Pooled association tests for rare variants in exon-resequencing studies.

By Alkes L Price, G. Kryukov, P. D. de Bakker, Shaun Purcell, Jeffrey Staples, Lee-Jen Wei, Shamil R. Sunyaev. American Journal of Human Genetics, 2010

651 citations recorded by the source corpus.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/2ac4798550e64fa1291ff9bd3af0ca5e23ba2fdb

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

Citations in the corpus

Rare-variant association analysis: study designs and statistical tests. (2014, background): “The variable threshold (VT) 58 is an adaptive extension that selects optimal frequency thresholds for burden tests of rare variants and estimates p values analytically or by permutation.”
dbNSFP: A Lightweight Database of Human Non-synonymous SNPs and Their Functional Predictions (2011, methodology): “The second is to facilitate the imputation of missing scores that are required in the weighted sum test (e.g., VT test) [Price et al., 2010] for detecting association between phenotypes and groups of rare variants.”
Rare-variant association testing for sequencing data with the sequence kernel association test. (2011, methodology): “Numerous alternative methods are largely variations on these approaches.(16,17,19) A limitation for all these burden tests is that they implicitly assume that all rare variants influence the phenotype in the same direction and with the same magnitude of effect (after incorporating known weights).”
Testing for an Unusual Distribution of Rare Variants (2011, methodology): “Two genes were simulated, and the mean liability value for an individual differed as a function of the number of rare alleles occurring at these genes [14,15].”
Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies. (2012, methodology): “and the p-values can be calculated using the (11).”
Dissecting the genetics of complex traits using summary association statistics (2016, background): “Burden tests may either assume that standardized effect sizes are the same for each rare variant 108 (i.e. per-allele effect sizes are proportional to 1/ 𝑝 F 1 − 𝑝 F , where p i is the allele frequency), or apply weights or thresholds based on allele frequency or functional information 109,110 .”
The Next-Generation Sequencing Revolution and Its Impact on Genomics (2013, neutral): “…2010; Lin and Tang, 2011; Wu et al., 2011; Zhang et al., 2011]), variants with heterogeneous direction of effect (Han and Pan, 2010; Lin and Tang, 2011; Neale et al., 2011; Wu et al., 2011; Zhang et al., 2011), and selection of the ideal frequency cutoff for rare variants (Price et al., 2010a).”
The genetics of Alzheimer disease: back to the future. (2010, background): “, to pool variants within the same coding regions (Price et al., 2010) or to measure general ‘‘mutational load’’ in case versus control subjects (International Schizophrenia Consortium, 2008).”
Optimal tests for rare variant effects in sequencing association studies. (2012, background): “The earliest and most commonly used class of region based rare variant tests are the burden tests, which collapse or summarize the rare variants within region as a single genetic variable which can then be tested for association with any trait of interest [6, 10, 11, 14].”