The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine

Mercer, T.R., Xu, J., Mason, C.E. et al. The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine. Genome Biol 22, 306 (2021). https://doi.org/10.1186/s13059-021-02528-3

Abstract

The MicroArray and Sequencing Quality Control (MAQC) consortium is a FDA-led, community-wide effort to evaluate the use of genomic technologies in clinical applications. This evaluation includes the benchmarking of NGS technologies, the development of reference materials, and understanding the experimental and bioinformatic variables that impact the accuracy and reproducibility of large genomic datasets. These outcomes are ultimately used to inform best-practice guidelines, regulatory considerations, and foster further improvements in genomic technologies and computational methods.

The MAQC consortium has been ongoing for almost 16 years with four projects (MAQC I-IV). The founding project, MAQC Phase I, was initiated in 2005 by the FDA’s National Center for Toxicological Research (NCTR) to evaluate the reliability of microarray technologies that were being increasingly used in research, clinical diagnosis, and drug development and thus posed an urgency for the FDA to address the regulatory implication of the technology. In 2010, the MAQC consortium launched the SEQC (Sequencing Quality Control, known as MAQC III) project to investigate emerging next-generation sequencing (NGS) technologies. This SEQC project established best-practice use of RNA sequencing (RNA-seq) for measuring gene expression, compared RNA-seq performance to microarrays, evaluated the inter-platform reproducibility of NGS technologies, and evaluated the bioinformatic tools increasingly required to analyze large and complex RNA-seq data-sets.