Gene-based Higher Criticism methods for large-scale exonic single-nucleotide polymorphism data

In genome-wide association studies, gene-based methods measure potential joint genetic effects of loci within genes and are promising for detecting causative genetic variations. Following recent theoretical research in statistical multiple-hypothesis testing, we propose to adapt the Higher Criticism procedures to develop novel gene-based methods that use the information of linkage disequilibrium for detecting weak and sparse genetic signals. With the large-scale exonic single-nucleotide polymorphism data from Genetic Analysis Workshop 17, we show that the new Higher-Criticism-type gene-based methods have higher statistical power to detect causative genes than the minimal P-value method, ridge regression, and the prototypes of Higher Criticism do.

• Publication year

  2011

• Venue

  BMC Proceedings

• Publication date

  2011-11-29

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/1753-6561-5-S9-S65PMID 22373436PMCID 3287904
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Statistical analysis of rare sequence variants: an overview of collapsing methods

  2011cited by this paper
• Gene and pathway-based second-wave analysis of genome-wide association studies

  2010cited by this paper
• Comparisons of multi‐marker association methods to detect association between a candidate region and disease

  2010cited by this paper
• Genome-wide gene and pathway analysis

  2010cited by this paper
• ATOM: a powerful gene-based association test by combining optimally weighted markers

  2009cited by this paper
• Association tests using kernel‐based measures of multi‐locus genotype similarity between individuals

  2009cited by this paper
• Innovated Higher Criticism for Detecting Sparse Signals in Correlated Noise

  2009influential reference
• A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic

  2009influential reference
• Considering dependence among genes and markers for false discovery control in eQTL mapping

  2008cited by this paper
• Kernel-Based Association Test

  2008cited by this paper
• A principal components regression approach to multilocus genetic association studies

  2008cited by this paper
• Pathway-based approaches for analysis of genomewide association studies.

  2007cited by this paper
• Two-Stage Designs in Case–Control Association Analysis

  2006cited by this paper
• Higher criticism for detecting sparse heterogeneous mixtures

  2004influential reference
• The future of association studies: gene-based analysis and replication.

  2004cited by this paper
• Trimming, weighting, and grouping SNPs in human case-control association studies.

  2001cited by this paper
• The Higher Criticism

  year unknowncited by this paper
• The Higher Criticism: An Inaugural.

  year unknowncited by this paper

• DNA hypomethylation mediates immune response in pan-cancer

  2023cites this paper
• Signal-noise ratio of genetic associations and statistical power of SNP-set tests

  2023cites this paper
• The general goodness-of-fit tests for correlated data

  2022cites this paper
• Rare and Weak effects in Large-Scale Inference: methods and phase diagrams

  2014cites this paper
• Detecting epistasis in human complex traits

  2014cites this paper
• Higher Criticism for Large-Scale Inference: especially for Rare and Weak effects

  2014cites this paper
• Detection boundary and Higher Criticism approach for rare and weak genetic effects

  2014cites this paper
• OPTIMAL CLASSIFICATION IN SPARSE GAUSSIAN GRAPHIC MODEL

  2012cites this paper
• Effect of linkage disequilibrium on the identification of functional variants

  2011cites this paper