2022 Citation Impact
0.914 - SNIP (Source Normalized Impact per Paper)
0.506 - SJR (SCImago Journal Rank)
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Here we describe the data provided for Problem 1 of Genetic Analysis Workshop 15. The data provided for Problem 1 were unusual in two ways. First, the phenotype was the level of gene expression for each gene, ...
Several methods to identify tagging single-nucleotide polymorphisms (SNPs) are in common use for genetic epidemiologic studies; however, there may be loss of information when using only a subset of SNPs. We so...
Genotype-expression association analysis using linear regression may produce different test results depending on whether founders only or all pedigreed members are used. This difference is not due to the corre...
The Genetic Analysis Workshop 15 rheumatoid arthritis data included a set of 460 cases and 460 controls genotyped at 2300 closely spaced markers on a 10 megabase region of chromosome 18q. We conducted a multil...
Rheumatoid arthritis (RA, MIM 180300) is a common and complex inflammatory disorder. The North American Rheumatoid Arthritis Consortium (NARAC) data, as part of the Genetic Analysis Workshop 15 data, consists ...
Family-based association approaches such as the transmission-disequilibrium test (TDT) are used extensively in the study of genetic traits because they are generally robust to the presence of population struct...
We compared and evaluated several variable and model selection methods using Bayesian and non-Bayesian approaches for three replicates of the Genetic Analysis Workshop 15 (GAW15) simulated data. In doing so, t...
In a small chromosomal region, a number of polymorphisms may be both linked to and associated with a disease. Potentially directly associated causal loci may be distinguished from indirectly associated loci by...
There has been a growing interest in developing strategies for identifying single-nucleotide polymorphisms (SNPs) that explain a linkage signal by joint modeling of linkage and association. We compare several ...
This study evaluated the utility of unrelated controls and flanking markers when performing joint modeling of linkage and association by the LAMP software (version 0.0.6) [Am J Hum Genet 2005, 76:934ā949; Am J Hu...
The influence of certain alleles of the HLA-DRB1 locus on risk for rheumatoid arthritis has been well established through linkage and association studies. In addition, other loci in the HLA region on 6p21 may ...
A family-based association study design is not only able to localize causative genes more precisely than linkage analysis, but it also helps explain the genetic mechanism underlying the trait under study. Ther...
Performing linkage and association analyses on a large set of correlated data presents an interesting set of problems. In the current setting, we have 3554 expression levels from lymphoblastoid cell lines in 1...
Extensive studies have been performed to analyze variation in gene expression data by using multistage approaches, including a combination of microarray and linkage analysis. Such a method was recently used in...
About 28% of genes appear to have an expression pattern that follows a mixture distribution. We use first- and second-order partial correlation coefficients to identify trios and quartets of non-sex-linked gen...
The Genetic Analysis Workshop 15 (GAW15) Problem 1 contained baseline expression levels of 8793 genes in immortalized B cells from 194 individuals in 14 Centre d'Etude du Polymorphisme Humain (CEPH) Utah pedig...
In this report, we compared haplotyping approaches using families and unrelated individuals on the simulated rheumatoid arthritis (RA) data in Problem 3 from Genetic Analysis Workshop (GAW) 15. To investigate ...
Modern genetic epidemiology faces the challenge of dealing with hundreds of thousands of genetic markers. The selection of a small initial subset of interesting markers for further investigation can greatly fa...
We recently proposed a new strategy: 2-locus TDT for detecting two susceptibility genes through their interaction in trio families. We apply our method to two candidate genes, A and C, on the Genetic Analysis ...
Many genes with major effects on quantitative traits have been reported to interact with other genes. However, finding a group of interacting genes from thousands of SNPs is challenging. Hence, an efficient an...
We incorporate population effects of sex and antibodies directed against cyclic citrullinated peptides (anti-CCP) into the linkage analysis of rheumatoid arthritis (RA) with microsatellites data provided by th...
Clinical heterogeneity of a disease may reflect an underlying genetic heterogeneity, which may hinder the detection of trait loci. Consequently, many statistical methods have been developed that allow for the ...
The goal of this paper is to investigate the effect of using principal components as a data reduction method for expression data in linkage analysis. We used 45 probes normalized using the Affymetrix Global Sc...
Microarray technologies allow the measurement of the expression levels of thousands of transcripts at the same time. As part of Genetic Analysis Workshop 15 (GAW15), we analyzed a data set that measured the ex...
With the availability of high-throughput microarray technologies, investigators can simultaneously measure the expression levels of many thousands of genes in a short period. Although there are rich statistica...
We propose a method to perform linkage genome scans for many correlated traits in the Genetic Analysis Workshop 15 (GAW15) data. The proposed method has two steps: first, we use a clustering method to find the...
In order to identify regulatory genes, we determined the heritability of gene transcripts, performed linkage analysis to identify quantitative trait loci (QTLs), and evaluated the evidence for shared genetic e...
Three LOD score statistics are often used for genome-wide linkage analysis: the maximum LOD score, the LOD score statistic proposed by Kong and Cox, both based on the allele-sharing between affected sib pairs,...
To evaluate whether there is evidence for two rheumatoid arthritis (RA) susceptibility genes on chromosome 6, we applied new robust methods for two-locus multipoint identical-by-descent mapping to the rheumato...
We applied nonparametric quantitative trait linkage analysis to two rheumatoid arthritis quantitative phenotypes, IgM rheumatoid factor (RF) and anti-cyclic citrullinated peptide autoantibody titer measurement...
The CEPH samples are an invaluable resource for mapping genes that contribute to traits that can be measured in cell lines. With the many markers that have already been genotyped for the Centre d'Etude du Poly...
Although rheumatoid arthritis, a chronic and inflammatory disease affecting numerous adults, has a complex genetic component involving the human leukocyte antigen region, additional genomic regions most likely...
Our aim is to develop methods for identifying a (causal) variant or variants from a dense panel of single-nucleotide polymorphisms (SNPs) that are genotyped on the evidence of previous studies. Because a large...
We studied rheumatoid arthritis (RA) in the North American Rheumatoid Arthritis Consortium (NARAC) data (1499 subjects; 757 families). Identical methods were applied for studying RA in the Genetic Analysis Wor...
Rheumatoid arthritis is a complex disease that appears to involve multiple genetic and environmental factors. Using the Genetic Analysis Workshop 15 simulated rheumatoid arthritis data and the structural equat...
We sought to i) identify putative genetic determinants of the severity of rheumatoid arthritis in the NARAC (North American Rheumatoid Arthritis Consortium) data, ii) assess whether known candidate genes for d...
Inter-individual variation in gene expression levels can arise as an effect of variation in DNA markers. When associating multiple gene expression variables with multiple DNA marker variables, multivariate tec...
Non-inherited maternal antigens encoded by specific HLA-DRB1 alleles (NIMA) have been implicated as a rheumatoid arthritis (RA) risk factor. Using genotype data from North American Rheumatoid Arthritis Consortium...
Haplotypes are composed of specific combinations of alleles at the several loci on the same chromosome. Because haplotypes incorporate linkage disequilibrium (LD) information from multiple loci, haplotype-base...
Morley et al. (Nature 2004, 430:743ā747) detected significant linkages to the expression levels of 142 genes (of 3554) at a reported threshold of genome-wide p = 0.001 (LOD ā 5.3), using 14 three-generation Centr...
A new type of test is presented for genome-wide association studies using a case-control design. It is referred to as the adaptive two-stage (ATS) analysis, being based on both the Hardy-Weinberg disequilibriu...
With technological advances in high-throughput genotyping, it is not unusual to perform hundreds of thousands of tests for each phenotype. Thus, correction to control type I error is essential. The false-disco...
By applying an association test to analyze the data sets from Genetic Analysis Workshop 15 Problem 3, we compare power using different haplotype-block information. The results from using both of the two differ...
The goal of this paper is to investigate the effects of normalization procedures for expression data on linkage results. We selected the two most commonly used expression data extraction and normalization meth...
We evaluate the impact of three pre-processing methods for Affymetrix microarray data on expression quantitative trait locus (eQTL) mapping, using 14 CEPH Utah families (GAW Problem 1 data). Different sets of ...
To explore the mapping of factors regulating gene expression, we have carried out linkage studies using expression data from individual transcripts (from Affymetrix microarrays; Genetic Analysis Workshop 15 Pr...
In the fast-developing field of expression quantitative traits loci (eQTL) studies, much interest has been concentrated on detecting genomic regions containing transcriptional regulators that influence multipl...
Recent studies have shown that linkage disequilibrium (LD) between single-nucleotide polymorphism (SNP) markers is widespread. Assuming linkage equilibrium has been shown to cause false positives in linkage st...
The presence of linkage disequilibrium violates the underlying assumption of linkage equilibrium in most traditional multipoint linkage approaches. Studies have shown that such violation leads to bias in quali...
A number of autoimmune and other diseases have well established HLA associations; in many cases there is strong evidence for the direct involvement of the HLA class II peptide-presenting antigens, e.g., HLA DR...
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