LASSO model selection with post-processing for a genome-wide association study data set
نویسندگان
چکیده
Model selection procedures for simultaneous analysis of all single-nucleotide polymorphisms in genome-wide association studies are most suitable for making full use of the data for a complex disease study. In this paper we consider a penalized regression using the LASSO procedure and show that post-processing of the penalized-regression results with subsequent stepwise selection may lead to improved identification of causal single-nucleotide polymorphisms.
منابع مشابه
Combining least absolute shrinkage and selection operator (LASSO) and principal-components analysis for detection of gene-gene interactions in genome-wide association studies
Variable selection in genome-wide association studies can be a daunting task and statistically challenging because there are more variables than subjects. We propose an approach that uses principal-component analysis (PCA) and least absolute shrinkage and selection operator (LASSO) to identify gene-gene interaction in genome-wide association studies. A PCA was used to first reduce the dimension...
متن کاملThe Impact of Different Genetic Architectures on Accuracy of Genomic Selection Using Three Bayesian Methods
Genome-wide evaluation uses the associations of a large number of single nucleotide polymorphism (SNP) markers across the whole genome and then combines the statistical methods with genomic data to predict the genetic values. Genomic predictions relieson linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) in a population. Methods that use all markers simultaneo...
متن کاملEvaluation of the lasso and the elastic net in genome-wide association studies
The number of publications performing genome-wide association studies (GWAS) has increased dramatically. Penalized regression approaches have been developed to overcome the challenges caused by the high dimensional data, but these methods are relatively new in the GWAS field. In this study we have compared the statistical performance of two methods (the least absolute shrinkage and selection op...
متن کاملPenalized Regression for Genome-Wide Association Screening of Sequence Data
Whole exome and whole genome sequencing are likely to be potent tools in the study of common diseases and complex traits. Despite this promise, some very difficult issues in data management and statistical analysis must be squarely faced. The number of rare variants identified by sequencing is apt to be much larger than the number of common variants encountered in current association studies. T...
متن کاملGenome-wide Association Study to Identify Genes and Biological Pathways Associated with Type Traits in Cattle using Pathway Analysis
Extended Abstract Introduction and Objective: Type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlate with other economically important traits in cattle including fertility, longevity and carcass traits. The present study aimed to conduct a genome wide association studies (GWAS) based on gene-set enrichment analysis for identifying the ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره 5 شماره
صفحات -
تاریخ انتشار 2011