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Digital PCR as a New Method for Minimal Residual Disease Monitoring and Treatment Free Remission Management in Chronic Myeloid Leukemia Patients: Is It Reliable? HEMATO 2022. [DOI: 10.3390/hemato4010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The effective and sensitive monitoring of Minimal Residual Disease or Measurable Residual Disease (MRD) is a very important aspect in the management of patients affected by hematologic malignancies. The recent availability of new technologies has opened to the improvement of MRD monitoring. It is particularly relevant in patients affected by Chronic Myeloid Leukemia (CML). MRD monitoring is key in the management of CML patients thanks to the efficacy of TKIs therapy. Moreover, the policies of TKIs discontinuation aimed at treatment free remission are strongly based on the good selection of patients eligible for stopping TKIs therapy. The recently described application of digital PCR in CML patients monitoring seems to improve the accuracy and precision in the identification of optimal responders. The present review reports an overview on the application of digital PCR in the monitoring of MRD in CML and its impact on TKIs discontinuation trials and, consequently, on TFR success.
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Galimberti S, Balducci S, Guerrini F, Del Re M, Cacciola R. Digital Droplet PCR in Hematologic Malignancies: A New Useful Molecular Tool. Diagnostics (Basel) 2022; 12:1305. [PMID: 35741115 PMCID: PMC9221914 DOI: 10.3390/diagnostics12061305] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/21/2022] [Accepted: 05/22/2022] [Indexed: 01/27/2023] Open
Abstract
Digital droplet PCR (ddPCR) is a recent version of quantitative PCR (QT-PCR), useful for measuring gene expression, doing clonality assays and detecting hot spot mutations. In respect of QT-PCR, ddPCR is more sensitive, does not need any reference curve and can quantify one quarter of samples already defined as "positive but not quantifiable". In the IgH and TCR clonality assessment, ddPCR recapitulates the allele-specific oligonucleotide PCR (ASO-PCR), being not adapt for detecting clonal evolution, that, on the contrary, does not represent a pitfall for the next generation sequencing (NGS) technique. Differently from NGS, ddPCR is not able to sequence the whole gene, but it is useful, cheaper, and less time-consuming when hot spot mutations are the targets, such as occurs with IDH1, IDH2, NPM1 in acute leukemias or T315I mutation in Philadelphia-positive leukemias or JAK2 in chronic myeloproliferative neoplasms. Further versions of ddPCR, that combine different primers/probes fluorescences and concentrations, allow measuring up to four targets in the same PCR reaction, sparing material, time, and money. ddPCR is also useful for quantitating BCR-ABL1 fusion gene, WT1 expression, donor chimerism, and minimal residual disease, so helping physicians to realize that "patient-tailored therapy" that is the aim of the modern hematology.
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Affiliation(s)
- Sara Galimberti
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Serena Balducci
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Francesca Guerrini
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Marzia Del Re
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Rossella Cacciola
- Department of Clinical and Experimental Medicine, Section of Hemostasis, University of Catania, 95123 Catania, Italy
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3
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Rosvall BR, Kostiuk M, Williams J, Matkin A, Harris J, Seikaly H, O'Connell DA, Biron VL. Utility of droplet digital polymerase chain reaction for TERT and BRAF mutational profiling of thyroid nodules. BMC Cancer 2021; 21:1142. [PMID: 34702207 PMCID: PMC8547072 DOI: 10.1186/s12885-021-08810-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/22/2021] [Indexed: 12/07/2022] Open
Abstract
Background Mutations involving BRAF and TERT are important predictors of disease severity in thyroid cancer, but molecular testing is limited by cost and lack of adequate tissue sample. This study aimed to assess the utility of BRAFV600E and TERT testing using droplet digital PCR (ddPCR) as a diagnostic and prognostic tool for thyroid fine needle aspirate biopsy (FNAB). Methods Patients with thyroid nodules were prospectively enrolled from March 2015 to September 2018. Pre-operative FNAB was collected for standard cytology and molecular testing. BRAFV600E and TERT levels were analyzed by ddPCR. Cytology (Bethesda system) and ddPCR results were correlated to surgical pathology. Results A total of 222 patients were enrolled, of which 124 received thyroid surgery. Pre-operative cytology alone with Bethesda ≥5 was 100% specific and 70% sensitive for malignancy on final surgical pathology. BRAFV600E positivity or TERT overexpression was 100% specific and 60.0% sensitive. Combining cytology (Bethesda ≥5) with BRAFV600E and TERT testing increased the sensitivity of a malignant diagnosis to 80.0%. High TERT levels and/or BRAFV600E was associated with aggressive or advanced stage pathology. Conclusions Combining cytology with ddPCR analysis of BRAFV600E and TERT can improve the diagnostic accuracy of thyroid FNAB, and help predict aggressive pathology. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08810-8.
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Affiliation(s)
- Brandon R Rosvall
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada
| | - Morris Kostiuk
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada
| | - Jordana Williams
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada
| | - Ashlee Matkin
- Division of Plastic and Reconstructive Surgery, Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Jeffrey Harris
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada
| | - Hadi Seikaly
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada
| | - Daniel A O'Connell
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada
| | - Vincent L Biron
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4 Walter Mackenzie Center, 8440 112 St, Edmonton, Alberta, T6G 2B7, Canada.
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4
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Moncada A, Pancrazzi A. Lab tests for MPN. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 366:187-220. [PMID: 35153004 DOI: 10.1016/bs.ircmb.2021.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecular laboratory investigations for myeloproliferative neoplasm (MPN) can ideally be divided into two distincts groups, those for the detection of the BCR-ABL rearrangement (suspect of chronic myeloid leukemia) and those for the variants determination of the driver genes of the negative Philadelphia forms (MPN Ph neg). The BCR-ABL detection is based on RT-Polymerase Chain Reaction techniques and more recently on droplet digital PCR (ddPCR). For this type of analysis, combined with chromosome banding analysis (CBA) and Fluorescent in situ hybridization (FISH), it is essential to quantify BCR-ABL mutated copies by standard curve method. The investigation on driver genes for MPN Ph neg forms includes activity for erythroid forms such as Polycythemia Vera (test JAK2V617F and JAK2 exon 12), for non-erythroid forms such as essential thrombocythemia and myelofibrosis (test JAK2V617F, CALR exon 9, MPL exon 10), for "atypical" ones such as mastocytosis (cKIT D816V test) and for hypereosinophilic syndrome (FIP1L1-PDGFRalpha test). It's crucial to assign prognosis value through calculating allelic burden of JAK2 V617F variant and determining CALR esone 9 variants (type1/1like, type2/2like and atypical ones). A fundamental innovation for investigating triple negative cases for JAK2, CALR, MPL and for providing prognostic score is the use of Next Generation Sequencing panels containing high molecular risk genes as ASXL1, EZH2, TET2, IDH1/IDH2, SRSF2. This technique allows to detect additional or subclonal mutations which are usually acquired in varying sized sub-clones of hematopoietic progenitors. These additional variants have a prognostic significance and should be indagated to exclude false negative cases.
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Affiliation(s)
- Alice Moncada
- Laboratory Medicine Department, Molecular and Clinical Pathology Sector, Azienda USL Toscana Sudest, Ospedale San Donato, Arezzo, Italy
| | - Alessandro Pancrazzi
- Laboratory Medicine Department, Molecular and Clinical Pathology Sector, Azienda USL Toscana Sudest, Ospedale San Donato, Arezzo, Italy.
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5
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Tellinghuisen J. dPCR vs. qPCR: The role of Poisson statistics at low concentrations. Anal Biochem 2020; 611:113946. [DOI: 10.1016/j.ab.2020.113946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/14/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
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6
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Soverini S, Bernardi S, Galimberti S. Molecular Testing in CML between Old and New Methods: Are We at a Turning Point? J Clin Med 2020; 9:E3865. [PMID: 33261150 PMCID: PMC7760306 DOI: 10.3390/jcm9123865] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 12/18/2022] Open
Abstract
Molecular monitoring of minimal residual disease (MRD) and BCR-ABL1 kinase domain (KD) mutation testing have a well consolidated role in the routine management of chronic myeloid leukemia (CML) patients, as they provide precious information for therapeutic decision-making. Molecular response levels are used to define whether a patient has an "optimal", "warning", or "failure" response to tyrosine kinase inhibitor (TKI) therapy. Mutation status may be useful to decide whether TKI therapy should be changed and which alternative TKI (or TKIs) are most likely to be effective. Real-time quantitative polymerase chain reaction (RQ-qPCR) and Sanger sequencing are currently the gold standard for molecular response monitoring and mutation testing, respectively. However, in recent years, novel technologies such as digital PCR (dPCR) and next-generation sequencing (NGS) have been evaluated. Here, we critically describe the main features of these old and novel technologies, provide an overview of the recently published studies assessing the potential clinical value of dPCR and NGS, and discuss how the state of the art might evolve in the next years.
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Affiliation(s)
- Simona Soverini
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology “Lorenzo e Ariosto Seràgnoli”, University of Bologna, 40138 Bologna, Italy;
| | - Simona Bernardi
- Department of Clinical and Experimental Sciences, University of Brescia, Bone Marrow Transplant Unit, ASST Spedali Civili, 25123 Brescia, Italy
- Centro di Ricerca Emato-Oncologica AIL (CREA), ASST Spedali Civili, 25123 Brescia, Italy
| | - Sara Galimberti
- Department of Clinical and Experimental Medicine, Hematology Unit, University of Pisa, 56126 Pisa, Italy;
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Coccaro N, Tota G, Anelli L, Zagaria A, Specchia G, Albano F. Digital PCR: A Reliable Tool for Analyzing and Monitoring Hematologic Malignancies. Int J Mol Sci 2020; 21:ijms21093141. [PMID: 32365599 PMCID: PMC7247671 DOI: 10.3390/ijms21093141] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
The digital polymerase chain reaction (dPCR) is considered to be the third-generation polymerase chain reaction (PCR), as it yields direct, absolute and precise measures of target sequences. dPCR has proven particularly useful for the accurate detection and quantification of low-abundance nucleic acids, highlighting its advantages in cancer diagnosis and in predicting recurrence and monitoring minimal residual disease, mostly coupled with next generation sequencing. In the last few years, a series of studies have employed dPCR for the analysis of hematologic malignancies. In this review, we will summarize these findings, attempting to focus on the potential future perspectives of the application of this promising technology.
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Affiliation(s)
| | | | | | | | | | - Francesco Albano
- Correspondence: ; Tel.: +39-(0)80-5478031; Fax: +39-(0)80-5508369
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8
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La Rocca F, Grieco V, Ruggieri V, Zifarone E, Villani O, Zoppoli P, Russi S, Laurino S, Falco G, Calice G, Marinaccio A, Natalicchio MI, Albano F, Musto P. Superiority of Droplet Digital PCR Over Real-Time Quantitative PCR for JAK2 V617F Allele Mutational Burden Assessment in Myeloproliferative Neoplasms: A Retrospective Study. Diagnostics (Basel) 2020; 10:diagnostics10030143. [PMID: 32150880 PMCID: PMC7151190 DOI: 10.3390/diagnostics10030143] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/11/2022] Open
Abstract
JAK2V617F mutational status is an essential diagnostic index in myeloproliferative neoplasms (MPNs). Although widely used for detection of JAK2 V617F mutation in peripheral blood (PB), sensitive real-time quantitative PCR (qPCR) presents some methodological limitations. Recently, emerging alternative technologies, like digital droplet PCR (ddPCR), have been reported to overcome some of qPCR’s technical drawbacks. The purpose of this study was to compare the diagnostic utility of ddPCR to qPCR for JAK2 V617F detection and quantification in samples from MPNs patients. Sensitivity and specificity of qPCR and ddPCR in the detection of the mutation were assessed by using a calibrator panel of mutated DNA on 195 JAK2 positive MPN samples. Based on our results, ddPCR proved to be a suitable, precise, and sensitive method for detection and quantification of the JAK2 V617F mutation.
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Affiliation(s)
- Francesco La Rocca
- Laboratory of Clinical Research and Advanced Diagnostics, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture (Pz), Italy; (F.L.R.); (V.G.)
| | - Vitina Grieco
- Laboratory of Clinical Research and Advanced Diagnostics, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture (Pz), Italy; (F.L.R.); (V.G.)
| | - Vitalba Ruggieri
- Laboratory of Preclinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata (CROB); 85028 Rionero in Vulture (Pz), Italy; (P.Z.); (S.R.); (S.L.); (G.C.)
- Correspondence:
| | - Emanuela Zifarone
- Trial Office, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture (Pz), Italy;
| | - Oreste Villani
- Hematology and Stem Cell Transplantation Unit, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture (Pz), Italy;
| | - Pietro Zoppoli
- Laboratory of Preclinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata (CROB); 85028 Rionero in Vulture (Pz), Italy; (P.Z.); (S.R.); (S.L.); (G.C.)
| | - Sabino Russi
- Laboratory of Preclinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata (CROB); 85028 Rionero in Vulture (Pz), Italy; (P.Z.); (S.R.); (S.L.); (G.C.)
| | - Simona Laurino
- Laboratory of Preclinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata (CROB); 85028 Rionero in Vulture (Pz), Italy; (P.Z.); (S.R.); (S.L.); (G.C.)
| | - Geppino Falco
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy;
- Biogem, Istituto di Biologia e Genetica Molecolare, Via Camporeale, 83031 Ariano Irpino (AV), Italy
| | - Giovanni Calice
- Laboratory of Preclinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata (CROB); 85028 Rionero in Vulture (Pz), Italy; (P.Z.); (S.R.); (S.L.); (G.C.)
| | - Anna Marinaccio
- Section of Clinic Pathology, OO.RR., 71122 Foggia, Italy; (A.M.); (M.I.N.)
| | | | - Francesco Albano
- Unit of Hematology and Stem Cell Transplantation, AOU Policlinico Consorziale “Giovanni XXIII”, “Aldo Moro” University, 70124 Bari, Italy; (F.A.); (P.M.)
| | - Pellegrino Musto
- Unit of Hematology and Stem Cell Transplantation, AOU Policlinico Consorziale “Giovanni XXIII”, “Aldo Moro” University, 70124 Bari, Italy; (F.A.); (P.M.)
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9
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Izzo B, Gottardi EM, Errichiello S, Daraio F, Baratè C, Galimberti S. Monitoring Chronic Myeloid Leukemia: How Molecular Tools May Drive Therapeutic Approaches. Front Oncol 2019; 9:833. [PMID: 31555590 PMCID: PMC6742705 DOI: 10.3389/fonc.2019.00833] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/13/2019] [Indexed: 12/25/2022] Open
Abstract
More than 15 years ago, imatinib entered into the clinical practice as a "magic bullet"; from that point on, the prognosis of patients affected by chronic myeloid leukemia (CML) became comparable to that of aged-matched healthy subjects. The aims of treatment with tyrosine kinase inhibitors (TKIs) are for complete hematological response after 3 months of treatment, complete cytogenetic response after 6 months, and a reduction of the molecular disease of at least 3 logs after 12 months. Patients who do not reach their goal can switch to another TKI. Thus, the molecular monitoring of response is the main consideration of management of CML patients. Moreover, cases in deep and persistent molecular response can tempt the physician to interrupt treatment, and this "dream" is possible due to the quantitative PCR. After great international effort, today the BCR-ABL1 expression obtained in each laboratory is standardized and expressed as "international scale." This aim has been reached after the establishment of the EUTOS program (in Europe) and the LabNet network (in Italy), the platforms where biologists meet clinicians. In the field of quantitative PCR, the digital PCR is now a new and promising, sensitive and accurate tool. Some authors reported that digital PCR is able to better classify patients in precise "molecular classes," which could lead to a better identification of those cases that will benefit from the interruption of therapy. In addition, digital PCR can be used to identify a point mutation in the ABL1 domain, mutations that are often responsible for the TKI resistance. In the field of resistance, a prominent role is played by the NGS that enables identification of any mutation in ABL1 domain, even at sub-clonal levels. This manuscript reviews how the molecular tools can lead the management of CML patients, focusing on the more recent technical advances.
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Affiliation(s)
- Barbara Izzo
- Department of Clinical Medicine and Surgery, Molecular Biology, University Federico II, Naples, Italy
| | | | - Santa Errichiello
- Department of Clinical Medicine and Surgery, Molecular Biology, University Federico II, Naples, Italy
| | - Filomena Daraio
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Claudia Baratè
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Sara Galimberti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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10
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Galimberti S, Genuardi E, Mazziotta F, Iovino L, Morabito F, Grassi S, Ciabatti E, Guerrini F, Petrini M. The Minimal Residual Disease in Non-Hodgkin's Lymphomas: From the Laboratory to the Clinical Practice. Front Oncol 2019; 9:528. [PMID: 31293969 PMCID: PMC6606710 DOI: 10.3389/fonc.2019.00528] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/31/2019] [Indexed: 01/05/2023] Open
Abstract
Minimal residual disease (MRD) in non-Hodgkin's lymphomas (NHLs) still represents matter of interest and debate: indeed, the new available treatments offer higher rates of complete responses and MRD negativity than in the past, with a positive impact on the long-term survival. Furthermore, the introduction of more sensitive and accurate molecular techniques, such as digital PCR (ddPCR) and the next generation sequencing techniques (NGS), increased the possibility of identifying molecular targets to be followed after therapy (such as rearrangement of immunoglobulins, fusion genes, or mutations). This review focused on how molecular biology can help to detect MRD in different types of NHLs and how MRD can change the clinical practice in 2019. In follicular lymphoma (FL), contamination of the grafts and molecular disease persistence after transplantation represent a negative prognostic factors. The combination of Rituximab or Obinutuzumab with Bendamustine seems to be the most effective way to clear MRD in FL patients receiving chemo-immunotherapy (further studies are in progress), and also 90Yttrium-Ibritumomab-Tiuxetan offers a deep clearance of molecular disease. Finally, molecular MRD can further stratify PET-negative cases, with subjects both PET- and MRD-negative presenting the best outcome. In aggressive lymphomas, MRD has a relevant prognostic power and can represent the platform for immunotherapy (such as CAR-T). In diffuse large B-cell lymphoma (DLBCL), the assessment of MRD in the plasma (where cell-free DNA and exosomes circulate) seems to be more predictive than the bone marrow analysis or peripheral blood mononuclear cells. Finally, NGS technologies could be more useful than the classical "patient allele-specific PCR" because they can identify any possible clone emerging during the treatment or follow-up, even if different from that identified at diagnosis, thus predicting relapse. After all, the present available molecular approaches can move MRD from the bench side to the clinical practice.
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Affiliation(s)
- Sara Galimberti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Elisa Genuardi
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Turin, Italy
| | - Francesco Mazziotta
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,GeNOMEC School of Doctorate, University of Siena, Siena, Italy
| | - Lorenzo Iovino
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,Clinical and Translational Sciences School of Doctorate, University of Pisa, Pisa, Italy
| | - Fortunato Morabito
- Hematology Oncology Department, Augusta Victoria Hospital, East Jerusalem, Israel.,Biotechnology Research Unit, Cosenza, Italy
| | - Susanna Grassi
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,GeNOMEC School of Doctorate, University of Siena, Siena, Italy
| | - Elena Ciabatti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesca Guerrini
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Mario Petrini
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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11
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Digital PCR in Myeloid Malignancies: Ready to Replace Quantitative PCR? Int J Mol Sci 2019; 20:ijms20092249. [PMID: 31067725 PMCID: PMC6540058 DOI: 10.3390/ijms20092249] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 01/13/2023] Open
Abstract
New techniques are on the horizon for the detection of small leukemic clones in both, acute leukemias and myeloproliferative disorders. A promising approach is based on digital polymerase chain reaction (PCR). Digital PCR (dPCR) is a breakthrough technology designed to provide absolute nucleic acid quantification. It is particularly useful to detect a low amount of target and therefore it represents an alternative method for detecting measurable residual disease (MRD). The main advantages are the high precision, the very reliable quantification, the absolute quantification without the need for a standard curve, and the excellent reproducibility. Nowadays the main disadvantages of this strategy are the costs that are still higher than standard qPCR, the lack of standardized methods, and the limited number of laboratories that are equipped with instruments for dPCR. Several studies describing the possibility and advantages of using digital PCR for the detection of specific leukemic transcripts or mutations have already been published. In this review we summarize the available data on the use of dPCR in acute myeloid leukemia and myeloproliferative disorders.
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12
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Palumbo GA, Stella S, Pennisi MS, Pirosa C, Fermo E, Fabris S, Cattaneo D, Iurlo A. The Role of New Technologies in Myeloproliferative Neoplasms. Front Oncol 2019; 9:321. [PMID: 31106152 PMCID: PMC6498877 DOI: 10.3389/fonc.2019.00321] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/09/2019] [Indexed: 12/17/2022] Open
Abstract
The hallmark of BCR-ABL1-negative myeloproliferative neoplasms (MPNs) is the presence of a driver mutation in JAK2, CALR, or MPL gene. These genetic alterations represent a key feature, useful for diagnostic, prognostic and therapeutical approaches. Molecular biology tests are now widely available with different specificity and sensitivity. Recently, the allele burden quantification of driver mutations has become a useful tool, both for prognostication and efficacy evaluation of therapies. Moreover, other sub-clonal mutations have been reported in MPN patients, which are associated with poorer prognosis. ASXL1 mutation appears to be the worst amongst them. Both driver and sub-clonal mutations are now taken into consideration in new prognostic scoring systems and may be better investigated using next generation sequence (NGS) technology. In this review we summarize the value of NGS and its contribution in providing a comprehensive picture of mutational landscape to guide treatment decisions. Finally, discussing the role that NGS has in defining the potential risk of disease development, we forecast NGS as the standard molecular biology technique for evaluating these patients.
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Affiliation(s)
- Giuseppe A Palumbo
- Department of Scienze Mediche, Chirurgiche e Tecnologie Avanzate "G.F. Ingrassia," University of Catania, Catania, Italy
| | - Stefania Stella
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico-Vittorio Emanuele, Catania, Italy.,Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Maria Stella Pennisi
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico-Vittorio Emanuele, Catania, Italy.,Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Cristina Pirosa
- Postgraduate School of Hematology, University of Catania, Catania, Italy
| | - Elisa Fermo
- Hematology Division, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sonia Fabris
- Hematology Division, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniele Cattaneo
- Hematology Division, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandra Iurlo
- Hematology Division, Myeloproliferative Syndromes Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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13
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Milosevic D, Mills JR, Campion MB, Vidal-Folch N, Voss JS, Halling KC, Highsmith WE, Liu MC, Kipp BR, Grebe SKG. Applying Standard Clinical Chemistry Assay Validation to Droplet Digital PCR Quantitative Liquid Biopsy Testing. Clin Chem 2018; 64:1732-1742. [DOI: 10.1373/clinchem.2018.291278] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/23/2018] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Droplet digital PCR (ddPCR) is an emerging technology for quantitative cell-free DNA oncology applications. However, assay performance criteria must be established in a standardized manner to harness this potential. We reasoned that standard protocols used in clinical chemistry assay validation should be able to fill this need.
METHODS
We validated KRAS, EGFR, and BRAF quantitative ddPCR assays based on the Clinical Laboratory Improvement Act regulations for laboratory-developed tests in clinical chemistry and the matching Clinical and Laboratory Standards Institute guidelines. This included evaluation of limit of the blank (LOB), limit of detection (LOD), limit of quantification (LOQ), intraassay and interassay imprecision, analytical range, dilution linearity, accuracy (including comparison with orthogonal platforms), reference range study, interference, and stability studies.
RESULTS
For the ddPCR assays, the LOB was 4 mutant copies, LODs were 12 to 22 copies, and LOQs were 35 to 64 copies. The upper limit of the dynamic range was 30000 copies, and dilutions were linear down to the LOQs with good accuracy of spike recovery of Horizon reference material. Method comparisons with next-generation sequencing and an alternative ddPCR platform showed complete qualitative agreement and quantitative concordance, with slopes of 0.73 to 0.97 and R2s of 0.83 to 0.99. No substantial interferences were discovered. Wild-type copy numbers in plasma ranged from 462 to 6169/mL in healthy individuals.
CONCLUSIONS
Standard clinical chemistry assay validation protocols can be applied to quantitative ddPCR assays. This should facilitate comparison of the performance of different assays and allow establishment of minimal significant change thresholds in monitoring applications.
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Affiliation(s)
- Dragana Milosevic
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN
| | - John R Mills
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN
| | - Michael B Campion
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Noemi Vidal-Folch
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Jesse S Voss
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - W Edward Highsmith
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Minetta C Liu
- Department of Laboratory Meidicne and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN
- Department of Oncology, Division of Medical Oncology Mayo Clinic, Rochester, MN
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Stefan K G Grebe
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN
- Department of Medicine, Division of Endocrinology, Mayo Clinic, Rochester, MN
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14
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Quan PL, Sauzade M, Brouzes E. dPCR: A Technology Review. SENSORS (BASEL, SWITZERLAND) 2018; 18:E1271. [PMID: 29677144 PMCID: PMC5948698 DOI: 10.3390/s18041271] [Citation(s) in RCA: 334] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 04/13/2018] [Accepted: 04/15/2018] [Indexed: 12/17/2022]
Abstract
Digital Polymerase Chain Reaction (dPCR) is a novel method for the absolute quantification of target nucleic acids. Quantification by dPCR hinges on the fact that the random distribution of molecules in many partitions follows a Poisson distribution. Each partition acts as an individual PCR microreactor and partitions containing amplified target sequences are detected by fluorescence. The proportion of PCR-positive partitions suffices to determine the concentration of the target sequence without a need for calibration. Advances in microfluidics enabled the current revolution of digital quantification by providing efficient partitioning methods. In this review, we compare the fundamental concepts behind the quantification of nucleic acids by dPCR and quantitative real-time PCR (qPCR). We detail the underlying statistics of dPCR and explain how it defines its precision and performance metrics. We review the different microfluidic digital PCR formats, present their underlying physical principles, and analyze the technological evolution of dPCR platforms. We present the novel multiplexing strategies enabled by dPCR and examine how isothermal amplification could be an alternative to PCR in digital assays. Finally, we determine whether the theoretical advantages of dPCR over qPCR hold true by perusing studies that directly compare assays implemented with both methods.
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Affiliation(s)
- Phenix-Lan Quan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Martin Sauzade
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA.
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15
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Perricone M, Palandri F, Ottaviani E, Angelini M, Bagli L, Bellesia E, Donati M, Gemmati D, Zucchini P, Mancini S, Marchica V, Trubini S, De Matteis G, Di Zacomo S, Favarato M, Fioroni A, Bolzonella C, Maccari G, Navaglia F, Gatti D, Toffolatti L, Orlandi L, Laloux V, Manfrini M, Galieni P, Giannini B, Tieghi A, Barulli S, Serino ML, Maccaferri M, Scortechini AR, Giuliani N, Vallisa D, Bonifacio M, Accorsi P, Salbe C, Fazio V, Gusella M, Toffoletti E, Salvucci M, Svaldi M, Gherlinzoni F, Cassavia F, Orsini F, Martinelli G. Assessment of the interlaboratory variability and robustness of JAK2V617F mutation assays: A study involving a consortium of 19 Italian laboratories. Oncotarget 2018; 8:32608-32617. [PMID: 28427233 PMCID: PMC5464813 DOI: 10.18632/oncotarget.15940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/22/2017] [Indexed: 11/25/2022] Open
Abstract
To date, a plenty of techniques for the detection of JAK2V617F is used over different laboratories, with substantial differences in specificity and sensitivity. Therefore, to provide reliable and comparable results, the standardization of molecular techniques is mandatory. A network of 19 centers was established to 1) evaluate the inter- and intra-laboratory variability in JAK2V617F quantification, 2) identify the most robust assay for the standardization of the molecular test and 3) allow consistent interpretation of individual patient analysis results. The study was conceived in 3 different rounds, in which all centers had to blindly test DNA samples with different JAK2V617F allele burden (AB) using both quantitative and qualitative assays. The positivity of samples with an AB < 1% was not detected by qualitative assays. Conversely, laboratories performing the quantitative approach were able to determine the expected JAK2V617F AB. Quantitative results were reliable across all mutation loads with moderate variability at low AB (0.1 and 1%; CV = 0.46 and 0.77, respectively). Remarkably, all laboratories clearly distinguished between the 0.1 and 1% mutated samples. In conclusion, a qualitative approach is not sensitive enough to detect the JAK2V617F mutation, especially at low AB. On the contrary, the ipsogen JAK2 MutaQuant CE-IVD kit resulted in a high, efficient and sensitive quantification detection of all mutation loads. This study sets the basis for the standardization of molecular techniques for JAK2V617F determination, which will require the employment of approved operating procedures and the use of certificated standards, such as the recent WHO 1st International Reference Panel for Genomic JAK2V617F.
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Affiliation(s)
- Margherita Perricone
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Francesca Palandri
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Emanuela Ottaviani
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Mario Angelini
- Molecular Hematology Laboratory U.O.C of Hematology Hospital Mazzoni, Ascoli Piceno, Italy
| | - Laura Bagli
- Medical Genetics Unit- Hub Laboratory AUSL Romagna, Pievesestina di Cesena, Italy
| | - Enrica Bellesia
- Imaging and Laboratory Diagnostic Department, Clinical Chemistry and Endocrinology Laboratory, Hematology Unit, Oncology and Technology Department, Hospital S. Maria Nuova, IRCCS, Reggio Emilia, Italy
| | - Meris Donati
- Clinical Pathology Laboratory, A.O. Ospedali Riuniti Marche Nord, Pesaro, Italy
| | - Donato Gemmati
- Center Hemostasis and Thrombosis, Section of Medical Biochemistry, Molecular Biology and Genetics, Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Patrizia Zucchini
- Department of Medical and Surgical Sciences, Division of Hematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefania Mancini
- Clinical Hematology Laboratory, Department of Molecular and Clinical Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Valentina Marchica
- Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Serena Trubini
- Clinical Pathology, Molecular Biology Laboratory, and Hematology/Bone Marrow Transplantation Unit, AUSL Piacenza, Piacenza, Italy
| | - Giovanna De Matteis
- Section of Clinical Biochemistry and Section of Hematology, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Silvia Di Zacomo
- Department of Hematology, Blood Bank and Biotechnology, Ospedale Civile Pescara, Pescara, Italy
| | - Mosè Favarato
- UOS Molecular Diagnostics, Department of Clinical Pathology, ULSS12 Venetian, Venice, Italy
| | - Annamaria Fioroni
- UOC laboratory medicine, P.O. San Salvatore, Sulmona, L'Aquila, Italy
| | - Caterina Bolzonella
- Department of Oncology, Laboratory of Pharmacology and Molecular Biology, ULSS 18, Rovigo, Italy
| | - Giorgia Maccari
- Clinical Hematology, Department of Experimental and Clinical Medical Sciences, University of Udine, Udine, Italy
| | - Filippo Navaglia
- Department of Laboratory Medicine, University-Hospital of Padova, Padova, Italy
| | - Daniela Gatti
- Department of Haematology and BMT, Healthcare Company of South Tyrol, District of Bolzano, Bolzano, Italy
| | - Luisa Toffolatti
- Department of Pathology and Haematology, Treviso General Hospital, Treviso, Italy
| | | | - Vèronique Laloux
- QIAGEN GmbH, Hilden, Germany (Member of The European LeukemiaNet (ELN) Foundation Circle)
| | - Marco Manfrini
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Piero Galieni
- Molecular Hematology Laboratory U.O.C of Hematology Hospital Mazzoni, Ascoli Piceno, Italy
| | - Barbara Giannini
- Medical Genetics Unit- Hub Laboratory AUSL Romagna, Pievesestina di Cesena, Italy
| | - Alessia Tieghi
- Imaging and Laboratory Diagnostic Department, Clinical Chemistry and Endocrinology Laboratory, Hematology Unit, Oncology and Technology Department, Hospital S. Maria Nuova, IRCCS, Reggio Emilia, Italy
| | - Sara Barulli
- Clinical Pathology Laboratory, A.O. Ospedali Riuniti Marche Nord, Pesaro, Italy
| | - Maria Luisa Serino
- Center Hemostasis and Thrombosis, Section of Medical Biochemistry, Molecular Biology and Genetics, Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Monica Maccaferri
- Department of Medical and Surgical Sciences, Division of Hematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Anna Rita Scortechini
- Clinical Hematology Laboratory, Department of Molecular and Clinical Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Nicola Giuliani
- Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Daniele Vallisa
- Clinical Pathology, Molecular Biology Laboratory, and Hematology/Bone Marrow Transplantation Unit, AUSL Piacenza, Piacenza, Italy
| | - Massimiliano Bonifacio
- Section of Clinical Biochemistry and Section of Hematology, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Patrizia Accorsi
- Department of Hematology, Blood Bank and Biotechnology, Ospedale Civile Pescara, Pescara, Italy
| | - Cristina Salbe
- UOS Molecular Diagnostics, Department of Clinical Pathology, ULSS12 Venetian, Venice, Italy
| | - Vinicio Fazio
- UOC laboratory medicine, P.O. San Salvatore, Sulmona, L'Aquila, Italy
| | - Milena Gusella
- Department of Oncology, Laboratory of Pharmacology and Molecular Biology, ULSS 18, Rovigo, Italy
| | - Eleonora Toffoletti
- Clinical Hematology, Department of Experimental and Clinical Medical Sciences, University of Udine, Udine, Italy
| | - Marzia Salvucci
- Medical Genetics Unit- Hub Laboratory AUSL Romagna, Pievesestina di Cesena, Italy
| | - Mirija Svaldi
- Department of Haematology and BMT, Healthcare Company of South Tyrol, District of Bolzano, Bolzano, Italy
| | - Filippo Gherlinzoni
- Department of Pathology and Haematology, Treviso General Hospital, Treviso, Italy
| | | | | | - Giovanni Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
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16
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Perricone M, Polverelli N, Martinelli G, Catani L, Ottaviani E, Zuffa E, Franchini E, Dizdari A, Forte D, Sabattini E, Cavo M, Vianelli N, Palandri F. The relevance of a low JAK2V617F allele burden in clinical practice: a monocentric study. Oncotarget 2018; 8:37239-37249. [PMID: 28422729 PMCID: PMC5514906 DOI: 10.18632/oncotarget.16744] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 03/20/2017] [Indexed: 02/02/2023] Open
Abstract
Since low JAK2V617F allele burden (AB) has been detected also in healthy subjects, its clinical interpretation may be challenging in patients with chronic myeloproliferative neoplasms (MPNs). We tested 1087 subjects for JAK2V617F mutation on suspicion of hematological malignancy. Only 497 (45.7%) patients were positive. Here we present clinical and laboratory parameters of a cohort of 35/497 patients with an AB ≤ 3%. Overall, 22/35 (62.9%) received a WHO-defined diagnosis of MPN and in 14/35 cases (40%) diagnosis was supported by bone marrow (BM) histology (‘’Histology-based’’ diagnosis). In patients that were unable or refused to perform BM evaluation, diagnosis relied on prospective clinical observation (12 cases, 34.3%) and molecular monitoring (6 cases, 17.1%) (‘’Clinical-based’’ or ‘’Molecular-based’’ diagnosis, respectively). In 11/35 (31.4%) patients, a low JAK2V617F AB was not conclusive of MPN. The probability to have a final hematological diagnosis (ET/PV/MF) was higher in patients with thrombocytosis than in patients with polyglobulia (73.7% vs 57.1%, respectively). The detection of AB ≥ 0.8% always corresponded to an overt MPN phenotype. The repetition of JAK2V617F evaluation over time timely detected the spontaneous expansion (11 cases) or reduction (4 cases) of JAK2V617F-positive clones and significantly oriented the diagnostic process. Our study confirms that histology is relevant to discriminate small foci of clonal hematopoiesis with uncertain clinical significance from a full blown disease. Remarkably, our data suggest that a cut-off of AB ≥ 0.8% is very indicative for the presence of a MPN. Monitoring of the AB over time emerged as a convenient and non-invasive method to assess clonal hematopoiesis expansion.
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Affiliation(s)
- Margherita Perricone
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Nicola Polverelli
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Lucia Catani
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Emanuela Ottaviani
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Elisa Zuffa
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Eugenia Franchini
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Arbana Dizdari
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Dorian Forte
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Elena Sabattini
- Haematopathology Unit, Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Michele Cavo
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Nicola Vianelli
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Francesca Palandri
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology 'L. and A. Seràgnoli', University of Bologna, S. Orsola-Malpighi Hospital, Bologna, Italy
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17
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Nystrand CF, Ghanima W, Waage A, Jonassen CM. JAK2 V617F mutation can be reliably detected in serum using droplet digital PCR. Int J Lab Hematol 2017; 40:181-186. [PMID: 29150911 DOI: 10.1111/ijlh.12762] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 10/05/2017] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Detection of the JAK2 V617F mutation is a key step in the diagnosis of myeloproliferative neoplasms (MPN). Sensitive real-time quantitative PCR (qPCR) detection on peripheral blood (PB) is the most widely used method. The main objective of this study was to determine whether serum, the most common material available in archival biobanks, is a good liquid biopsy for detecting and quantifying the JAK2 V617F mutation using droplet digital PCR (ddPCR). METHODS Paired PB and serum samples from 66 patients with MPN were used. Serum samples were frozen at -25°C before analysis. DNA was extracted from 200 μL PB and 400 μL serum, and ddPCR analysis was performed. RESULTS Among the 47 patients with detectable mutation in their PB samples, the overall sensitivity for the detection of JAK2 mutation in serum was of 96% (45 of 47); V617F was detected in all cases where mutation load was above 1%. Our results showed very strong correlation between PB and serum (Spearman r: 0.989, P < .0001). Significantly higher allele burden was detected in serum compared to PB (Wilcoxon signed ranks test, Z = -5.672, P < .0001). CONCLUSION In our study, JAK2 V617F mutation load as low as 1% was reliably detected in serum using ddPCR.
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Affiliation(s)
- C F Nystrand
- Centre for Laboratory medicine, Østfold Hospital Trust, Kalnes, Norway
| | - W Ghanima
- Department of Oncology, Østfold Hospital Trust, Kalnes, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - A Waage
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Haematology, St. Olavs Hospital, Trondheim, Norway
| | - C M Jonassen
- Centre for Laboratory medicine, Østfold Hospital Trust, Kalnes, Norway.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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18
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Finazzi MC, Lussana F, Salmoiraghi S, Spinelli O, Rambaldi A. Detection of driver and subclonal mutations in myelofibrosis: clinical impact on pharmacologic and transplant based treatment strategies. Expert Rev Hematol 2017; 10:627-636. [PMID: 28504024 DOI: 10.1080/17474086.2017.1331125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Myelofibrosis (MF) is the most aggressive form among Philadelphia negative (Ph-) myeloproliferative neoplasms (MPNs). In the last years, the mutational landscape of MF has expanded remarkably by the identification of additional recurrent mutations, called subclonal mutations. Areas covered: Here we describe the available data about the currently identified subclonal mutations and their prognostic value in MF patients. We also review the practical value of including such molecular information in available prognostic models for both outcome prediction and possibly treatment decision with regards to transplant indication. Lastly, we covered the available data on the application of molecular markers for minimal residual disease (MRD) monitoring after transplantation. Expert commentary: The demonstration of the prognostic value of additional mutations suggests to define this molecular profile at diagnosis and when an allogeneic transplant can be advised, particularly in younger patients. The presence of molecular markers might offer the possibility to evaluate the depth of remission and to monitor MRD after transplantation. Prospective clinical studies are needed to validate the use of this molecular data in the routine clinical practice.
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Affiliation(s)
- Maria Chiara Finazzi
- a Hematology and Bone Marrow Transplant Unit, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII , Bergamo , Italy
| | - Federico Lussana
- a Hematology and Bone Marrow Transplant Unit, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII , Bergamo , Italy
| | - Silvia Salmoiraghi
- a Hematology and Bone Marrow Transplant Unit, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII , Bergamo , Italy
| | - Orietta Spinelli
- a Hematology and Bone Marrow Transplant Unit, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII , Bergamo , Italy
| | - Alessandro Rambaldi
- a Hematology and Bone Marrow Transplant Unit, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII , Bergamo , Italy.,b Department of Oncology and Hematology , Università degli Studi di Milano , Milan , Italy
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19
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20
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Guglielmelli P, Pietra D, Pane F, Pancrazzi A, Cazzola M, Vannucchi AM, Tura S, Barosi G. Recommendations for molecular testing in classical Ph1-neg myeloproliferative disorders-A consensus project of the Italian Society of Hematology. Leuk Res 2017; 58:63-72. [PMID: 28460339 DOI: 10.1016/j.leukres.2017.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/26/2017] [Accepted: 04/20/2017] [Indexed: 12/21/2022]
Abstract
The discovery that Philadelphia-negative classical myeloproliferative neoplasms (MPNs) present with several molecular abnormalities, including the mostly represented JAK2V617F mutation, opened new horizons in the diagnosis, prognosis, and monitoring of these disorders. However, the great strides in the knowledge on molecular genetics need parallel progresses on the best approach to methods for detecting and reporting disease-associated mutations, and to shape the most effective and rationale testing pathway in the diagnosis, prognosis and monitoring of MPNs. The MPN taskforce of the Italian Society of Hematology (SIE) assessed the scientific literature and composed a framework of the best, possibly evidence-based, recommendations for optimal molecular methods as well as insights about the applicability and interpretation of those tests in the clinical practice, and clinical decision for testing MPNs patients. The issues dealt with: source of samples and nucleic acid template, the most appropriate molecular abnormalities and related detection methods required for diagnosis, prognosis, and monitoring of MPNs, how to report a diagnostic molecular test, calibration and quality control. For each of these issues, practice recommendations were provided.
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Affiliation(s)
- Paola Guglielmelli
- CRIMM-Centro Ricerca e Innovazione delle Malattie Mieloproliferative, Azienda Ospedaliera-Universitaria Careggi, Florence, Italy; Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Daniela Pietra
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | - Alessandro Pancrazzi
- CRIMM-Centro Ricerca e Innovazione delle Malattie Mieloproliferative, Azienda Ospedaliera-Universitaria Careggi, Florence, Italy; Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Mario Cazzola
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Department of Haematology Oncology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia, Italy
| | - Alessandro M Vannucchi
- CRIMM-Centro Ricerca e Innovazione delle Malattie Mieloproliferative, Azienda Ospedaliera-Universitaria Careggi, Florence, Italy; Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Giovanni Barosi
- Center for the Study of Myelofibrosis, Biotechnology Research Area, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico S. Matteo, Pavia, Italy.
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21
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Isaac A, Kostiuk M, Zhang H, Lindsay C, Makki F, O'Connell DA, Harris JR, Cote DWJ, Seikaly H, Biron VL. Ultrasensitive detection of oncogenic human papillomavirus in oropharyngeal tissue swabs. J Otolaryngol Head Neck Surg 2017; 46:5. [PMID: 28088212 PMCID: PMC5237494 DOI: 10.1186/s40463-016-0177-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/06/2016] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The incidence of oropharyngeal squamous cell carcinoma (OPSCC) caused by oncogenic human papillomavirus (HPV) is rising worldwide. HPV-OPSCC is commonly diagnosed by RT-qPCR of HPV E6 and E7 oncoproteins or by p16 immunohistochemistry (IHC). Droplet digital PCR (ddPCR) has been recently reported as an ultra-sensitive and highly precise method of nucleic acid quantification for biomarker analysis. To validate the use of a minimally invasive assay for detection of oncogenic HPV based on oropharyngeal swabs using ddPCR. Secondary objectives were to compare the accuracy of ddPCR swabs to fresh tissue p16 IHC and RT-qPCR, and to compare the cost of ddPCR with p16 IHC. METHODS We prospectively included patients with p16+ oral cavity/oropharyngeal cancer (OC/OPSCC), and two control groups: p16- OC/OPSCC patients, and healthy controls undergoing tonsillectomy. All underwent an oropharyngeal swab with ddPCR for quantitative detection of E6 and E7 mRNA. Surgical specimens had p16 IHC performed. Agreement between ddPCR and p16 IHC was determined for patients with p16 positive and negative OC/OPSCC as well as for healthy control patients. The sensitivity and specificity of ddPCR of oropharyngeal swabs were calculated against p16 IHC for OPSCC. RESULTS 122 patients were included: 36 patients with p16+OPSCC, 16 patients with p16-OPSCC, 4 patients with p16+OCSCC, 41 patients with p16-OCSCC, and 25 healthy controls. The sensitivity and specificity of ddPCR of oropharyngeal swabs against p16 IHC were 92 and 98% respectively, using 20-50 times less RNA than that required for conventional RT-qPCR. Overall agreement between ddPCR of tissue swabs and p16 of tumor tissue was high at ĸ = 0.826 [0.662-0.989]. CONCLUSION Oropharyngeal swabs analyzed by ddPCR is a quantitative, rapid, and effective method for minimally invasive oncogenic HPV detection. This assay represents the most sensitive and accurate mode of HPV detection in OPSCC without a tissue biopsy in the available literature.
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Affiliation(s)
- Andre Isaac
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada
| | - Morris Kostiuk
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada
| | - Han Zhang
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada
| | - Cameron Lindsay
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada.,, 1E4 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada
| | - Fawaz Makki
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada
| | - Daniel A O'Connell
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada.,, 1E4 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada
| | - Jeffrey R Harris
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada.,, 1E4.29 WMC 8440 112 Street, Edmonton, AB, T6G 2A1, Canada
| | - David W J Cote
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada.,, 1E4 WMC 8440 112 Street, Edmonton, AB, T6G 2A1, Canada
| | - Hadi Seikaly
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada
| | - Vincent L Biron
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada.
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Usseglio F, Beaufils N, Calleja A, Raynaud S, Gabert J. Detection of CALR and MPL Mutations in Low Allelic Burden JAK2 V617F Essential Thrombocythemia. J Mol Diagn 2017; 19:92-98. [DOI: 10.1016/j.jmoldx.2016.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 08/05/2016] [Accepted: 08/12/2016] [Indexed: 12/11/2022] Open
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Monitoring Minimal Residual Disease in the Myeloproliferative Neoplasms: Current Applications and Emerging Approaches. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7241591. [PMID: 27840830 PMCID: PMC5093244 DOI: 10.1155/2016/7241591] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/05/2016] [Indexed: 11/18/2022]
Abstract
The presence of acquired mutations within the JAK2, CALR, and MPL genes in the majority of patients with myeloproliferative neoplasms (MPN) affords the opportunity to utilise these mutations as markers of minimal residual disease (MRD). Reduction of the mutated allele burden has been reported in response to a number of therapeutic modalities including interferon, JAK inhibitors, and allogeneic stem cell transplantation; novel therapies in development will also require assessment of efficacy. Real-time quantitative PCR has been widely adopted for recurrent point mutations with assays demonstrating the specificity, sensitivity, and reproducibility required for clinical utility. More recently, approaches such as digital PCR have demonstrated comparable, if not improved, assay characteristics and are likely to play an increasing role in MRD monitoring. While next-generation sequencing is increasingly valuable as a tool for diagnosis of MPN, its role in the assessment of MRD requires further evaluation.
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Guerrini F, Paolicchi M, Ghio F, Ciabatti E, Grassi S, Salehzadeh S, Ercolano G, Metelli MR, Del Re M, Iovino L, Petrini I, Carulli G, Cecconi N, Rousseau M, Cervetti G, Galimberti S. The Droplet Digital PCR: A New Valid Molecular Approach for the Assessment of B-RAF V600E Mutation in Hairy Cell Leukemia. Front Pharmacol 2016; 7:363. [PMID: 27790140 PMCID: PMC5061817 DOI: 10.3389/fphar.2016.00363] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 09/20/2016] [Indexed: 12/22/2022] Open
Abstract
Hairy cell leukemia (HCL) is a chronic lymphoproliferative B-cell disorder where the B-RAF V600E mutation has been recently detected, as reported for solid neoplasias but not for other B-cell lymphomas. The digital droplet PCR (dd-PCR) is a molecular technique that, without standard references, is able to accurately quantitate DNA mutations. ddPCR could be an useful instrument for the detection of the B-RAF V600E mutation in HCL, where the minimal residual disease monitoring is fundamental for planning a patients-targeted treatment in the era of new anti-CD20 and anti-RAF compounds. This retrospective study enrolled 47 patients observed at the Hematology Unit of the University of Pisa, Italy, from January 2005 to January 2014: 27 patients were affected by “classic” HCL, two by the variant HCL (vHCL), and 18 by splenic marginal zone lymphoma (SMZL). The aim of the study was to compare dd-PCR to “classic” quantitative PCR (QT-PCR) in terms of sensitivity and specificity and to demonstrate its possible use in HCL. Results showed that: (1) the sensitivity of dd-PCR is about half a logarithm superior to QT-PCR (5 × 10-5 vs. 2.5 × 10-4), (2) the specificity of the dd-PCR is comparable to QT-PCR (no patient with marginal splenic lymphoma or HCL variant resulted mutated), (3) its high sensitivity would allow to use dd-PCR in the monitoring of MRD. At the end of treatment, among patients in complete remission, 33% were still MRD-positive by dd-PCR versus 28% by QT-PCR versus 11% by the evaluation of the B-cell clonality, after 12 months, dd-PCR was comparable to QT-PCR and both detected the B-RAF mutation in 15% of cases defined as MRD-negative by IgH rearrangement. Moreover, (4) the feasibility and the costs of dd-PCR are comparable to those of QT-PCR. In conclusion, our study supports the introduction of dd-PCR in the scenario of HCL, also during the follow-up.
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Affiliation(s)
- Francesca Guerrini
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa Pisa, Italy
| | - Matteo Paolicchi
- UO hematology, Azienda Ospedaliero-Universitaria Pisana Pisa, Italy
| | - Francesco Ghio
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa Pisa, Italy
| | - Elena Ciabatti
- UO hematology, Azienda Ospedaliero-Universitaria Pisana Pisa, Italy
| | - Susanna Grassi
- Section of Hematology, Department of Clinical and Experimental Medicine, University of PisaPisa, Italy; GeNoMEC, University of SienaSiena, Italy
| | - Serena Salehzadeh
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa Pisa, Italy
| | - Giacomo Ercolano
- UO hematology, Azienda Ospedaliero-Universitaria Pisana Pisa, Italy
| | - Maria R Metelli
- UO hematology, Azienda Ospedaliero-Universitaria Pisana Pisa, Italy
| | - Marzia Del Re
- Clinical Pharmacology and Pharmacogenetic Unit, Department of Clinical and Experimental Medicine, University of Pisa Pisa, Italy
| | - Lorenzo Iovino
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa Pisa, Italy
| | - Iacopo Petrini
- Section of Pathology, Department of Translational Medicine and New Technologies, University of Pisa Pisa, Italy
| | - Giovanni Carulli
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa Pisa, Italy
| | - Nadia Cecconi
- UO hematology, Azienda Ospedaliero-Universitaria Pisana Pisa, Italy
| | - Martina Rousseau
- UO hematology, Azienda Ospedaliero-Universitaria Pisana Pisa, Italy
| | - Giulia Cervetti
- UO hematology, Azienda Ospedaliero-Universitaria Pisana Pisa, Italy
| | - Sara Galimberti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa Pisa, Italy
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Olmedillas López S, García-Olmo DC, García-Arranz M, Guadalajara H, Pastor C, García-Olmo D. KRAS G12V Mutation Detection by Droplet Digital PCR in Circulating Cell-Free DNA of Colorectal Cancer Patients. Int J Mol Sci 2016; 17:484. [PMID: 27043547 PMCID: PMC4848940 DOI: 10.3390/ijms17040484] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 03/21/2016] [Accepted: 03/24/2016] [Indexed: 12/14/2022] Open
Abstract
KRAS mutations are responsible for resistance to anti-epidermal growth factor receptor (EGFR) therapy in colorectal cancer patients. These mutations sometimes appear once treatment has started. Detection of KRAS mutations in circulating cell-free DNA in plasma (“liquid biopsy”) by droplet digital PCR (ddPCR) has emerged as a very sensitive and promising alternative to serial biopsies for disease monitoring. In this study, KRAS G12V mutation was analyzed by ddPCR in plasma DNA from 10 colorectal cancer patients and compared to six healthy donors. The percentage of KRAS G12V mutation relative to wild-type sequences in tumor-derived DNA was also determined. KRAS G12V mutation circulating in plasma was detected in 9 of 10 colorectal cancer patients whose tumors were also mutated. Colorectal cancer patients had 35.62 copies of mutated KRAS/mL plasma, whereas in healthy controls only residual copies were found (0.62 copies/mL, p = 0.0066). Interestingly, patients with metastatic disease showed a significantly higher number of mutant copies than M0 patients (126.25 versus 9.37 copies/mL, p = 0.0286). Wild-type KRAS was also significantly elevated in colorectal cancer patients compared to healthy controls (7718.8 versus 481.25 copies/mL, p = 0.0002). In conclusion, KRAS G12V mutation is detectable in plasma of colorectal cancer patients by ddPCR and could be used as a non-invasive biomarker.
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Affiliation(s)
- Susana Olmedillas López
- Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid 28040, Spain.
| | - Dolores C García-Olmo
- Experimental Research Unit, General University Hospital of Albacete, Albacete 02006, Spain.
| | - Mariano García-Arranz
- Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid 28040, Spain.
- Department of Surgery, School of Medicine, Autónoma University of Madrid, Madrid 28029, Spain.
| | - Héctor Guadalajara
- Department of Surgery, School of Medicine, Autónoma University of Madrid, Madrid 28029, Spain.
- Department of General Surgery, General Hospital of Villalba, Madrid 28400, Spain.
| | - Carlos Pastor
- Department of Surgery, Fundación Jiménez Díaz University Hospital, Madrid 28040, Spain.
| | - Damián García-Olmo
- Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid 28040, Spain.
- Department of Surgery, School of Medicine, Autónoma University of Madrid, Madrid 28029, Spain.
- Department of Surgery, Fundación Jiménez Díaz University Hospital, Madrid 28040, Spain.
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Biron VL, Kostiuk M, Isaac A, Puttagunta L, O'Connell DA, Harris J, Côté DWJ, Seikaly H. Detection of human papillomavirus type 16 in oropharyngeal squamous cell carcinoma using droplet digital polymerase chain reaction. Cancer 2016; 122:1544-51. [PMID: 26989832 DOI: 10.1002/cncr.29976] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/01/2015] [Accepted: 12/22/2015] [Indexed: 12/22/2022]
Abstract
BACKGROUND The incidence of oropharyngeal squamous cell carcinoma caused by oncogenic HPV (HPV-OPSCC) is rising worldwide. HPV-OPSCC is commonly diagnosed by RT-qPCR of HPV-16 E6 and E7 oncoproteins or by cyclin-dependent kinase inhibitor 2A, multiple tumor suppressor 1 (p16) immunohistochemistry (IHC). Droplet digital PCR (ddPCR) has been recently reported as ultra-sensitive and highly precise method of nucleic acid quantification for biomarker analysis. We aimed to validate this method for the detection of HPV-16 E6 and E7 in HPV-OPSCC. METHODS Participants were recruited from January 2015-November 2015 at initial presentation to the University of Alberta Head and Neck Oncology Clinic. RNA was extracted, purified and quantified from prospectively collected participant tissues, and ddPCR was performed with fluorescent probes detecting HPV-16 E6 and E7. Results from ddPCR were compared with p16 IHC performed by clinical pathology as standard of care. RESULTS Head and neck tissues were prospectively obtained from 68 participants including 29 patients with OPSCC, 29 patients with non-OPSCC and 10 patients without carcinoma. 79.2% of patients with OPSCC were p16 positive. The sensitivity and specificity of ddPCR HPV E6/E7 compared with p16 IHC in OPSCC was 91.3 and 100%, respectively. The amount of target RNA used was ≤1 ng, 20-50 times lower than reported by other for RT-qPCR HPV E6/E7. CONCLUSIONS The ddPCR of HPV E6/E7 is a novel and highly specific method of detecting HPV-16 in OPSCC. Cancer 2016;122:1544-51. © 2016 American Cancer Society.
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Affiliation(s)
- Vincent L Biron
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery University of Alberta, Edmonton, Alberta, Canada
| | - Morris Kostiuk
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery University of Alberta, Edmonton, Alberta, Canada
| | - Andre Isaac
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery University of Alberta, Edmonton, Alberta, Canada
| | - Lakshmi Puttagunta
- Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel A O'Connell
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery University of Alberta, Edmonton, Alberta, Canada
| | - Jeffrey Harris
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery University of Alberta, Edmonton, Alberta, Canada
| | - David W J Côté
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery University of Alberta, Edmonton, Alberta, Canada
| | - Hadi Seikaly
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery University of Alberta, Edmonton, Alberta, Canada
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Synovial Sarcoma Microvesicles Harbor the SYT-SSX Fusion Gene Transcript: Comparison of Different Methods of Detection and Implications in Biomarker Research. Stem Cells Int 2016; 2016:6146047. [PMID: 27069481 PMCID: PMC4812493 DOI: 10.1155/2016/6146047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/31/2016] [Accepted: 02/15/2016] [Indexed: 01/07/2023] Open
Abstract
Background. Synovial sarcoma is an aggressive soft-tissue malignancy. This study examines the presence of the SYT-SSX fusion transcript in synovial sarcoma microvesicles as well as its potential role as a biomarker for synovial sarcoma. Patients and Methods. Microvesicle release of synovial sarcoma cells was examined by transmission electron microscopy. RNA-content was analyzed by qPCR, nested PCR, nested qPCR, and droplet digital PCR to compare their sensitivity for detection of the SYT-SSX fusion gene transcript. Whole blood RNA, RNA of mononuclear cells, and microvesicle RNA of synovial sarcoma patients were analyzed for the presence of the fusion gene transcripts. Results. Electron microscopic analysis revealed synovial sarcoma cells releasing membrane-enclosed microvesicles. In vitro, the SYT-SSX fusion gene transcript was detected in both synovial sarcoma cells and microvesicles. Nested qPCR proved to be the most sensitive in detecting the SYT-SSX fusion gene mRNA. In contrast, the fusion gene transcript was not detected in peripheral blood cells and microvesicles of synovial sarcoma patients. Conclusion. Synovial sarcoma cells release microvesicles harboring the SYT-SSX fusion transcript. Nested qPCR proved to be the most sensitive in detecting the SYT-SSX fusion gene mRNA; however, more sensitive assays are needed to detect cancer-specific microvesicles in the peripheral blood of cancer patients.
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