[PDF] Top 20 Comparing gene set analysis methods on single nucleotide polymorphism data from Genetic Analysis Workshop 16
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Comparing gene set analysis methods on single nucleotide polymorphism data from Genetic Analysis Workshop 16
... Recently, gene set analysis (GSA) has been extended from use on gene expression data to use on single-nucleotide polymorphism (SNP) data in ... See full document
5
A framework for analyzing both linkage and association: an analysis of Genetic Analysis Workshop 16 simulated data
... linkage analysis in the simulated single-nucleotide polymorphism data provided for Genetic Analysis Workshop ...linkage analysis and regression ...All ... See full document
6
A combinatorial approach for detecting gene gene interaction using multiple traits of Genetic Analysis Workshop 16 rheumatoid arthritis data
... several single susceptibility genes, such as PTPN22, STAT4, and TRAF1-C5, have been ...the gene-gene interaction in the rheumatoid arthritis data using multiple traits: disease status, ... See full document
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Analysis of high density single nucleotide polymorphism data: three novel methods that control for linkage disequilibrium between markers in a linkage analysis
... initial graphical model is assumed, and given the observed genotypes, an imputation of the haplotypes is made. In the second stage, given the imputed haplotypes a new graphical model is estimated. These stages are iter- ... See full document
7
Analysis of Genetic Analysis Workshop 18 data with gene based penalized regression
... of methods. PeRC and Mendel were run on a data set comprised of all SNPs within genes plus the common SNPs (MAF ...RVs. Single marker analysis was performed in PLINK [13] on all SNPs, ... See full document
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A multistep approach to single nucleotide polymorphism–set analysis: an evaluation of power and type I error of gene based tests of association after pathway based association tests
... for data analysis, and Dordt College and its Summer Research Program in Statistical Genetics for their continued ...sequence data were provided by the Type 2 Diabetes Genetic Exploration by ... 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
... the gene FPGT , a gene in LD with a single nucleotide polymorphism (SNP) previously re- ported to be associated ( p = ...haplotype methods de- tected a much stronger association ... See full document
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Application of collapsing methods for continuous traits to the Genetic Analysis Workshop 17 exome sequence data
... 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 sequence data ... See full document
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SNP set analysis for detecting disease association using exon sequence data
... the genetic effects of both common and rare ...a single-nucleotide polymorphism (SNP) set based on logistic regression models and logistic kernel machine ...models. ... See full document
6
Genetic Analysis Workshop 18 single nucleotide variant prioritization based on protein impact, sequence conservation, and gene annotation
... GAW18 data set by additional quality filtering, these find- ings suggest that a more sophisticated annotation pipeline may be required to avoid false positive LOF variant anno- ... See full document
6
Case control association testing by graphical modeling for the Genetic Analysis Workshop 17 mini exome sequence data
... for genetic variation underlying complex diseases turns to rare variants of small effect ascertained from genome-wide or exome-wide sequence data, the need for methods of disease-gene ... See full document
5
A pathway analysis applied to Genetic Analysis Workshop 16 genome wide rheumatoid arthritis data
... identify genetic contributors to disease. Currently, single-nucleotide polymorphism (SNP) association analysis is the most widely used method of genome-wide association data, but ... See full document
8
Joint analysis of sequence data and single nucleotide polymorphism data using pedigree information for imputation and recombination inference
... of genetic studies ...collect data, either at the whole gen- ome level or for targeted ...downstream analysis are still prohibitively ...accumulated single-nucleotide ... See full document
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Development and validation of a novel single nucleotide polymorphism (SNP) panel for genetic analysis of Blastomyces spp and association analysis
... typing data, haplotypes were ascertained by identifying matching samples, and subsumed to a single representative using Genetic Analysis in Excel ...[16]. Genetic structure among ... See full document
11
Systematic comparative analysis of single nucleotide variant detection methods from single cell RNA sequencing data
... transcriptome data with quantified gene expression as features, which could be influenced by different technical factors such as se- quencing platforms, batch effects, and dropouts, while the detection of ... See full document
15
Propensity score analysis in the Genetic Analysis Workshop 17 simulated data set on independent individuals
... Genetic Analysis Workshop 17 provided simulated phenotypes and exome sequence data for 697 independent individuals (209 case subjects and 488 control ...these data was influenced by ... See full document
6
Gene hunting of the Genetic Analysis Workshop 16 rheumatoid arthritis data using rough set theory
... rough set theory to identify genes affecting rheumatoid arthritis risk from the data collected by the North American Rheumatoid Arthritis ...each gene, we employ generalized dynamic reducts in ... See full document
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The Genetic Analysis Workshop 16 Problem 3: simulation of heritable longitudinal cardiovascular phenotypes based on actual genome wide single nucleotide polymorphisms in the Framingham Heart Study
... interpreting data obtained as part of a genome-wide association study presents numerous challenges, as well as the promise of improved under- standing of the genetic factors influencing complex ...detailed ... See full document
7
Predictive modeling in case control single nucleotide polymorphism studies in the presence of population stratification: a case study using Genetic Analysis Workshop 16 Problem 1 dataset
... the data that are derived by clustering the subjects using the axis of genetic ...overall genetic variability, which is usually assumed to be reducing the underlying ethnicity ...the genetic ... See full document
5
Replication of recently identified associated single nucleotide polymorphisms from six autoimmune diseases in Genetic Analysis Workshop 16 rheumatoid arthritis data
... 17. Todd JA, Walker NM, Cooper JD, Smyth DJ, Downes K, Plagnol V, Bailey R, Nejentsev S, Field SF, Payne F, Lowe CE, Szeszko JS, Hafler JP, Zeitels L, Yang JH, Vella A, Nutland S, Stevens HE, Schuilenburg H, Coleman G, ... See full document
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