Detection boundary and higher criticism approach for rare and weak genetic effects
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Publication:400613
DOI10.1214/14-AOAS724zbMATH Open1454.62420arXiv1407.8382OpenAlexW1994005523MaRDI QIDQ400613FDOQ400613
Jiashun Jin, Zheyang Wu, Hongyu Zhao, Yiming Sun, Judy H. Cho, Shiquan He
Publication date: 22 August 2014
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
Abstract: Genome-wide association studies (GWAS) have identified many genetic factors underlying complex human traits. However, these factors have explained only a small fraction of these traits' genetic heritability. It is argued that many more genetic factors remain undiscovered. These genetic factors likely are weakly associated at the population level and sparsely distributed across the genome. In this paper, we adapt the recent innovations on Tukey's Higher Criticism (Tukey [The Higher Criticism (1976) Princeton Univ.]; Donoho and Jin [Ann. Statist. 32 (2004) 962-994]) to SNP-set analysis of GWAS, and develop a new theoretical framework in large-scale inference to assess the joint significance of such rare and weak effects for a quantitative trait. In the core of our theory is the so-called detection boundary, a curve in the two-dimensional phase space that quantifies the rarity and strength of genetic effects. Above the detection boundary, the overall effects of genetic factors are strong enough for reliable detection. Below the detection boundary, the genetic factors are simply too rare and too weak for reliable detection. We show that the HC-type methods are optimal in that they reliably yield detection once the parameters of the genetic effects fall above the detection boundary and that many commonly used SNP-set methods are suboptimal. The superior performance of the HC-type approach is demonstrated through simulations and the analysis of a GWAS data set of Crohn's disease.
Full work available at URL: https://arxiv.org/abs/1407.8382
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statistical powergenome-wide association studieshigher criticismlarge-scale inferencerare and weak effectsdetection boundarymultiple hypotheses testingSNP-set methods
Nonparametric hypothesis testing (62G10) Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10)
Cites Work
- Bayesian variable selection regression for genome-wide association studies and other large-scale problems
- Detection boundary in sparse regression
- Title not available (Why is that?)
- Global testing under sparse alternatives: ANOVA, multiple comparisons and the higher criticism
- Higher criticism for detecting sparse heterogeneous mixtures.
- Properties of higher criticism under strong dependence
- Higher criticism thresholding: Optimal feature selection when useful features are rare and weak
- Correlation and Large-Scale Simultaneous Significance Testing
- Innovated higher criticism for detecting sparse signals in correlated noise
- Large-Scale Simultaneous Hypothesis Testing
- Empirical Bayes Analysis of a Microarray Experiment
- Size, power and false discovery rates
- Sample size and power analysis for sparse signal recovery in genome-wide association studies
- Detection boundary and higher criticism approach for rare and weak genetic effects
- Hypothesis testing in semiparametric additive mixed models
- Limit theorems for the ratio of the empirical distribution function to the true distribution function
- Adaptive detection of a signal of growing dimension. II
- On model selection strategies to identify genes underlying binary traits using genome-wide association data
- Feature selection when there are many influential features
- Semiparametric Regression of Multidimensional Genetic Pathway Data: Least‐Squares Kernel Machines and Linear Mixed Models
Cited In (11)
- Detection boundary and higher criticism approach for rare and weak genetic effects
- An adaptive decorrelation procedure for signal detection
- Group feature screening via the F statistic
- Anomaly Detection for a Large Number of Streams: A Permutation-Based Higher Criticism Approach
- Powerful test based on conditional effects for genome-wide screening
- Signal-noise ratio of genetic associations and statistical power of SNP-set tests
- Omnibus testing approach for gene-based gene-gene interaction
- Global testing against sparse alternatives under Ising models
- TFisher: a powerful truncation and weighting procedure for combining \(p\)-values
- Higher criticism for large-scale inference, especially for rare and weak effects
- Accurate and Efficient P-value Calculation Via Gaussian Approximation: A Novel Monte-Carlo Method
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