Problems with the "omics"

omics studies involve the measurement of large numbers of parameters, typically genes (genomics), proteins (proteomics), lipids (lipidomics) or metabolites (metabolomics). Values associated with each of the measured parameters are searched to find examples that correlate with biological endpoints, often disease or cancer. Although the number of parameters being measured has increased dramatically with "omics" studies, the number of biological and methodological replicates has not. As with comparable classical biomedical studies, there exist limitations arising from whether or not the analytical methods are adequate for making the measurements needed and whether or not the measurements are implemented properly. In addition, because of the large number of measurements and the limited number of test subjects, unique problems arise in "omics" studies involving statistics and bias. Even though improvements in technology may well minimize measurement problems, the inherent difficulties associated with measuring so many parameters from a limited number of test subjects will remain. This review focuses on the four main problems with the "omics": bias, statistics, methodology, and method misuse. Although we give suggestions to minimize the impacts of these problems, some problems may not be solved unless the number of measurements is more consistent with the number of possible biological replicates. (c) 2006 Elsevier Ltd. All rights reserved.