%0 Journal Article
%T Integrative Genomics with Mediation Analysis in a Survival Context
%A Szil¨¢rd Nemes
%A Toshima Z. Parris
%A Anna Danielsson
%A Zakaria Einbeigi
%A Gunnar Steineck
%A Junmei Miao Jonasson
%A Khalil Helou
%J Computational and Mathematical Methods in Medicine
%D 2013
%I Hindawi Publishing Corporation
%R 10.1155/2013/413783
%X DNA copy number aberrations (DCNA) and subsequent altered gene expression profiles may have a major impact on tumor initiation, on development, and eventually on recurrence and cancer-specific mortality. However, most methods employed in integrative genomic analysis of the two biological levels, DNA and RNA, do not consider survival time. In the present note, we propose the adoption of a survival analysis-based framework for the integrative analysis of DCNA and mRNA levels to reveal their implication on patient clinical outcome with the prerequisite that the effect of DCNA on survival is mediated by mRNA levels. The specific aim of the paper is to offer a feasible framework to test the DCNA-mRNA-survival pathway. We provide statistical inference algorithms for mediation based on asymptotic results. Furthermore, we illustrate the applicability of the method in an integrative genomic analysis setting by using a breast cancer data set consisting of 141 invasive breast tumors. In addition, we provide implementation in R. 1. Introduction Concomitant analysis of the two biological levels, DNA and RNA, and elucidating their implication in cancer development and cancer-related mortality is a key objective of studies within the cancer genetics field. Integrative analysis of DNA copy number aberrations (DCNA) and mRNA levels has received considerable interest with studies employing a wide range of statistical methods [1¨C5]. Integrative genomic analyses aim to identify novel biomarkers that can distinguish between patients with favorable and unfavorable prognosis. However, the sole focus on DCNA-driven altered gene expression profiles falls short of this goal. To develop a better understanding of the impact DCNA-driven altered gene expression profiles have on tumor recurrence or cancer-specific mortality, we need to consider patient survival status and survival time, that is, survival analysis. However, the unique relationship between DNA and RNA raises the need to interpret the data from a more refined viewpoint. Ascertaining causality between two biological factors is far to be straightforward. However, no one would question that mRNA is transcribed from a DNA template. Thus, mRNA mediates the genetic information imprinted in DNA and possibly the effect copy number aberrations have on survival status. The chosen statistical-mathematical framework has to properly address this issue. Mediation assumes that an independent variable (DNA) causes the mediator (mRNA), which in turn causes the outcome (survival status). Thus, the mediator accounts partially or totally
%U http://www.hindawi.com/journals/cmmm/2013/413783/