robust detection and genotyping of single feature polymorphisms from gene expression data健壮的检测和基因分型的单一功能多态性基因表达数据.pdfVIP

Robust Detection and Genotyping of Single Feature Polymorphisms from Gene Expression Data 1. 1. 1 2 2 3 Minghui Wang , Xiaohua Hu , Gang Li , Lindsey J. Leach , Elena Potokina , Arnis Druka , Robbie 3 2 1,2 Waugh , Michael J. Kearsey , Zewei Luo * 1 Laboratory of Population Quantitative Genetics, The State Key Laboratory of Genetic Engineering, Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China, 2 School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, United Kingdom, 3 Scottish Crop Research Institute, Invergowrie, Dundee, United Kingdom Abstract It is well known that Affymetrix microarrays are widely used to predict genome-wide gene expression and genome-wide genetic polymorphisms from RNA and genomic DNA hybridization experiments, respectively. It has recently been proposed to integrate the two predictions by use of RNA microarray data only. Although the ability to detect single feature polymorphisms (SFPs) from RNA microarray data has many practical implications for genome study in both sequenced and unsequenced species, it raises enormous challenges for statistical modelling and analysis of microarray gene expression data for this objective. Several methods are proposed to predict SFPs from the gene expression profile. However, their performance is highly vulnerable to differential expression of genes. The SFPs thus predicted are eventually a reflection of differentially expressed genes rather than genuine sequence polymorphisms. To address the problem, we developed a novel statistical method to sepa