Across the landscape of clinical medicine, drug development and genomic technology development, reproducibility is the foundation for their translation to clinical utility and regulatory application. Human or technical error leading to irreproducibility of biomedical research hampers clinical translation of biomarkers and therapeutics. These concerns pervade through the use of high-throughput genomic technologies such as microarrays and next-generation sequencing for both preclinical and clinical studies. In this presentation, The FDA-led community-wide MAQC/SEQC consortium projects will be discussed that is focused on promoting standardization and quality control efforts to address alarming concerns on irreproducibility in the generation, analysis, and interpretation of genomics data. Among issues encountered, computational reproducibility becomes increasingly challenging. Thus, the presentation will discuss some of advancements in this area based on the data generated from MAQC/SEQC and beyond. A set of lessons-learned and general guideline will also be provided to explicitly consider reproducibility, a fundamental hallmark of good science, in analysis of transcriptomics data.