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BRASS: permutation methods for binary traits in genetic association studies with structured samples

https://doi.org/10.1101/451377
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What this work says

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

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Association of a NovelACTA1Mutation With a Dominant Progressive Scapuloperoneal Myopathy in an Extended Family
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Statistical Methods for Genome‐Wide and Sequencing Association Studies of Complex Traits in Related Samples
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Estimation of significance thresholds for genomewide association scans
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Permutation Testing in the Presence of Polygenic Variation
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Robust Inference of Population Structure for Ancestry Prediction and Correction of Stratification in the Presence of Relatedness
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Beyond the traditional simulation design for evaluating type 1 error control: From the “theoretical” null to “empirical” null
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A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity
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Rare-Variant Association Analysis: Study Designs and Statistical Tests
inferredcites →https://doi.org/10.1016/j.ajhg.2015.11.022openalex-snapshot
Model-free Estimation of Recent Genetic Relatedness
inferredcites →https://doi.org/10.1016/j.ajhg.2015.12.012openalex-snapshot
Retrospective Binary-Trait Association Test Elucidates Genetic Architecture of Crohn Disease
inferredcites →https://doi.org/10.1016/j.ajhg.2016.02.012openalex-snapshot
Control for Population Structure and Relatedness for Binary Traits in Genetic Association Studies via Logistic Mixed Models
inferredcites →https://doi.org/10.1038/ejhg.2012.173openalex-snapshot
Novel mutations in the sarcomeric protein myopalladin in patients with dilated cardiomyopathy
inferredcites →https://doi.org/10.1038/ncomms10460openalex-snapshot
Complex disease and phenotype mapping in the domestic dog
inferredcites →https://doi.org/10.1038/ng.2310openalex-snapshot
Genome-wide efficient mixed-model analysis for association studies
inferredcites →https://doi.org/10.1038/ng.2876openalex-snapshot
Advantages and pitfalls in the application of mixed-model association methods
inferredcites →https://doi.org/10.1038/ng1337openalex-snapshot
The effects of human population structure on large genetic association studies
inferredcites →https://doi.org/10.1038/ng1847openalex-snapshot
Principal components analysis corrects for stratification in genome-wide association studies
inferredcites →https://doi.org/10.1038/nmeth.2037openalex-snapshot
Improved linear mixed models for genome-wide association studies
inferredcites →https://doi.org/10.1038/s41588-020-00766-yopenalex-snapshot
Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power
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Genomic analyses implicate noncoding de novo variants in congenital heart disease
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Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments
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Gene–gene interaction detection with deep learning
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A Numerical Study of PQL Estimation Biases in Generalized Linear Mixed Models Under Heterogeneity of Random Effects
inferredcites →https://doi.org/10.1080/10618600.2000.10474870openalex-snapshot
Maximum Likelihood for Generalized Linear Models with Nested Random Effects via High-Order, Multivariate Laplace Approximation
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Quantitative-Trait Homozygosity and Association Mapping and Empirical Genomewide Significance in Large, Complex Pedigrees: Fasting Serum-Insulin Level in the Hutterites
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Disrupted in Schizophrenia 1 (DISC1): Association with Schizophrenia, Schizoaffective Disorder, and Bipolar Disorder
inferredcites →https://doi.org/10.1093/bioinformatics/btad139openalex-snapshot
The hidden factor: accounting for covariate effects in power and sample size computation for a binary trait
inferredcites →https://doi.org/10.1093/cvr/cvm015openalex-snapshot
Mutations in the Z-band protein myopalladin gene and idiopathic dilated cardiomyopathy
inferredcites →https://doi.org/10.1093/hmg/ddt043openalex-snapshot
Homozygous and heterozygous disruptions of ANK3: at the crossroads of neurodevelopmental and psychiatric disorders
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Neuronal deficiency ofARV1causes an autosomal recessive epileptic encephalopathy
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Improved Estimation Procedures for Multilevel Models with Binary Response: A Case-Study
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Reliable Estimation of Generalized Linear Mixed Models using Adaptive Quadrature
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Detecting gene-gene interactions using a permutation-based random forest method
inferredcites →https://doi.org/10.1214/09-sts307openalex-snapshot
Population Structure and Cryptic Relatedness in Genetic Association Studies
inferredcites →https://doi.org/10.1371/journal.pgen.1003475openalex-snapshot
Genome-Wide Analysis in German Shepherd Dogs Reveals Association of a Locus on CFA 27 with Atopic Dermatitis
inferredcites →https://doi.org/10.1371/journal.pgen.1003646openalex-snapshot
Genome-Wide Association Mapping in Dogs Enables Identification of the Homeobox Gene, NKX2-8, as a Genetic Component of Neural Tube Defects in Humans
inferredcites →https://doi.org/10.1371/journal.pgen.1006029openalex-snapshot
Genome-Wide Analysis Identifies Germ-Line Risk Factors Associated with Canine Mammary Tumours
inferredcites →https://doi.org/10.1371/journal.pgen.1006329openalex-snapshot
CERAMIC: Case-Control Association Testing in Samples with Related Individuals, Based on Retrospective Mixed Model Analysis with Adjustment for Covariates
inferredcites →https://doi.org/10.1371/journal.pone.0134720openalex-snapshot
A Multi-Breed Genome-Wide Association Analysis for Canine Hypothyroidism Identifies a Shared Major Risk Locus on CFA12
inferredcites →https://doi.org/10.1534/genetics.107.074609openalex-snapshot
Naive Application of Permutation Testing Leads to Inflated Type I Error Rates
inferredcites →https://doi.org/10.2307/2669868openalex-snapshot
Quasi-Likelihood and Its Application: A General Approach to Optimal Parameter Estimation
inferredcites →https://doi.org/10.5281/zenodo.16435756openalex-snapshot
A Statistical Method for Evaluating Systematic Relationships

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inferred← citeshttps://doi.org/10.21203/rs.3.rs-873449/v1openalex-snapshot
False discovery rates for genome-wide association tests in biobanks with thousands of phenotypes
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