Analysing biological pathways in genome-wide association studies

K Wang, M Li, H Hakonarson - Nature Reviews Genetics, 2010 - nature.com
Genome-wide association (GWA) studies have typically focused on the analysis of single
markers, which often lacks the power to uncover the relatively small effect sizes conferred by …

Pathway analysis of genomic data: concepts, methods, and prospects for future development

VK Ramanan, L Shen, JH Moore, AJ Saykin - TRENDS in Genetics, 2012 - cell.com
Genome-wide data sets are increasingly being used to identify biological pathways and
networks underlying complex diseases. In particular, analyzing genomic data through sets …

Polygenic modeling with Bayesian sparse linear mixed models

X Zhou, P Carbonetto, M Stephens - PLoS genetics, 2013 - journals.plos.org
Both linear mixed models (LMMs) and sparse regression models are widely used in
genetics applications, including, recently, polygenic modeling in genome-wide association …

How far from the SNP may the causative genes be?

A Brodie, JR Azaria, Y Ofran - Nucleic acids research, 2016 - academic.oup.com
While GWAS identify many disease-associated SNPs, using them to decipher disease
mechanisms is hindered by the difficulty in mapping SNPs to genes. Most SNPs are in non …

High-dimensional LASSO-based computational regression models: regularization, shrinkage, and selection

F Emmert-Streib, M Dehmer - Machine Learning and Knowledge …, 2019 - mdpi.com
Regression models are a form of supervised learning methods that are important for
machine learning, statistics, and general data science. Despite the fact that classical …

[HTML][HTML] Gene set analysis of genome-wide association studies: methodological issues and perspectives

L Wang, P Jia, RD Wolfinger, X Chen, Z Zhao - Genomics, 2011 - Elsevier
Recent studies have demonstrated that gene set analysis, which tests disease association
with genetic variants in a group of functionally related genes, is a promising approach for …

Network-based multiple sclerosis pathway analysis with GWAS data from 15,000 cases and 30,000 controls

SE Baranzini, P Khankhanian, NA Patsopoulos… - The American Journal of …, 2013 - cell.com
Multiple sclerosis (MS) is an inflammatory CNS disease with a substantial genetic
component, originally mapped to only the human leukocyte antigen (HLA) region. In the last …

Gene set analysis of SNP data: benefits, challenges, and future directions

BL Fridley, JM Biernacka - European Journal of Human Genetics, 2011 - nature.com
The last decade of human genetic research witnessed the completion of hundreds of
genome-wide association studies (GWASs). However, the genetic variants discovered …

Gene set analysis: a step‐by‐step guide

MA Mooney, B Wilmot - … Journal of Medical Genetics Part B …, 2015 - Wiley Online Library
To maximize the potential of genome‐wide association studies, many researchers are
performing secondary analyses to identify sets of genes jointly associated with the trait of …

Gene set analysis of GWAS data for human longevity highlights the relevance of the insulin/IGF-1 signaling and telomere maintenance pathways

J Deelen, HW Uh, R Monajemi, D van Heemst… - Age, 2013 - Springer
In genome-wide association studies (GWAS) of complex traits, single SNP analysis is still
the most applied approach. However, the identified SNPs have small effects and provide …