A versatile gene-based test for genome-wide association studies.

By Jimmy Zhenli Liu, A. McRae, Dale R. Nyholt, S. Medland, Naomi R. Wray, K. Brown, N. Hayward, G. Montgomery, Peter M. Visscher, Nicholas G. Martin and 1 more. American Journal of Human Genetics, 2010

843 citations recorded by the source corpus.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/9b24feb35b129ca3027de573bbb04095283bda44

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Citations in the corpus

Multivariate Rank-Based Distribution-Free Nonparametric Testing Using Measure Transportation (2019, background): “The independence testing problem has found applications in a wide variety of disciplines such as in statistical genetics [88], marketing and finance [53], survival analysis [95], ecological risk assessment [34], independent component analysis [91], etc.”
GATES: a rapid and powerful gene-based association test using extended Simes procedure. (2011, methodology): “tests, GATES has comparable power but is much faster than the best-SNP test proposed by Liu et al.(16) and can be more powerful than the original Simes test when the SNPs within a gene are in strong LD.”
Genome-partitioning of genetic variation for complex traits using common SNPs (2011, methodology): “We mapped SNPs to 17,787 genes according to positions on the UCSC Genome Browser hg18 assembl”
Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics (2016, methodology): “To compare the gene scores computed by the two methods, we increased the maximum number of Monte Carlo runs for VEGAS to 108, at a high computational cost (about 9 days of runtime).”
MAGMA: Generalized Gene-Set Analysis of GWAS Data (2015, positive): “The CD data set was then analysed using MAGMA and with five commonly used other tools for gene and gene-set analyses, specifically VEGAS [17], PLINK [8], ALIGATOR [9], INRICH [10] and MAGENTA [12].”
Selecting causal genes from genome-wide association studies via functionally-coherent subnetworks (2014, background): “…may in the future be included to augment network-based prioritization methods (for example, by placing prior probability weights on candidate genes 37 ); however, such analyses at large scale will require a (currently unavailable) catalog of annotated effect sizes for markers across all tested…”
Genome-Wide Association Studies in Dogs and Humans Identify ADAMTS20 as a Risk Variant for Cleft Lip and Palate (2015, background): “VEGAS is a versatile gene-based test designed to handle any type of data input as long as a p-value can be generated for each individual marker[51].”
Understanding multicellular function and disease with human tissue-specific networks (2015, positive): “We converted SNP-level association statistics into gene-level statistics 19 for each of three recorded phenotypes – diastolic blood pressure (DBP), systolic blood pressure (SBP) and hypertension (HTN).”