International Interlaboratory Digital PCR Study Demonstrating High Reproducibility for the Measurement of a Rare Sequence Variant

• Published in: Analytical chemistry (Washington) Vol. 89; no. 3; pp. 1724 - 1733
• Main Authors: Whale, Alexandra S, Devonshire, Alison S, Karlin-Neumann, George, Regan, Jack, Javier, Leanne, Cowen, Simon, Fernandez-Gonzalez, Ana, Jones, Gerwyn M, Redshaw, Nicholas, Beck, Julia, Berger, Andreas W, Combaret, Valérie, Dahl Kjersgaard, Nina, Davis, Lisa, Fina, Frederic, Forshew, Tim, Fredslund Andersen, Rikke, Galbiati, Silvia, González Hernández, Álvaro, Haynes, Charles A, Janku, Filip, Lacave, Roger, Lee, Justin, Mistry, Vilas, Pender, Alexandra, Pradines, Anne, Proudhon, Charlotte, Saal, Lao H, Stieglitz, Elliot, Ulrich, Bryan, Foy, Carole A, Parkes, Helen, Tzonev, Svilen, Huggett, Jim F
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 07.02.2017
• Subjects: Analytical chemistry; Calibration; Cancer; Digital; DNA - chemistry; DNA - metabolism; Genetics; Humans; Laboratories; Markers; Molecules; Polymerase chain reaction; Polymorphism, Single Nucleotide; Proto-Oncogene Proteins p21(ras) - genetics; Real-Time Polymerase Chain Reaction - methods; Reproducibility; Reproducibility of Results; Sequence Analysis, DNA; Stratification; Therapy
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/acs.analchem.6b03980

This study tested the claim that digital PCR (dPCR) can offer highly reproducible quantitative measurements in disparate laboratories. Twenty-one laboratories measured four blinded samples containing different quantities of a KRAS fragment encoding G12D, an important genetic marker for guiding therapy of certain cancers. This marker is challenging to quantify reproducibly using quantitative PCR (qPCR) or next generation sequencing (NGS) due to the presence of competing wild type sequences and the need for calibration. Using dPCR, 18 laboratories were able to quantify the G12D marker within 12% of each other in all samples. Three laboratories appeared to measure consistently outlying results; however, proper application of a follow-up analysis recommendation rectified their data. Our findings show that dPCR has demonstrable reproducibility across a large number of laboratories without calibration. This could enable the reproducible application of molecular stratification to guide therapy and, potentially, for molecular diagnostics.