title: Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges.
abstract: The development and progression of cancer, a collection of diseases with complex genetic architectures, is facilitated by the interplay of multiple etiological factors. This complexity challenges the traditional single-platform study design and calls for an integrated approach to data analysis. However, integration of heterogeneous measurements of biological variation is a non-trivial exercise due to the diversity of the human genome and the variety of output data formats and genome coverage obtained from the commonly used molecular platforms. This review article will provide an introduction to integration strategies used for analyzing genetic risk factors for cancer. We critically examine the ability of these strategies to handle the complexity of the human genome and also accommodate information about the biological and functional interactions between the elements that have been measured-making the assessment of disease risk against a composite genomic factor possible. The focus of this review is to provide an overview and introduction to the main strategies and to discuss where there is a need for further development.
authors: Department of Pathology, The University of MelbourneMelbourne, VIC, Australia; Department of Biomedicine, The University of AarhusAarhus, Denmark.
authors: Louise B
authors: LB
authors: Thingholm
authors: Department of Clinical Genetics, Odense University Hospital Odense, Denmark.
authors: Lars
authors: L
authors: Andersen
authors: Centre for Epidemiology and Biostatistics, The University of Melbourne Melbourne, VIC, Australia.
authors: Enes
authors: E
authors: Makalic
authors: Department of Pathology, The University of Melbourne Melbourne, VIC, Australia.
authors: Melissa C
authors: MC
authors: Southey
authors: Department of Clinical Genetics, Odense University Hospital Odense, Denmark.
authors: Mads
authors: M
authors: Thomassen
authors: Department of Biomedicine, The University of Aarhus Aarhus, Denmark.
authors: Lise Lotte
authors: LL
authors: Hansen
keywords: DNA methylation; array data; gene expression; integrated analysis; massive parallel sequencing (MPS)