Embracing the complexity of genomic data for personalized medicine

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Abstract
Numerous recent studies have demonstrated the use of genomic data, particularly gene expression signatures, as clinical prognostic factors in cancer and other complex diseases. Such studies herald the future of genomic medicine and the opportunity for personalized prognosis in a variety of clinical contexts that utilizes genome-scale molecular information. The scale, complexity, and information content of high-throughput gene expression data, as one example of complex genomic information, is often under-appreciated as many analyses continue to focus on defining individual rather than multiplex biomarkers for patient stratification. Indeed, this complexity of genomic data is often—rather paradoxically—viewed as a barrier to its utility. To the contrary, the complexity and scale of global genomic data, as representing the many dimensions of biology, must be embraced for the development of more precise clinical prognostics. The need is for integrated analyses—approaches that embrace the complexity of genomic data, including multiple forms of genomic data, and aim to explore and understand multiple, interacting, and potentially conflicting predictors of risk, rather than continuing on the current and traditional path that oversimplifies and ignores the information content in the complexity. All forms of potentially relevant data should be examined, with particular emphasis on understanding the interactions, complementarities, and possible conflicts among gene expression, genetic, and clinical markers of risk.