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Lynch C, Fleming R. A review of direct polymerase chain reaction of DNA and RNA for forensic purposes. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Courtney Lynch
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd Auckland New Zealand
- School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Rachel Fleming
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd Auckland New Zealand
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Taira C, Matsuda K, Takeichi N, Furukawa S, Sugano M, Uehara T, Okumura N, Honda T. Rapid ABO genotyping by high-speed droplet allele-specific PCR using crude samples. J Clin Lab Anal 2017; 32. [PMID: 28295603 DOI: 10.1002/jcla.22196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/13/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND ABO genotyping has common tools for personal identification of forensic and transplantation field. We developed a new method based on a droplet allele-specific PCR (droplet-AS-PCR) that enabled rapid PCR amplification. We attempted rapid ABO genotyping using crude DNA isolated from dried blood and buccal cells. METHODS We designed allele-specific primers for three SNPs (at nucleotides 261, 526, and 803) in exons 6 and 7 of the ABO gene. We pretreated dried blood and buccal cells with proteinase K, and obtained crude DNAs without DNA purification. RESULTS Droplet-AS-PCR allowed specific amplification of the SNPs at the three loci using crude DNA, with results similar to those for DNA extracted from fresh peripheral blood. The sensitivity of the methods was 5%-10%. The genotyping of extracted DNA and crude DNA were completed within 8 and 9 minutes, respectively. The genotypes determined by the droplet-AS-PCR method were always consistent with those obtained by direct sequencing. CONCLUSION The droplet-AS-PCR method enabled rapid and specific amplification of three SNPs of the ABO gene from crude DNA treated with proteinase K. ABO genotyping by the droplet-AS-PCR has the potential to be applied to various fields including a forensic medicine and transplantation medical care.
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Affiliation(s)
- Chiaki Taira
- Laboratory of Clinical Chemistry and Immunology, Department of Biomedical Laboratory Sciences, School of Health Sciences, Shinshu University, Matsumoto, Japan
| | - Kazuyuki Matsuda
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Naoya Takeichi
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Satomi Furukawa
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Mitsutoshi Sugano
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Takeshi Uehara
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Nobuo Okumura
- Laboratory of Clinical Chemistry and Immunology, Department of Biomedical Laboratory Sciences, School of Health Sciences, Shinshu University, Matsumoto, Japan
| | - Takayuki Honda
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
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Asaka S, Yoshizawa A, Matsuda K, Yamaguchi A, Yamamoto H, Shiina T, Nakata R, Ogawa K, Zhang M, Honda T. A novel, rapid point-of-care test for lung cancer patients to detect epidermal growth factor receptor gene mutations by using real-time droplet-PCR and fresh liquid cytology specimens. Oncol Rep 2016; 37:1020-1026. [PMID: 27922678 DOI: 10.3892/or.2016.5287] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/08/2016] [Indexed: 11/06/2022] Open
Abstract
Epidermal growth factor receptor gene (EGFR) mutations are associated with response to tyrosine kinase inhibitors (TKIs) in patients with non-small cell lung cancer (NSCLC). We developed a novel, rapid EGFR mutation assay using a real-time droplet-polymerase chain reaction machine (EGFR d-PCR assay). The purpose of this study was to validate the performance of the EGFR d-PCR assay using fresh liquid cytology specimens. We analyzed three major EGFR mutations (L858R in exon 21, E746_A750del in exon 19 and T790M in exon 20) in 80 fresh liquid cytology specimens of adenocarcinoma (ADC) or NSCLC-not otherwise specified (NOS) via the EGFR d-PCR assay and conventional real-time PCR assay using the therascreen® EGFR RGQ PCR kit (Therascreen assay). In addition, we performed sensitivity assays using cell lines with EGFR mutations. The EGFR d-PCR assay detected 16 L858Rs, 8 E746_A750dels and 1 T790M mutation and the Therascreen assay detected 16 L858Rs, 11 deletions in exon 19 and 1 T790M mutation. The results were concordant between the two assays. The reaction time of the EGFR d-PCR assay was 8 min and 10 sec, but that of the Therascreen assay was 1 h and 45 min. Sensitivity, as assessed by the detection limit of the EGFR d-PCR assay was 0.5, 0.05 and 0.5% for L858R, E746_A750del and T790M, respectively. The EGFR d-PCR assay markedly reduced the detection time of major EGFR mutations with high sensitivity compared with the conventional Therascreen assay and is expected to expedite EGFR-TKI therapy for lung cancer patients, especially those in advanced stages.
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Affiliation(s)
- Shiho Asaka
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Akihiko Yoshizawa
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Kazuyuki Matsuda
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Akemi Yamaguchi
- Graduate School of Science and Technology, Shinshu University, Wakasato, Nagano 380-8553, Japan
| | - Hiroshi Yamamoto
- First Department of Internal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Takayuki Shiina
- Department of Thoracic Surgery, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Rie Nakata
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Kaoru Ogawa
- Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Meng Zhang
- Department of Thoracic Surgery, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Takayuki Honda
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
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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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Yamaguchi A, Matsuda K, Uehara M, Honda T, Saito Y. A novel automated device for rapid nucleic acid extraction utilizing a zigzag motion of magnetic silica beads. Anal Chim Acta 2016; 906:1-6. [DOI: 10.1016/j.aca.2015.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/08/2015] [Accepted: 10/17/2015] [Indexed: 01/06/2023]
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