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bioRxiv · 10.1101/077917

AN INTERNATIONAL INTER-LABORATORY DIGITAL PCR STUDY DEMONSTRATES HIGH REPRODUCIBILITY FOR THE MEASUREMENT OF A RARE SEQUENCE VARIANT

Alexandra S Whale·Alison S Devonshire·George Karlin-Neumann·Jack Regan·Leanne Javier·Simon Cowen·Ana Fernandez-Gonzalez·Gerwyn M Jones·Nicholas Redshaw·Julia Beck·Andreas W Berger·Valerie Combaret·Nina Dahl Kjersgaard·Lisa Davis·Frederic Fina·Tim Forshew·Rikke Fredslund Andersen·Silvia Galbiati·Alvaro Gonzalez Hernandez·Charles Haynes·Filip Janku·Roger Lacave·Justin Lee·Vilas Mistry·Alexandra Pender·Anne Pradines·Charlotte Proudhon·Lao Saal·Elliot Stieglitz·Bryan Ulrich·Carole A Foy·Helen Parkes·Svilen Tzonev·Jim Huggett
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Abstract

This study tested the claim that digital PCR (dPCR) can offer highly reproducible quantitative measurements in disparate labs. 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 qPCR or NGS due to the presence of competing wild type sequences and the need for calibration. Using dPCR, eighteen 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 and could enable the reproducible application of molecular stratification to guide therapy, and potentially for molecular diagnostics.\n\nSIGNIFICANCE STATEMENTThe poor reproducibility of molecular diagnostic methods limits their application in part due to the challenges associated with calibration of what are relative measurement approaches. In this study we investigate the performance of one of the only absolute measurement methods available today, digital PCR (dPCR), and demonstrated that when compared across twenty-one laboratories, dPCR has unprecedented reproducibility. These results were achieved when measuring a challenging single nucleotide variant and without calibration to any reference samples. This opens the possibility for dPCR to offer a method to transform reproducibility in the molecular diagnostic field, both by direct use as well as in support of other currently used clinical methods.

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Alexandra S Whale, Alison S Devonshire, George Karlin-Neumann, Jack Regan, Leanne Javier, Simon Cowen, Ana Fernandez-Gonzalez, Gerwyn M Jones, Nicholas Redshaw, Julia Beck, Andreas W Berger, Valerie Combaret, Nina Dahl Kjersgaard, Lisa Davis, Frederic Fina, Tim Forshew, Rikke Fredslund Andersen, Silvia Galbiati, Alvaro Gonzalez Hernandez, Charles Haynes, Filip Janku, Roger Lacave, Justin Lee, Vilas Mistry, Alexandra Pender, Anne Pradines, Charlotte Proudhon, Lao Saal, Elliot Stieglitz, Bryan Ulrich, Carole A Foy, Helen Parkes, Svilen Tzonev, Jim Huggett. 2016-09-28. AN INTERNATIONAL INTER-LABORATORY DIGITAL PCR STUDY DEMONSTRATES HIGH REPRODUCIBILITY FOR THE MEASUREMENT OF A RARE SEQUENCE VARIANT. https://doi.org/10.1101/077917

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