2022 Citation Impact
0.914 - SNIP (Source Normalized Impact per Paper)
0.506 - SJR (SCImago Journal Rank)
2023 Usage
640,615 downloads
196 Altmetric mentions
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We performed a multipoint linkage analysis for rheumatoid arthritis (RA) using high-density single-nucleotide polymorphism (SNP) data for chromosome 6 and chromosome 21 using Genetic Analysis Workshop 15 (GAW1...
Variance-components and regression-based methods are frequently used to map quantitative trait loci. The normality of the trait values is usually assumed and violation of this assumption can have a detrimental...
Several studies have been conducted to assess the influence of genetic variation on genome-wide gene expression profiles measured by the microarray technologies. Due to substantial noise in microarray-based ex...
"Genetical genomics", the study of natural genetic variation combining data from genetic marker-based studies with gene expression analyses, has exploded with the recent development of advanced microarray tech...
Using the Problem 1 data set made available for Genetic Analysis Workshop 15, we assessed sensitivity of linkage results to a correlation-based feature extraction method as well as to different normalization p...
Construction of precise confidence sets of disease gene locations after initial identification of linked regions can improve the efficiency of the ensuing fine mapping effort. We took the confidence set infere...
We applied a simple and efficient two-step method to analyze a family-based association study of gene expression quantitative trait loci (eQTL) in a mixed model framework. This two-step method produces very si...
In this report, we focused on the multiplicity issue in Problem 1 of Genetic Analysis Workshop 15. We investigated and compared the performance of the stratified false-discovery rate control method with the tr...
Multiple testing is a problem in genome-wide or region-wide association studies. In this report, we consider a study design given by the Genetic Analysis Workshop 15 (GAW15) Problem 3 ā nuclear families (paren...
The incorporation of disease-associated covariates into studies aiming to identify susceptibility genes for complex human traits is a challenging problem. Accounting for such covariates in genetic linkage and ...
Large-scale genome-wide association studies are increasingly common, due in large part to recent advances in genotyping technology. Despite a dramatic drop in genotyping costs, it is still too expensive to gen...
We present a class of haplotype-sharing statistics useful for association mapping in case-parent trio data. The framework presented allows derivation of novel tests as well as new simplified variance estimator...
When the number of phenotypes in a genetic study is on the scale of thousands, such as in studies concerning thousands of gene expression levels, the single-trait analysis is computationally intensive, and hea...
There is a growing interest in studying natural variation in human gene expression. Studies mapping genetic determinants of expression profiles are often carried out considering the expression of one gene at a...
We explored approaches to using multiple related traits (gene expression levels) in linkage analysis. We first grouped mRNA transcripts according to their functions annotated in biological process of gene onto...
Standard genetic mapping techniques scan chromosomal segments for location of genetic linkage and association signals. The majority of these methods consider only correlations at single markers and/or phenotyp...
Bayesian methods continue to permeate genetic epidemiology investigations of genetic markers associated with or linked to causal genes for complex diseases. The attraction of these methods is an ability to cap...
We describe a hierarchical Bayes model for the influence of constitutional genotypes from a linkage scan on the expression of a large number of genes. The model comprises linear regression models for the means...
Genome-wide association studies usually involve several hundred thousand of single-nucleotide polymorphisms (SNPs). Conventional approaches face challenges when there are enormous number of SNPs but a relative...
Rheumatoid arthritis is a clinically and genetically heterogeneous disease. Anti-cyclic citrullinated (anti-CCP) antibodies have a high specificity for rheumatoid arthritis and levels correlate with disease se...
Parametric linkage methods for quantitative trait locus mapping require explicit specification of the probability model of the quantitative trait and hence can lead to misleading linkage inferences when the mo...
We performed linkage analysis on families with rheumatoid arthritis, stratifying by ethnic origin. We compared results using either Kong and Cox nonparametric LOD scores or MOD score analysis using the softwar...
The genetic factors underlying many complex traits are not well understood. The Genetic Analysis Workshop 15 Problem 1 data present the opportunity to explore whether gene expression data from microarrays can ...
Heterogeneity poses a challenge to linkage mapping. Here, we apply a latent class extension of Haseman-Elston regression to expression phenotypes with significant evidence of linkage to trans regulators in 14 lar...
Focusing on chromosome 1, a recursive partitioning linkage algorithm (RP) was applied to perform linkage analysis on the rheumatoid arthritis NARAC data, incorporating covariates such as HLA-DRB1 genotype, age...
Understanding the genetic basis of human variation is an important goal of biomedical research. In this study, we used structural equation models (SEMs) to construct genetic networks to model how specific sing...
Identifying gene-environment (G Ć E) interactions has become a crucial issue in the past decades. Different methods have been proposed to test for G Ć E interactions in the framework of linkage or association ...
The restricted partition method (RPM) provides a way to detect qualitative factors (e.g. genotypes, environmental exposures) associated with variation in quantitative or binary phenotypes, even if the contribu...
The identification of susceptibility genes for common, chronic disease presents great challenges. The development of novel statistical and computational methodologies to help identify these genes is an area of...
Rheumatoid arthritis (RA) is a multifactorial disease with complex genetic etiology, about which little is known. Here, we apply a two-stage procedure in which a quick first-stage analysis was used to narrow d...
Non-parametric linkage methods have had limited success in detecting gene by gene interactions. Using affected sibling-pair (ASP) data from all replicates of the simulated data from Problem 3, we assessed the ...
When two genes interact to cause a clinically important phenotype, it would seem reasonable to expect that we could leverage genotypic information at one of the loci in order to improve our ability to detect t...
Gene expression profiles and single-nucleotide polymorphism (SNP) profiles are modern data for genetic analysis. It is possible to use the two types of information to analyze the relationships among genes by s...
We carried out an analysis of the Genetic Analysis Workshop 15 simulated Problem 3 data. We restricted ourselves to the present/absent phenotype. Linkage analysis revealed a very strong signal on chromosome 6....
After genetic linkage has been identified for a complex disease, the next step is often fine-mapping by association analysis, using single-nucleotide polymorphisms (SNPs) within a linkage region. If a SNP show...
To detect association of the DR1 allele with rheumatoid arthritis (RA) given linkage in the affected sibling pairs of the replicates of Problem 3 of Genetic Analysis Workshop 15 (GAW15), we propose a new score...
In order to model the effect of PTPN22 on rheumatoid arthritis (RA), we determined the combination of single-nucleotide-polymorphisms (SNPs) showing the strongest association with RA. Three SNPs (rs2476601-rs1273...
We propose a nonparametric association analysis combining both family and unrelated case-control genotype data. Under the assumption of Hardy-Weinberg equilibrium, we formed an affected group to compare with a...
We performed a case-control association analysis of rheumatoid arthritis (RA) for several candidate genes using the North American Rheumatoid Arthritis Consortium (NARAC) data provided in Genetic Analysis Work...
The goal of this analysis is to compare different test strategies for genetic association in case-control studies using related individuals. The first test is the trend test that is corrected for related indiv...
Related cases may be included in case-control association studies if correlations between related individuals due to identity-by-descent (IBD) sharing are taken into account. We derived a framework to test for...
Clustering of related haplotypes in haplotype-based association mapping has the potential to improve power by reducing the degrees of freedom without sacrificing important information about the underlying gene...
Several recent papers have suggested that two-locus tests of association that incorporate gene Ć gene interaction can be more powerful than marginal, single-locus tests across a broad range of multilocus inter...
PedGenie beta version 2.1 is a unique, flexible, and easily implemented analysis software tool that is enhanced significantly by incorporation of meta-statistics to allow valid combined analysis of multiple st...
The mRNA expression levels of genes have been shown to have discriminating power for the classification of breast cancer. Studying the heritability of gene expression levels on breast cancer related transcript...
Mutual information (MI) is a robust nonparametric statistical approach for identifying associations between genotypes and gene expression levels. Using the data of Problem 1 provided for the Genetic Analysis W...
Assuming multiple loci play a role in regulating the expression level of a single phenotype, we propose a new approach to identify cis- and trans-acting loci that regulate gene expression. Using the Problem 1 dat...
While genome-wide linkage studies have been successful in mapping variants underlying rare monogenic disorders, genome-wide association studies may be more appropriate for detecting common variants of modest e...
For Genetic Analysis Workshop 15 Problem 2, we organized data from several ongoing studies designed to identify genetic and environmental risk factors for rheumatoid arthritis. Data were derived from the North...
2022 Citation Impact
0.914 - SNIP (Source Normalized Impact per Paper)
0.506 - SJR (SCImago Journal Rank)
2023 Usage
640,615 downloads
196 Altmetric mentions