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Kaprou GD, Papadopoulos V, Papageorgiou DP, Kefala I, Papadakis G, Gizeli E, Chatzandroulis S, Kokkoris G, Tserepi A. Ultrafast, low-power, PCB manufacturable, continuous-flow microdevice for DNA amplification. Anal Bioanal Chem 2019; 411:5297-5307. [PMID: 31161322 DOI: 10.1007/s00216-019-01911-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/25/2019] [Accepted: 05/09/2019] [Indexed: 12/12/2022]
Abstract
The design and fabrication of a continuous-flow μPCR device with very short amplification time and low power consumption are presented. Commercially available, 4-layer printed circuit board (PCB) substrates are employed, with in-house designed yet industrially manufactured embedded Cu micro-resistive heaters lying at very close distance from the microfluidic network, where DNA amplification takes place. The 1.9-m-long microchannel in combination with desirably high flow velocities (for fast amplification) challenged the robustness of the sealing that was overcome with the development of a novel bonding method rendering the microdevice robust even at extreme pressure drops (12 bars). The proposed fabrication methods are PCB compatible, allowing for mass and reliable production of the μPCR device in the established PCB industry. The μPCR chip was successfully validated during the amplification of two different DNA fragments (and with different target DNA copies) corresponding to the exon 20 of the BRCA1 gene, and to the plasmid pBR322, a commonly used cloning vector in E. coli. Successful DNA amplification was demonstrated at total reaction times down to 2 min, with a power consumption of 2.7 W, rendering the presented μPCR one of the fastest and lowest power-consuming devices, suitable for implementation in low-resource settings. Detailed numerical calculations of the DNA residence time distributions, within an acceptable temperature range for denaturation, annealing, and extension, performed for the first time in the literature, provide useful information regarding the actual on-chip PCR protocol and justify the maximum volumetric flow rate for successful DNA amplification. The calculations indicate that the shortest amplification time is achieved when the device is operated at its enzyme kinetic limit (i.e., extension rate). Graphical abstract.
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Affiliation(s)
- Georgia D Kaprou
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, Patr. Gregoriou E' and 27 Neapoleos Str., PO Box 60037, 15341, Agia Paraskevi, Attica, Greece.,Department of Biology, University of Crete, Voutes, 70013, Heraklion, Greece
| | - Vasileios Papadopoulos
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, Patr. Gregoriou E' and 27 Neapoleos Str., PO Box 60037, 15341, Agia Paraskevi, Attica, Greece
| | - Dimitris P Papageorgiou
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, Patr. Gregoriou E' and 27 Neapoleos Str., PO Box 60037, 15341, Agia Paraskevi, Attica, Greece.,Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ioanna Kefala
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, Patr. Gregoriou E' and 27 Neapoleos Str., PO Box 60037, 15341, Agia Paraskevi, Attica, Greece
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - Electra Gizeli
- Department of Biology, University of Crete, Voutes, 70013, Heraklion, Greece.,Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - Stavros Chatzandroulis
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, Patr. Gregoriou E' and 27 Neapoleos Str., PO Box 60037, 15341, Agia Paraskevi, Attica, Greece
| | - George Kokkoris
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, Patr. Gregoriou E' and 27 Neapoleos Str., PO Box 60037, 15341, Agia Paraskevi, Attica, Greece.
| | - Angeliki Tserepi
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, Patr. Gregoriou E' and 27 Neapoleos Str., PO Box 60037, 15341, Agia Paraskevi, Attica, Greece.
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Jaure O, Alonso EN, Braico DA, Nieto A, Orozco M, Morelli C, Ferro AM, Barutta E, Vincent E, Martínez D, Martínez I, Maegli MI, Frizza A, Kowalyzyn R, Salvadori M, Ginestet P, Gonzalez Donna ML, Balogh GA. BRCA1 polymorphism in breast cancer patients from Argentina. Oncol Lett 2014; 9:845-850. [PMID: 25624909 PMCID: PMC4301546 DOI: 10.3892/ol.2014.2772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 04/16/2014] [Indexed: 01/19/2023] Open
Abstract
Breast cancer is the most common type of cancer in females in Argentina, with an incidence rate similar to that in the USA. However, the contribution of the BRCA1 or BRCA2 mutation in breast cancer incidence has not yet been investigated in Argentina. In order to evaluate which BRCA1 polymorphisms or mutations characterize female breast cancer in Argentina, the current study enrolled 206 females with breast cancer from several hospitals from the southeast of Argentina. A buccal smear sample was obtained in duplicate from each patient and the DNA samples were processed for polymorphism analysis using the single-strand conformational polymorphism technique. The polymorphisms in BRCA1 were investigated using a combination of 15 primers to analyze exons 2, 3, 5, 20 and 11 (including the 11.1 to 11.12 regions). The BRCA1 mutations were confirmed by direct sequencing. Samples were successfully examined from 154 females and, among these, 16 mutations were identified in the BRCA1 gene representing 13.9% of the samples analyzed. One patient was identified with a polymorphism in exon 2 (0.86%), four in exon 20 (3.48%), four in exon 11.3 (3.48%), one in exon 11.7 (0.86%), two in exon 11.8 (1.74%), one in exon 11.10 (0.86%) and one in exon 11.11 (0.86%). The most prevalent alteration in BRCA1 was located in exon 11 (11 out of 16 patients; 68.75%). The objective of our next study is to evaluate the prevalence of mutations in the BRCA2 gene and analyze the BRCA1 gene in the healthy relatives of BRCA1 mutation carriers.
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Affiliation(s)
- Omar Jaure
- Biotechnology Laboratory, Center of Research and Technology, CERZOS-CONICET, Bahía Blanca, Buenos Aires 8000, Argentina
| | - Eliana N Alonso
- Biotechnology Laboratory, Center of Research and Technology, CERZOS-CONICET, Bahía Blanca, Buenos Aires 8000, Argentina
| | - Diego Aguilera Braico
- Biotechnology Laboratory, Center of Research and Technology, CERZOS-CONICET, Bahía Blanca, Buenos Aires 8000, Argentina
| | - Alvaro Nieto
- Biotechnology Laboratory, Center of Research and Technology, CERZOS-CONICET, Bahía Blanca, Buenos Aires 8000, Argentina
| | - Manuela Orozco
- Biotechnology Laboratory, Center of Research and Technology, CERZOS-CONICET, Bahía Blanca, Buenos Aires 8000, Argentina
| | - Cecilia Morelli
- Biotechnology Laboratory, Center of Research and Technology, CERZOS-CONICET, Bahía Blanca, Buenos Aires 8000, Argentina
| | - Alejandro M Ferro
- South Regional Italian Hospital, Bahía Blanca, Buenos Aires 8000, Argentina
| | - Elena Barutta
- Female Medical Institute MEDIFEM, Dr Leonidas Lucero's Hospital, Bahía Blanca, Buenos Aires 8000, Argentina
| | - Esteban Vincent
- Lavalle Institute of Diagnostics, Dr Leonidas Lucero's Hospital, Bahía Blanca, Buenos Aires 8000, Argentina
| | - Domingo Martínez
- Gynecology Services, Dr Leonidas Lucero's Hospital, Bahía Blanca, Buenos Aires 8000, Argentina
| | - Ignacio Martínez
- Gynecology Services, Dr Leonidas Lucero's Hospital, Bahía Blanca, Buenos Aires 8000, Argentina
| | - Maria Ines Maegli
- Gynecology Services, Dr Leonidas Lucero's Hospital, Bahía Blanca, Buenos Aires 8000, Argentina
| | - Alejandro Frizza
- Lavalle Institute of Diagnostics, Dr Leonidas Lucero's Hospital, Bahía Blanca, Buenos Aires 8000, Argentina
| | | | | | - Paul Ginestet
- Pigue Municipal's Hospital, Pigue, Buenos Aires 8170, Argentina
| | | | - Gabriela A Balogh
- Biotechnology Laboratory, Center of Research and Technology, CERZOS-CONICET, Bahía Blanca, Buenos Aires 8000, Argentina
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Zhou L, Palais RA, Ye F, Chen J, Montgomery JL, Wittwer CT. Symmetric snapback primers for scanning and genotyping of the cystic fibrosis transmembrane conductance regulator gene. Clin Chem 2013; 59:1052-61. [PMID: 23503723 DOI: 10.1373/clinchem.2013.202689] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND High-resolution melting of PCR products is an efficient and analytically sensitive method to scan for sequence variation, but detected variants must still be identified. Snapback primer genotyping uses a 5' primer tail complementary to its own extension product to genotype the resulting hairpin via melting. If the 2 methods were combined to analyze the same PCR product, the residual sequencing burden could be reduced or even eliminated. METHODS The 27 exons and neighboring splice sites of the CFTR [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)] gene were amplified by the PCR in 39 fragments. Primers included snapback tails for genotyping 7 common variants and the 23 CFTR mutations recommended for screening by the American College of Medical Genetics. After symmetric PCR, the amplicons were analyzed by high-resolution melting to scan for variants. Then, a 5-fold excess of H2O was added to each reaction to produce intramolecular hairpins for snapback genotyping by melting. Each melting step required <10 min. Of the 133 DNA samples analyzed, 51 were from CFTR patient samples or cell lines. RESULTS As expected, the analytical sensitivity of heterozygote detection in blinded studies was 100%. Snapback genotyping reduced the need for sequencing from 7.9% to 0.5% of PCR products; only 1 amplicon every 5 patients required sequencing to identify nonanticipated rare variants. We identified 2 previously unreported variants: c.3945A>G and c.4243-5C>T. CONCLUSIONS CFTR analysis by sequential scanning and genotyping with snapback primers is a good match for targeted clinical genetics, for which high analytical accuracy and rapid turnaround times are important.
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Affiliation(s)
- Luming Zhou
- Department of Pathology, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA.
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Hondow HL, Fox SB, Mitchell G, Scott RJ, Beshay V, Wong SQ, Dobrovic A. A high-throughput protocol for mutation scanning of the BRCA1 and BRCA2 genes. BMC Cancer 2011; 11:265. [PMID: 21702907 PMCID: PMC3146935 DOI: 10.1186/1471-2407-11-265] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 06/24/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Detection of mutations by DNA sequencing can be facilitated by scanning methods to identify amplicons which may have mutations. Current scanning methods used for the detection of germline sequence variants are laborious as they require post-PCR manipulation. High resolution melting (HRM) is a cost-effective rapid screening strategy, which readily detects heterozygous variants by melting curve analysis of PCR products. It is well suited to screening genes such as BRCA1 and BRCA2 as germline pathogenic mutations in these genes are always heterozygous. METHODS Assays for the analysis of all coding regions and intron-exon boundaries of BRCA1 and BRCA2 were designed, and optimised. A final set of 94 assays which ran under identical amplification conditions were chosen for BRCA1 (36) and BRCA2 (58). Significant attention was placed on primer design to enable reproducible detection of mutations within the amplicon while minimising unnecessary detection of polymorphisms. Deoxyinosine residues were incorporated into primers that overlay intronic polymorphisms. Multiple 384 well plates were used to facilitate high throughput. RESULTS 169 BRCA1 and 239 BRCA2 known sequence variants were used to test the amplicons. We also performed an extensive blinded validation of the protocol with 384 separate patient DNAs. All heterozygous variants were detected with the optimised assays. CONCLUSIONS This is the first HRM approach to screen the entire coding region of the BRCA1 and BRCA2 genes using one set of reaction conditions in a multi plate 384 well format using specifically designed primers. The parallel screening of a relatively large number of samples enables better detection of sequence variants. HRM has the advantages of decreasing the necessary sequencing by more than 90%. This markedly reduced cost of sequencing will result in BRCA1 and BRCA2 mutation testing becoming accessible to individuals who currently do not undergo mutation testing because of the significant costs involved.
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Affiliation(s)
- Heather L Hondow
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, Melbourne, Victoria, 8006, Australia
| | - Stephen B Fox
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, Melbourne, Victoria, 8006, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Gillian Mitchell
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, Melbourne, Victoria, 8006, Australia
| | - Rodney J Scott
- School of Biomedical Sciences, University of Newcastle, New South Wales, 2308, Australia
| | - Victoria Beshay
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, Melbourne, Victoria, 8006, Australia
| | - Stephen Q Wong
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, Melbourne, Victoria, 8006, Australia
| | | | - Alexander Dobrovic
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, Melbourne, Victoria, 8006, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia
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Vorkas PA, Poumpouridou N, Agelaki S, Kroupis C, Georgoulias V, Lianidou ES. PIK3CA hotspot mutation scanning by a novel and highly sensitive high-resolution small amplicon melting analysis method. J Mol Diagn 2010; 12:697-704. [PMID: 20616362 DOI: 10.2353/jmoldx.2010.100008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Somatic mutations in the PIK3CA gene have been discovered in many human cancers, and their presence correlates to therapy response. Three "hotspot" mutations within the PIK3CA gene are localized in exons 9 and 20. High-resolution melting analysis (HRMA) is a highly sensitive, robust, rapid, and cost-effective mutation analysis technique. We developed a novel methodology for the detection of hotspot mutations in exons 9 and 20 of the PIK3CA gene that is based on a combination of PCR and HRMA. The PIK3CA HRMA assay was evaluated by performing repeatability, sensitivity, and comparison with DNA sequencing studies and was further validated in 129 formalin-fixed paraffin-embedded breast tissue samples: 99 tumors, 20 noncancerous, and 10 fibroadenomas. The developed methodology was further applied in a selected group of 75 breast cancer patients who underwent Trastuzumab treatment. In sensitivity studies, the assay presented a capability to detect as low as 1% of mutated dsDNA in the presence of wtDNA for both exons. In the 99 tumor samples (validation group), 12/99 (12.1%) exon 9 mutations and 20/99 (20.2%) exon 20 mutations were found. No mutations were found in noncancerous tissues. In fibroadenomas, we report one PIK3CA mutation for the first time. In the selected group, 30/75 (40%) samples were detected as mutants. The PIK3CA HRMA assay is highly sensitive, reliable, cost-effective, and easy-to-perform, and therefore can be used as a screening test in a high-throughput pharmacodiagnostic setting.
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Affiliation(s)
- Panagiotis A Vorkas
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
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