte Antigen Risk Alleles in Celiac Disease Using Tag Single Nucleotide Polymorphisms
inferredcites →https://doi.org/10.1371/journal.pone.0071203openalex-snapshot
Properties of Local Interactions and Their Potential Value in Complementing Genome-Wide Association Studies
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot
Scikit-learn: Machine Learning in Python

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2217/pme-2016-0015openalex-snapshot
Can we Predict Those at Higher Risk for Migraine?
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