1. Multiplex Detection of Rare Mutations by Picoliter Droplet Based Digital PCR: Sensitivity and Specificity Considerations
- Author
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Elizabeth Fabre, Coren A. Milbury, Fanny Garlan, Audrey Didelot, Eleonora Zonta, Karla Perez-Toralla, Nicolas Pécuchet, Ouriel Caen, Valérie Taly, Pierre Laurent-Puig, Hélène Blons, Médecine Personnalisée, Pharmacogénomique, Optimisation Thérapeutique (MEPPOT - U1147), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Sorbonne Paris Cité (USPC), Département d'oncologie médicale [Centre Georges-François Leclerc], Centre Régional de Lutte contre le cancer Georges-François Leclerc [Dijon] (UNICANCER/CRLCC-CGFL), UNICANCER-UNICANCER, RainDance Technologies, Inc. [Lexington, MA, USA], Service de biochimie [AP-HP Hôpital Européen Georges Pompidou], Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), This work was supported by the Ministère de l’Enseignement Supérieur et de la Recherche, the Université Paris-Descartes, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé et de la Recherche Médicale (INSERM), the Institut National du Cancer (INCA, no. 2009-1-RT-03-US-1 and 2009-RT-03-UP5-1), the Agence Nationale de la Recherche (ANR Nanobiotechnologies, no. ANR-10-NANO-0002-09), the SIRIC CARPEM and canceropole funding (no.2011-1 LABEL-UP5-2). Eleonora Zonta receives salary through the INSERM Physicancer program (no. PC201423). Fanny Garlan thanks the Fondation Servier for a fellowship within the Frontiers in Life Science PhD program (FdV). Karla Perez-Toralla receives salary through the Merieux Institution (Merieux Institute Advanced research Grant to VT/PLP). Ouriel Caen receives salary through the Association pour la recherche contre le cancer (ARC, no. SL220100601375)., and TALY, Valerie
- Subjects
0301 basic medicine ,Lung Neoplasms ,Physiology ,[SDV]Life Sciences [q-bio] ,DNA Mutational Analysis ,Gene Identification and Analysis ,Cancer Treatment ,lcsh:Medicine ,Artificial Gene Amplification and Extension ,medicine.disease_cause ,Polymerase Chain Reaction ,Lung and Intrathoracic Tumors ,0302 clinical medicine ,Medicine and Health Sciences ,Multiplex ,Digital polymerase chain reaction ,lcsh:Science ,DNA extraction ,Multidisciplinary ,DNA, Neoplasm ,Hematology ,3. Good health ,Body Fluids ,[SDV] Life Sciences [q-bio] ,ErbB Receptors ,Blood ,Oncology ,030220 oncology & carcinogenesis ,KRAS ,Anatomy ,Research Article ,Context (language use) ,[SDV.CAN]Life Sciences [q-bio]/Cancer ,Computational biology ,Biology ,Research and Analysis Methods ,Sensitivity and Specificity ,Blood Plasma ,Proto-Oncogene Proteins p21(ras) ,03 medical and health sciences ,Extraction techniques ,[SDV.CAN] Life Sciences [q-bio]/Cancer ,Multiplex polymerase chain reaction ,medicine ,[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Genetics ,Humans ,Point Mutation ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Molecular Biology Techniques ,Mutation Detection ,Molecular Biology ,COLD-PCR ,lcsh:R ,Biology and Life Sciences ,Cancers and Neoplasms ,Molecular biology ,030104 developmental biology ,Mutation ,lcsh:Q ,Tumor Suppressor Protein p53 ,Multiplex Polymerase Chain Reaction - Abstract
International audience; In cancer research, the accuracy of the technology used for biomarkers detection is remarkably important. In this context, digital PCR represents a highly sensitive and reproducible method that could serve as an appropriate tool for tumor mutational status analysis. In particular, droplet-based digital PCR approaches have been developed for detection of tumor-specific mutated alleles within plasmatic circulating DNA. Such an approach calls for the development and validation of a very significant quantity of assays, which can be extremely costly and time consuming. Herein, we evaluated assays for the detection and quantification of various mutations occurring in three genes often misregulated in cancers: the epidermal growth factor receptor (EGFR), the v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) and the Tumoral Protein p53 (TP53) genes. In particular, commercial competitive allele-specific TaqMan® PCR (castPCR™) technology, as well as TaqMan® and ZEN™ assays, have been evaluated for EGFR p.L858R, p.T790M, p.L861Q point mutations and in-frame deletions Del19. Specificity and sensitivity have been determined on cell lines DNA, plasmatic circulating DNA of lung cancer patients or Horizon Diagnostics Reference Standards. To show the multiplexing capabilities of this technology, several multiplex panels for EGFR (several three- and four-plexes) have been developed, offering new "ready-to-use" tests for lung cancer patients.
- Published
- 2016
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