Many ethical and legal issues surround genomic technologies, some of which are present for other kinds of medical data, but some of which are specific to genomic data. Specifically the global nature of genomic data and the life-long implications of genetic defects on the health of the individual subject produce challenges in the ethical and legal handling of this data. In general, data derived from transcriptome analysis, which studies gene expression, as well as proteomics and metabolomics, carry less ethically-charged information than measures of the germ line genome. However, theoretical issues that have been raised related to withholding therapy based on a specific genotype which could also apply to a specific expression profile. Potential solutions for these challenges are discussed, such as maintaining a connection with research participants through a trusted third party, using electronic means to manage that contact and reconsent subjects. A flexible, secure information technology infrastructure is proposed to manage and search consent forms, provide the ability to collect additional data and consent while maintaining participant confidentiality.