Cambridge Healthtech Institute’s Ann Nguyen recently interviewed Dr. Sarah A. Munro of the National Institute of Standards and Technology (NIST). Dr. Munro shares her presentation “Making and Using RNA Standards: Can You Trust Your Genome-Scale Measurements?” at The Liquid Biopsy Summit, taking place June 21-23, 2017 in San Francisco, California.
“Built-In Truth”: NIST, RNA Standards and the Joint Initiative for Metrology in Biology
Q1: Can you describe the creation and use of RNA standards: their purpose, advantages, and limitations?
The External RNA Controls Consortium (ERCC) RNA spike-in controls are used in assays that are designed to measure RNA molecules such as gene expression microarray or RNA-Seq experiments. The ERCC RNA spike-in controls are added to total RNA samples at the start of a gene expression experiment to assess the technical performance of the measurement process. The library of ERCC controls are produced from a plasmid library, that was developed as a NIST standard reference material (SRM 2374 - DNA Sequence Library for External RNA Controls). ERCC RNA is produced from SRM 2374 using in vitro transcription. The RNA is combined in mixtures with known abundance ratios for use in gene expression experiments.
The ERCC was formed in response to challenges in interpreting gene expression measurement results. Appropriate controls would allow a scientist to confidently assess their results. The ERCC spike-in controls provide a way of assessing assay technical performance regardless of the sample of interest. Mixtures of ERCC controls with known abundance ratios serve as true positive and true negative controls -- “built-in truth” -- to evaluate diagnostic performance. Spike-in RNA controls will either indicate that the technical performance of the assay is consistent with expectation or provide a “red flag” that there is a problem with the assay. The ERCC controls can’t be used to directly evaluate the validity of a biological hypothesis, but by providing information on technical performance of the measurement process, the controls do act as an important indicator of whether one can confidently proceed in evaluating a biological hypothesis.
Q2: What are your activities and goals with the Joint Initiative for Metrology in Biology, as they relate to liquid biopsies and genome-scale measurements?
The Joint Initiative for Metrology in Biology (JIMB) is a partnership between NIST, Stanford University, and industry entrepreneurs. At JIMB we are unified to develop the standards-based measurement innovations that will support science and technology breakthroughs in genomics and synthetic biology. A major focus of JIMB is developing genomic and transcriptomic measurement science infrastructure, which is relevant to liquid biopsies and any other application that requires trustworthy genome-scale measurements. JIMB measurement science products include RNA and DNA reference materials, reference data, such as the Genome in a Bottle variant call set, and analysis tools and software, such as the ‘erccdashboard’ Bioconductor package for evaluating any gene expression experiment using the ERCC controls.
Q3: What kind of impact could all this work have on patient care in the next decade?
We hope that JIMB standards and measurement science innovations will underpin genomic and transcriptomic measurements that impact patient care in the next decade. JIMB is helping to answer important questions including “Are my gene expression measurement results trustworthy?” and “You’ve sequenced my genome; how well did you do?”.
Sarah A. Munro, Ph.D., Team Leader, Genome-Scale Measurements Group, Joint Initiative for Metrology in Biology, National Institute of Standards and Technology (NIST)
Dr. Munro leads a team developing measurement science for genomics and synthetic biology as part of the Joint Initiative for Metrology in Biology (JIMB), a new joint scientific initiative that NIST has launched in partnership with Stanford University and Bay Area industry (http://jimb.stanford.edu). In her work, Dr. Munro develops method validation tools, analysis software, new measurement technologies, and leads JIMB public-private-academic standards development consortia. Dr. Munro received her Ph.D. and BS degrees in Biological and Environmental Engineering from Cornell University.
Learn more about Dr. Munro’s presentation during The Liquid Biopsy Summit.