[PDF] Top 20 Powerful association test combining rare variant and gene expression using family data from Genetic Analysis Workshop 19
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Powerful association test combining rare variant and gene expression using family data from Genetic Analysis Workshop 19
... The rare variants here are defined as genetic variants with a minor allele frequency of less than 1 ...one variant at a time is oftentimes underpowered for rare variant detection unless ... See full document
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Exploration and comparison of methods for combining population and family based genetic association using the Genetic Analysis Workshop 17 mini exome
... a rare disease and the absence of population ...the rare disease assumption and adjusting for population ...estimated from the data and incorporated into the variance of the test ... See full document
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Application of noncollapsing methods to the gene based association test: a comparison study using Genetic Analysis Workshop 18 data
... A family-wise error rate (FWER) proce- dure was used to adjust for multiple hypothesis ...standard rare variants analysis meth- ods: SKAT [12] and famSKAT [13] in our ...analyze rare ... See full document
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Evaluation of association tests for rare variants using simulated data sets in the Genetic Analysis Workshop 17 data
... four association tests for rare variants — the combined multivariate and collapsing (CMC) method, two weighted-sum methods, and a variable threshold method — by applying them to the simulated data ... See full document
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Evaluation of pooled association tests for rare variant identification
... Genome-wide association studies have successfully identified many common variants associated with complex human ...Exploring rare variants associated with diseases is now catching more ...in ... See full document
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A combined association test for rare variants using family and case control data
... [1]. Rare variant association tests can be clas- sified as the burden test [2] and the sequence kernel association test (SKAT) ...burden test, assuming variants have the ... See full document
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Evaluation of gene based association tests for analyzing rare variants using Genetic Analysis Workshop 18 data
... rich data for the analysis of the role of rare variants in complex human diseases and ...single rare variant, many pooled association tests have been proposed for joint ... See full document
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Evaluating methods for combining rare variant data in pathway based tests of genetic association
... pathway analysis using two opposing ...by combining all SNPs within genes in a set or pathway of interest, and then we apply recently proposed rare variant methods to these ...use ... See full document
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A general method for combining different family based rare variant tests of association to improve power and robustness of a wide range of genetic architectures
... Current rare-variant, gene-based tests of association often suffer from a lack of statistical power to detect genotype – phenotype associations as a result of a lack of prior knowledge ... See full document
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Joint analysis of multiple blood pressure phenotypes in GAW19 data by using a multivariate rare variant association test
... more powerful, especially when there exist pleiotropic effects or highly correlated traits, but it is also subject to possible power loss when many neutral variants exist, or when variants are only asso- ciated ... See full document
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Comparison of multiple single nucleotide variant association tests in a meta analysis of Genetic Analysis Workshop 19 family and unrelated data
... estimated from genotypes using an expectation–maximization algorithm (R Package ...we test the global null hypothesis that all haplotype effects are equal (ie, H 0 : β 1 = ⋯ = β K ' ... See full document
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Rare variant analysis of blood pressure phenotypes in the Genetic Analysis Workshop 18 whole genome sequencing data using sequence kernel association test
... analyzing rare variants because it is fast and because nonburden tests are shown to be more powerful when most variants are noncausal or the effects of causal variants are in different ...directions. ... See full document
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Rare variant collapsing in conjunction with mean log p value and gradient boosting approaches applied to Genetic Analysis Workshop 17 data
... the data, and failure of replication is ...information from rare variants into the analysis by aggregating across SNPs that are in close proximity to each ...information from SNPs that ... See full document
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Detecting rare functional variants using a wavelet based test on quantitative and qualitative traits
... genome-wide association study on the Genetic Analysis Workshop 17 simulated unrelated individuals data using a multilocus score test based on wavelet transformation that ... See full document
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A LASSO penalized regression approach for genome wide association analyses using related individuals: application to the Genetic Analysis Workshop 19 simulated data
... new association method that combines LMM and LASSO to capitalize on the bene- fits of both ...common genetic back- ground among individuals through the use of a random polygenic ...simulated family ... See full document
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Challenges and directions: an analysis of Genetic Analysis Workshop 17 data by collapsing rare variants within family data
... all rare variants than when collapsing only nonsynonymous ...simulation data were chosen based on PolyPhen and SIFT predic- tions of the likelihood that the variant would be deleter- ... See full document
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Rare variant density across the genome and across populations
... the rare variant load for the Luhya population compared to the rest of the populations for these RGPD4 and RANBP2 ...the gene remains unchanged from population to ... See full document
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Analysis of Genetic Analysis Workshop 18 data with gene based penalized regression
... this data set, suggesting that most of our top findings were most likely false ...corrected using genomic control), sug- gesting that either (a) family structure needs to be taken into account, (b) ... See full document
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A Powerful and Adaptive Association Test for Rare Variants
... adaptive test, called KBAC, was proposed by Liu and Leal ...KBAC test is to detect not only the main effects of, but also possible interactions among, ...its test statistic is a weighted sum of the ... See full document
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Case control association testing by graphical modeling for the Genetic Analysis Workshop 17 mini exome sequence data
... The final estimated graphical model for the first repli- cate is shown in Figure 2. For this data set, our method detected five causal variants on four genes. Our model found three variants associated with disease ... See full document
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