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Kasapoğlu Aksoy M, Altan L, Görükmez O, Güner A, Ayar K. The relationship between CRP gene polymorphism (rs2794521, rs3091244), ASDAS-CRP and ASDAS-ESR in ankylosing spondylitis. Mod Rheumatol 2019; 30:715-720. [PMID: 31267817 DOI: 10.1080/14397595.2019.1639916] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background: We aimed to investigate the haplotypes and alleles of two variants (rs2794521 and rs3091244) in AS patients and to examine their relationship with ASDAS-CRP and ASDAS-ESR values.Methods: We evaluated 160 AS patients diagnosed according to the ASAS criteria. ASDAS-CRP and ASDAS-ESR values were calculated. ESR and CRP were examined. The restriction fragment length polymorphism (RFLP) method was used for detecting the rs2794521 and rs3091244 regions on the CRP gene.Results: As a result of the evaluation of rs2794521 gene polymorphism using PCR, TT, TC and CC genotypes were observed in 90, 81 and 9 individuals, respectively. As a result of the evaluation of rs3091244 gene polymorphism, CC, AC and TT genotypes were observed in 104, 51 and 5 individuals, respectively. T allele and C allele were found in rs2794521 gene by 75% and 25%, respectively. In addition, T allele, C allele and A allele were found in rs3091244 gene by 80%, 17% and 3%, respectively. With the help of regression equation, ASDAS-CRP level was 0.34 units higher in cases with rs3091244 C allele than cases without rs3091244 C alleles.Conclusion: CRP rs3091244 C allele may be associated with the increased relative risk for ASDAS-CRP.
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Affiliation(s)
- Meliha Kasapoğlu Aksoy
- Department of Physical Medicine and Rehabilitation, Bursa Yüksek İhtisas Training and Research Hospital, University of Health Sciences, Bursa, Turkey
| | - Lale Altan
- Department of Physical Medicine and Rehabilitation, Bursa Yüksek İhtisas Training and Research Hospital, University of Health Sciences, Bursa, Turkey.,Department of Physical Medicine and Rehabilitation, Faculty of Medicine, Uludağ University, Bursa, Turkey
| | - Orhan Görükmez
- Department of Genetics, Bursa Yüksek İhtisas Training and Research Hospital, University of Health Sciences, Bursa, Turkey
| | - Altuğ Güner
- Department of Physical Medicine and Rehabilitation, Bursa Yüksek İhtisas Training and Research Hospital, University of Health Sciences, Bursa, Turkey
| | - Koray Ayar
- Department of Romatology, Bursa Yüksek İhtisas Training and Research Hospital, University of Health Sciences, Bursa, Turkey
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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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Yamanaka ES, Tortajada-Genaro LA, Maquieira Á. Low-cost genotyping method based on allele-specific recombinase polymerase amplification and colorimetric microarray detection. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2144-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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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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High-speed droplet-allele-specific polymerase chain reaction for genotyping of single nucleotide polymorphisms. Methods Mol Biol 2016; 1310:29-35. [PMID: 26024623 DOI: 10.1007/978-1-4939-2690-9_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Single nucleotide alternations such as single nucleotide polymorphisms (SNPs) or single nucleotide mutations are useful genetic markers for molecular diagnosis, prognosis, drug response, and predisposition to diseases. Rapid identification of SNPs or mutations is clinically important, especially for determining drug responses and selection of molecular-targeted therapy. Here, we describe a rapid genotyping assay based on the allele-specific polymerase chain reaction (AS-PCR) by using our droplet-PCR machine (droplet-AS-PCR).
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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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Yamaguchi A, Matsuda K, Sueki A, Taira C, Uehara M, Saito Y, Honda T. Development of a rapid and sensitive one-step reverse transcription-nested polymerase chain reaction in a single tube using the droplet-polymerase chain reaction machine. Clin Chim Acta 2015; 448:150-4. [PMID: 26148723 DOI: 10.1016/j.cca.2015.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/02/2015] [Indexed: 11/25/2022]
Abstract
BACKGROUND Reverse transcription (RT)-nested polymerase chain reaction (PCR) is a time-consuming procedure because it has several handling steps and is associated with the risk of cross-contamination during each step. Therefore, a rapid and sensitive one-step RT-nested PCR was developed that could be performed in a single tube using a droplet-PCR machine. METHODS The K562 BCR-ABL mRNA-positive cell line as well as bone marrow aspirates from 5 patients with chronic myelogenous leukemia (CML) and 5 controls without CML were used. We evaluated one-step RT-nested PCR using the droplet-PCR machine. RESULTS One-step RT-nested PCR performed in a single tube using the droplet-PCR machine enabled the detection of BCR-ABL mRNA within 40min, which was 10(3)-fold superior to conventional RT nested PCR using three steps in separate tubes. The sensitivity of the one-step RT-nested PCR was 0.001%, with sample reactivity comparable to that of the conventional assay. CONCLUSIONS One-step RT-nested PCR was developed using the droplet-PCR machine, which enabled all reactions to be performed in a single tube accurately and rapidly and with high sensitivity. This one-step RT-nested PCR may be applicable to a wide spectrum of genetic tests in clinical laboratories.
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Affiliation(s)
- Akemi Yamaguchi
- Graduate School of Science and Technology, Shinshu University, Nagano, Japan; Core Technology Development Center, Seiko Epson Corporation, Suwa, Japan
| | - Kazuyuki Matsuda
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan.
| | - Akane Sueki
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Chiaki Taira
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Masayuki Uehara
- Core Technology Development Center, Seiko Epson Corporation, Suwa, Japan
| | - Yasunori Saito
- Institute of Engineering, Academic Assembly, Shinshu University, Nagano, Japan
| | - Takayuki Honda
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
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Taira C, Matsuda K, Yamaguchi A, Uehara M, Sugano M, Okumura N, Honda T. Rapid single nucleotide polymorphism based method for hematopoietic chimerism analysis and monitoring using high-speed droplet allele-specific PCR and allele-specific quantitative PCR. Clin Chim Acta 2015; 445:101-6. [PMID: 25797898 DOI: 10.1016/j.cca.2015.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 02/27/2015] [Accepted: 03/07/2015] [Indexed: 11/25/2022]
Abstract
BACKGROUND Chimerism analysis is important for the evaluation of engraftment and predicting relapse following hematopoietic stem cell transplantation (HSCT). We developed a chimerism analysis for single nucleotide polymorphisms (SNPs), including rapid screening of the discriminable donor/recipient alleles using droplet allele-specific PCR (droplet-AS-PCR) pre-HSCT and quantitation of recipient DNA using AS-quantitative PCR (AS-qPCR) following HSCT. METHODS SNP genotyping of 20 donor/recipient pairs via droplet-AS-PCR and the evaluation of the informativity of 5 SNP markers for chimerism analysis were performed. Samples from six follow-up patients were analyzed to assess the chimerism via AS-qPCR. These results were compared with that determined by short tandem repeat PCR (STR-PCR). RESULTS Droplet-AS-PCR could determine genotypes within 8min. The total informativity using all 5 loci was 95% (19/20). AS-qPCR provided the percentage of recipient DNA in all 6 follow-up patients without influence of the stutter peak or the amplification efficacy, which affected the STR-PCR results. CONCLUSION The droplet-AS-PCR had an advantage over STR-PCR in terms of rapidity and simplicity for screening before HSCT. Furthermore, AS-qPCR had better accuracy than STR-PCR for quantification of recipient DNA following HSCT. The present chimerism assay compensates for the disadvantages of STR-PCR and is readily performable in clinical laboratories.
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Affiliation(s)
- Chiaki Taira
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Kazuyuki Matsuda
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan.
| | - Akemi Yamaguchi
- Core Technology Development Center, Seiko Epson Corporation, Fujimi, Japan
| | - Masayuki Uehara
- Core Technology Development Center, Seiko Epson Corporation, Fujimi, Japan
| | - Mitsutoshi Sugano
- 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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