The FDA weighs in on RNA-Seq

The rapid advancement of emerging genomics technologies and their application for assessing safety and efficacy of FDA-regulated products require a high standard of reliability and robustness supporting regulatory decision-making in the FDA. To facilitate the regulatory application, the FDA implemented a novel data submission program, Voluntary Genomics Data Submission (VGDS), and also to engage the stakeholders. As part of the endeavor, for the past 10 years, the FDA has led an international consortium (MAQC)of regulatory agencies, academia, pharmaceutical companies, and genomics platform providers. The latest MAQC project is also called the SEquencing Quality Control (SEQC) project focused on RNA-seq. Due to rapid advances in NGS technologies, the third phase of the MAQC Project was initiated while the second phase was still under the way. Over 180 participants from 73 different organizations across 12 different countries participated in the SEQC project. The project generated over 10 TB of data with over 100 billion reads. On submission of this dataset to the Gene Expression Omnibus (GEO) repository in June 2014, it represented around 6% of the total RNA-seq data in the repository at that time. This rich data provides ample opportunities for RNA-seq data analysis method development. Under this project, four different datasets were generated. The first dataset was generated from six reference samples. These reference samples were sequenced by various laboratories using different RNA-seq platforms such as Illumina HiSeq, Life Technologies SOLiD, and Roche 454. The second dataset was composed of sequencing data for about 500 neuroblastoma samples from pediatric patients. The third dataset was from 100 rat liver samples. The last dataset was a survey of rat transcriptomes using 11 different organs across 4 different developmental stages for both male and female rat. The SEQC project evaluated technical performance, quality control, and cross lab and cross platform reproducibility of RNA-seq. RNA-seq data was also compared with data generated from the same samples by mature microarray technologies. In addition to that, evaluations were made on the use of RNA-seq for clinical applications and safety assessments. The observations from these efforts were published in 10 manuscripts

(read more about the findings…)

Xu J, Thakkar S, Gong B, Tong W. (2016) The FDA’s Experience with Emerging Genomics Technologies-Past, Present, and Future. AAPS J [Epub ahead of print] [article]

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