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Article
Open AccessModern simulation utilities for genetic analysis
Statistical geneticists employ simulation to estimate the power of proposed studies, test new analysis tools, and evaluate properties of causal models. Although there are existing trait simulators, there is am...
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Article
Open AccessPro-inflammatory cytokine polymorphisms and interactions with dietary alcohol and estrogen, risk factors for invasive breast cancer using a post genome-wide analysis for gene–gene and gene–lifestyle interaction
Molecular and genetic immune-related pathways connected to breast cancer and lifestyles in postmenopausal women are not fully characterized. In this study, we explored the role of pro-inflammatory cytokines su...
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Article
OpenMendel: a cooperative programming project for statistical genetics
Statistical methods for genome-wide association studies (GWAS) continue to improve. However, the increasing volume and variety of genetic and genomic data make computational speed and ease of data manipulation...
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Article
Open AccessEffect of genetic variants and traits related to glucose metabolism and their interaction with obesity on breast and colorectal cancer risk among postmenopausal women
Impaired glucose metabolism–related genetic variants and traits likely interact with obesity and related lifestyle factors, influencing postmenopausal breast and colorectal cancer (CRC), but their interconnect...
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Article
Open AccessGenome-wide QTL and eQTL analyses using Mendel
Pedigree genome-wide association studies (GWAS) (Option 29) in the current version of the Mendel software is an optimized subroutine for performing large-scale genome-wide quantitative trait locus (QTL) analys...
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Article
Open AccessFast genome-wide pedigree quantitative trait loci analysis using MENDEL
The linkage era left a rich legacy of pedigree samples that can be used for modern genome-wide association sequencing (GWAS) or next-generation sequencing (NGS) studies. Family designs are naturally equipped t...
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Article
Open AccessIntegrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue Syndrome
Systems biologic approaches such as Weighted Gene Co-expression Network Analysis (WGCNA) can effectively integrate gene expression and trait data to identify pathways and candidate biomarkers. Here we show tha...
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Article
Open AccessMerging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis
Correctly merged data sets that have been independently genotyped can increase statistical power in linkage and association studies. However, alleles from microsatellite data sets genotyped with different expe...
