Emerging technologies facilitate basic science research, but their value in regulatory applications requires rigorous assessment and consensus within the research community. Next-generation sequencing (NGS) represents an advanced genomic approach with a far-reaching impact in drug development, personalized medicine, food safety and beyond. Rapid progress in NGS over the last few years has demonstrated its translation from an exploratory to an applied stage. As a result, the FDA has received an increasing amount of NGS data supporting the evidence for the safety and efficacy of new medical products and the agency is now facing challenges with respect to developing standards for receiving data and ensuring reproducible results. This presentation will discuss the FDA-led community wide consortium project, known as the SEquencing Quality Control (SEQC) project, which developed a comprehensive plan to assess the power and limitations of RNA-seq. The project involved >180 participants from ~80 organizations and generated large RNA-seq data sets covering a broad range of biological samples (human, rat, and reference samples) with which many critical issues of applying RNA-Seq in clinical application and safety assessment were evaluated and discussed. The presentation will provide an overview and main conclusions of the SEQC project. In addition, the new SEQC project (SEQC2) which is in the planning stage will be also explained. SEQC2 is focused on whole-genome sequencing and target gene sequencing.