[PDF] Top 20 Collapsing based and kernel based single gene analyses applied to Genetic Analysis Workshop 17 mini exome data
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Collapsing based and kernel based single gene analyses applied to Genetic Analysis Workshop 17 mini exome data
... of collapsing- and kernel-based methods After obtaining the simulation answers from the GAW17 meetings, we analyzed 200 simulated data sets and then counted how many causal genes and ... 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 ...The analyses were performed on the mini-exome data set provided by Genetic Analysis Workshop ... See full document
6
Large scale risk prediction applied to Genetic Analysis Workshop 17 mini exome sequence data
... Genetic Analysis Workshop 17 (GAW17) provided a large-scale mini-exome sequence data set with a high proportion of rare ...this data set the number of genes far ... See full document
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Application of collapsing methods for continuous traits to the Genetic Analysis Workshop 17 exome sequence data
... evaluate collapsing methods using sequence ...a single SNP, for which a collapsing method is identical to a single-SNP ...GAW17 data were based on the real targeted exome ... See full document
5
Old lessons learned anew: family based methods for detecting genes responsible for quantitative and qualitative traits in the Genetic Analysis Workshop 17 mini exome sequence data
... entire data set and also split the set of subpedigrees into one file for each pedigree, to get overall nonparametric linkage and LOD scores for each of the eight ...nonparametric single-point linkage ... See full document
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Gene based multiple trait analysis for exome sequencing data
... common genetic variants identified through genome-wide association studies explain only a small proportion of the genetic risk for complex ...Some genetic association studies provide multiple ... See full document
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Collapsing ROC approach for risk prediction research on both common and rare variants
... emerging genetic findings holds great promise for improving public health and clinical ...common genetic loci, including those from genome-wide association studies, have lacked sufficient accuracy for ... 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
... our analysis, we explore both rare and common ...a gene, we use the results of collapsing and association ...a gene can have multiple p-values associated with it, especially in the rare ... 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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Detecting functional rare variants by collapsing and incorporating functional annotation in Genetic Analysis Workshop 17 mini exome data
... variants based on the number of replicates that provide nonzero parameter estimates for ...the data-adaptive collapsing method performs better than the other two ...proportion collapsing ... See full document
6
Search for compound heterozygous effects in exome sequence of unrelated subjects
... variant collapsing procedure for the analysis of DNA sequence ...a gene, knowing the phase of each variant may provide additional statistical power to detect associations with phenotypes that follow ... See full document
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Whole genome sequence analysis of the simulated systolic blood pressure in Genetic Analysis Workshop 18 family data: long term average and collapsing methods
... in gene MAP4 , single-marker analysis also provided high ...that collapsing multiple variants did worse than single-marker analysis for several genes when they contained causal ... See full document
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Genetic Analysis Workshop 18 single nucleotide variant prioritization based on protein impact, sequence conservation, and gene annotation
... for Applied Genomics; SWS and CM: University of Toronto, McLaughlin ...WGS data were provided by the T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-generation sequencing in Ethnic Samples) ... See full document
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A comparison of whole genome sequencing with exome sequencing for family based association studies
... Nevertheless, exome sequencing also has several intrinsic ...capability, exome sequencing might introduce bias as a result of fragment size and GC content, which could result in ambiguous mapping and reduce ... See full document
6
Gene based partial least squares approaches for detecting rare variant associations with complex traits
... the analysis of structural equation models with latent ...same gene are combined into a single LV (i. e., gene score) by constructing a linear function of the SNPs in X t [ ] i , ( i = 1, 2, ... See full document
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Pathway based joint effects analysis of rare genetic variants using Genetic Analysis Workshop 17 exon sequence data
... the Genetic Analysis Workshop 17 (GAW17) ...phenotype data, there are three quanti- tative risk factors (Q1, Q2, and Q4), which are simulated as normally distributed phenotypes, and one ... See full document
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A variance component based gene burden test
... sequence data were provided by the T2D-GENES Consortium, which is supported by NIH grants U01 DK085524, U01 DK085584, U01 DK085501, U01 DK085526, and U01 ...other genetic and phenotypic data for ... See full document
5
Identity by descent and association analysis of dichotomous traits based on large pedigrees
... in genetic research. Recent large GWAS have shown that common genetic variants are involved in common diseases, but most of the variants found in this way account for only a small portion of the trait ... See full document
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Addition of multiple rare SNPs to known common variants improves the association between disease and gene in the Genetic Analysis Workshop 17 data
... After the GAW17 conference, we compared the per- formance of our method to the simulated answers. For the correctly identified gene PTK2B, removal of simu- lated SNP C8S900 actually improved the disease associa- ... See full document
5
Gaussian graphical models for phenotypes using pedigree data and exploratory analysis using networks with genetic and nongenetic factors based on Genetic Analysis Workshop 18 data
... real data. We also explored binary sparse graphical models of single-nucleotide polymorphisms (SNPs), covariates, and quantitative traits for exploratory analysis of the ...association data ... See full document
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