[PDF] Top 20 Penalized regression based multimarker genotype analysis of Genetic Analysis Workshop 17 data
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Penalized regression based multimarker genotype analysis of Genetic Analysis Workshop 17 data
... of penalized regression methods is that strong sparsity penalties, such as the L1 norm (or LASSO), select only a small subset of a group of highly correlated ...the penalized meth- ods are detecting ... See full document
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Genetic signal maximization using environmental regression
... ics regression method that accounts for a portion of the environmental component using the Genetic Analysis Workshop 17 (GAW17) 1000 Genomes Project simu- lated family data ... See full document
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Pathway based joint effects analysis of rare genetic variants using Genetic Analysis Workshop 17 exon sequence data
... This data- base includes 888 gene sets collected from 186 pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) ...our data set, which left 472 pathways for fol- low-up ...three data- ... 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
... Epstein et al. [6] generalized this work by relaxing the assumptions of HWE, random mating, and the assumed multiplicative mode of inheritance. In addition, they described a formal test for the appropriateness of combin- ... See full document
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Genetic association analysis for common variants in the Genetic Analysis Workshop 18 data: a Dirichlet regression approach
... association analysis is performed using the penalized regression described above for different levels of c (0, ...The analysis is conducted utilizing both the GWAS and the dosage imputed ... See full document
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Pairwise shared genomic segment analysis in high risk pedigrees: application to Genetic Analysis Workshop 17 exome sequencing SNP data
... same genotype data, and because selected replicates in our study were all derived from the same structure, the genotype data were consistent across all 18 ...mean based on the number of ... See full document
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Propensity score analysis in the Genetic Analysis Workshop 17 simulated data set on independent individuals
... approach based on the propensity score, strata can be created to allow for multiple matches and retention of larger sample sizes if perfect matches cannot be found ...logistic regression model predicting ... See full document
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Use of Bayesian networks to dissect the complexity of genetic disease: application to the Genetic Analysis Workshop 17 simulated data
... network analysis. To accomplish this task, we construct simple regression models in which the weighted gene score (described in the previous subsection) and the smoking status are the explanatory ...real ... See full document
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Collapsing based and kernel based single gene analyses applied to Genetic Analysis Workshop 17 mini exome data
... Table 2 lists the top 10 genes associated with disease identified by the different methods. The true causal gene PIK3C3 was identified by all methods, probably because of its relatively large effect size and MAF. The ... See full document
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Genetic Analysis Workshop 17 mini exome simulation
... called genotype data distributed for GAW17 included the inferred genotypes, such that all individuals had genotypes for all base-pair positions, and phenotypes were simulated on the basis of these ...in ... See full document
9
Evaluation of a LASSO regression approach on the unrelated samples of Genetic Analysis Workshop 17
... The association is tested on the gene level. Within a gene, the dependent variable is Q2 of the GAW17 data set, and the independent variables are the genotypes of all the SNPs in the gene. We use a model, with a ... See full document
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Different approaches for dealing with rare variants in family based genetic studies: application of a Genetic Analysis Workshop 17 problem
... for genetic variants that predispose individuals to a phenotype of ...mini-exome data set provided by Genetic Analysis Workshop ...in regression models, imposes a barrier to ... See full document
6
Analysis of human mini exome sequencing data from Genetic Analysis Workshop 17 using a Bayesian hierarchical mixture model
... of genetic epidemiology and enabling exploration of the full allele frequency spectrum underlying complex ...rare genetic variants, statistical methods traditionally used in genetic association ... See full document
8
A LASSO penalized regression approach for genome wide association analyses using related individuals: application to the Genetic Analysis Workshop 19 simulated data
... analyses based on LMM to remove the effects of related- ness among individuals and then use the residuals of these analyses to fit the LASSO models ...common genetic back- ground among individuals through ... See full document
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Analysis of Genetic Analysis Workshop 18 data with gene based penalized regression
... imputed data, a possible strategy is to use the software package ProA- BEL [14] to construct the inverse variance-covariance matrix on the basis of the relationship matrix, which is made up of the kinship ... See full document
5
Using LASSO regression to detect predictive aggregate effects in genetic studies
... simulation data with a range of causal allele frequencies in the presence of quantitative and phenotypic ...LASSO regression model may be an effi- cient means to determine truly associated variants, but it ... See full document
5
Confidence set of putative quantitative trait loci in whole genome scans with application to the Genetic Analysis Workshop 17 simulated data
... dense genetic maps of single-nucleotide polymorphisms (SNPs) covering the whole ...genome. Based on these maps and using a variety of statistical methods, scientists nowa- days routinely scan the human ... See full document
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Identity by descent and association analysis of dichotomous traits based on large pedigrees
... stratified analysis on the 200 simu- lated population case-control data ...genes based on the outputs from the PLINK computer pro- ...large genetic effects, is the only gene with a detection ... See full document
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Using gene expression data to identify causal pathways between genotype and phenotype in a complex disease: application to Genetic Analysis Workshop 19
... Two methods for causal inference were implemented to identify causal pathways between SNP, gene expression, and phenotype. Attempting causal analysis without a stringent filtering process would not be possible and ... See full document
6
Evaluation of association tests for rare variants using simulated data sets in the Genetic Analysis Workshop 17 data
... The FWER of the variable threshold method is 0 in Table 3. This is a little surprising. To verify the validity of the results, we also perform the standard permutation procedure with 10 6 permutations. The standard ... See full document
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