1
|
Delobel D, Furutani Y, Nagoshi S, Tsubota A, Miyasaka A, Watashi K, Wakita T, Matsuura T, Usui K. SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV. BMC Infect Dis 2022; 22:516. [PMID: 35659601 PMCID: PMC9164387 DOI: 10.1186/s12879-022-07458-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background SmartAmp-Eprimer Binary code (SEB) Genotyping is a novel isothermal amplification method for rapid genotyping of any variable target of interest. Methods After in silico alignment of a large number of sequences and computational analysis to determine the smallest number of regions to be targeted by SEB Genotyping, SmartAmp primer sets were designed to obtain a binary code of On/Off fluorescence signals, each code corresponding to a unique genotype. Results Applied to HBV, we selected 4 targets for which fluorescence amplification signals produce a specific binary code unique to each of the 8 main genotypes (A–H) found in patients worldwide. Conclusions We present here the proof of concept of a new genotyping method specifically designed for complex and highly variable targets. Applied here to HBV, SEB Genotyping can be adapted to any other pathogen or disease carrying multiple known mutations. Using simple preparation steps, SEB Genotyping provides accurate results quickly and will enable physicians to choose the best adapted treatment for each of their patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07458-4.
Collapse
|
2
|
Liu X, Zhang C, Liu K, Wang H, Lu C, Li H, Hua K, Zhu J, Hui W, Cui Y, Zhang X. Multiple SNPs Detection Based on Lateral Flow Assay for Phenylketonuria Diagnostic. Anal Chem 2018; 90:3430-3436. [PMID: 29451781 DOI: 10.1021/acs.analchem.7b05113] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are closely related to genetic diseases, but current SNP detection methods, such as DNA microarrays that include tedious procedures and expensive, sophisticated instruments, are unable to perform rapid SNPs detection in clinical practice, especially for those multiple SNPs related to genetic diseases. In this study, we report a sensitive, low cost, and easy-to-use point-of-care testing (POCT) system formed by combining amplification refractory mutation system (ARMS) polymerase chain reaction with gold magnetic nanoparticles (GMNPs) and lateral flow assay (LFA) noted as the ARMS-LFA system, which allow us to use a uniform condition for multiple SNPs detection simultaneously. The genotyping results can be explained by a magnetic reader automatically or through visual interpretation according to the captured GMNPs probes on the test and control lines of the LFA device. The high sensitivity (the detection limit of 0.04 pg/μL with plasmid) and specificity of this testing system were found through genotyping seven pathogenic SNPs in phenylalanine hydroxylase gene ( PAH, the etiological factor of phenylketonuria). This system can also be applied in DNA quantification with a linear range from 0.02 to 2 pg/μL of plasmid. Furthermore, this ARMS-LFA system was applied to clinical trials for screening the seven pathogenic SNPs in PAH of 23 families including 69 individuals. The concordance rate of the genotyping results detected by the ARMS-LFA system was up to 97.8% compared with the DNA sequencing results. This method is a very promising POCT in the detection of multiple SNPs caused by genetic diseases.
Collapse
Affiliation(s)
- Xiaonan Liu
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Chao Zhang
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Kewu Liu
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Han Wang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005 , China
| | - Chaoxia Lu
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005 , China
| | - Hang Li
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Kai Hua
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China.,National Engineering Research Center for Miniaturized Detection System , Xi'an , Shaanxi 710069 , China
| | - Juanli Zhu
- Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection , Xi'an , Shaanxi 710077 , China
| | - Wenli Hui
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China.,National Engineering Research Center for Miniaturized Detection System , Xi'an , Shaanxi 710069 , China
| | - Yali Cui
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China.,National Engineering Research Center for Miniaturized Detection System , Xi'an , Shaanxi 710069 , China.,Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection , Xi'an , Shaanxi 710077 , China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005 , China
| |
Collapse
|
3
|
Enokida Y, Shimizu K, Atsumi J, Kakegawa S, Takase Y, Kaira K, Yashima H, Araki T, Nakazawa S, Ohtaki Y, Nagashima T, Alexander L, Usui K, Ishikawa T, Hayashizaki Y, Takeyoshi I. Prognostic potential of the MDM2 309T>G polymorphism in stage I lung adenocarcinoma. Cancer Med 2016; 5:1791-801. [PMID: 27228500 PMCID: PMC4884639 DOI: 10.1002/cam4.750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 03/27/2016] [Accepted: 04/04/2016] [Indexed: 11/08/2022] Open
Abstract
The MDM2 protein plays an important role in the regulation of cell proliferation and apoptosis via ubiquitination and proteasome‐mediated degradation of p53. The genetic polymorphism rs2279744 (c.309T>G) of the MDM2 gene is reportedly associated with susceptibility and/or prognosis in various cancers. In this study, we investigated the risk factors for worse survival in patients with lung adenocarcinoma (AC). We examined the association between c.309T>G and the prognosis of lung cancer by retrospectively reviewing 453 lung cancer patients. We studied both, clinicopathological and genetic characteristics, including the c.309T>G, p53 Arg72Pro, EGFR,KRAS, and p53 mutations. Associations between these factors and survival outcome were analyzed using Cox proportional hazards models. The frequencies of MDM2 polymorphisms were T/T, 20.8%; T/G, 48.6%, and G/G, 30.7%. The overall survival (OS) of AC patients with pathological stage I disease and the MDM2 T/T genotype was significantly shorter than that of those with the T/G or G/G genotypes (P = 0.02). Multivariate analysis revealed that the MDM2 T/T genotype was an independent, significant prognostic factor (hazard ratio [HR] = 2.23; 95% confidence interval [CI]: 1.07–4.65; P = 0.03). The MDM2 T/T genotype was predictive of poorer survival in a Japanese population. Genotyping for this polymorphism might predict the clinical outcomes of stage I AC patients.
Collapse
Affiliation(s)
- Yasuaki Enokida
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Kimihiro Shimizu
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Jun Atsumi
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Seiichi Kakegawa
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Yoshiaki Takase
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Kyoichi Kaira
- Department of Oncology Clinical Development, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Hideaki Yashima
- Department of Clinical Pharmacology, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Takuya Araki
- Department of Clinical Pharmacology, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Seshiru Nakazawa
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Yoichi Ohtaki
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Toshiteru Nagashima
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Lezhava Alexander
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Kengo Usui
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Toshihisa Ishikawa
- NGO Personalized Medicine & Healthcare, Yokohama, Kanagawa, 226-0016, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa, 230-0045, Japan
| | - Izumi Takeyoshi
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| |
Collapse
|
4
|
Hui W, Zhang S, Zhang C, Wan Y, Zhu J, Zhao G, Wu S, Xi D, Zhang Q, Li N, Cui Y. A novel lateral flow assay based on GoldMag nanoparticles and its clinical applications for genotyping of MTHFR C677T polymorphisms. NANOSCALE 2016; 8:3579-3587. [PMID: 26804455 DOI: 10.1039/c5nr07547e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Current techniques for single nucleotide polymorphism (SNP) detection require tedious experimental procedures and expensive and sophisticated instruments. In this study, a visual genotyping method has been successfully established via combining ARMS-PCR with gold magnetic nanoparticle (GoldMag)-based lateral flow assay (LFA) and applied to the genotyping of methylenetetrahydrofolate reductase (MTHFR) C677T. C677T substitution of the gene MTHFR leads to an increased risk of diseases. The genotyping result is easily achievable by visual observation within 5 minutes after loading of the PCR products onto the LFA device. The system is able to accurately assess a broad detection range of initial starting genomic DNA amounts from 5 ng to 1200 ng per test sample. The limit of detection reaches 5 ng. Furthermore, our PCR-LFA system was applied to clinical trials for screening 1721 individuals for the C677T genotypes. The concordance rate of the genotyping results detected by PCR-LFA was up to 99.6% when compared with the sequencing results. Collectively, our PCR-LFA has been proven to be rapid, accurate, sensitive, and inexpensive. This new method is highly applicable for C677T SNP screening in laboratories and clinical practices. More promisingly, it could also be extended to the detection of SNPs of other genes.
Collapse
Affiliation(s)
- Wenli Hui
- College of Life Sciences, Northwest University, Xi'an, 710069, China.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Enokida Y, Shimizu K, Kakegawa S, Atsumi J, Takase Y, Miyamae Y, Nagashima T, Ohtaki Y, Kaira K, Sunaga N, Yanagitani N, Yoshino R, Tsunekawa K, Igai H, Kamiyoshihara M, Usui K, Lezhava A, Tomizawa Y, Ishikawa T, Murakami M, Hayashizaki Y, Takeyoshi I. Single-nucleotide polymorphism (c.309T>G) in the MDM2 gene and lung cancer risk. Biomed Rep 2014; 2:719-724. [PMID: 25054017 DOI: 10.3892/br.2014.305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 06/13/2014] [Indexed: 02/03/2023] Open
Abstract
Murine double minute 2 (MDM2) is a negative regulator of p53. A single-nucleotide polymorphism (SNP) (rs2279744: c.309T>G) in the promoter region of the MDM2 gene has been shown to result in higher levels of MDM2 RNA and protein. Regarding the contribution of c.309T>G in the MDM2 gene to the lung cancer risk, previous studies are conflicting. In order to evaluate the association between c.309T>G and the lung cancer risk, a case-control study was performed. The MDM2 genotypes were determined in 762 lung cancer patients and in 700 cancer-free control subjects using the Smart Amplification Process. Statistical adjustment was performed for gender, age and pack-years of smoking. The distributions of c.309T>G (T/T, T/G, G/G) were 20.1, 49.7, 30.2% in the case group and 21.7, 47.9, 30.4% in the healthy-control group. There were no overall associations between the MDM2 genotypes and the risk of lung cancer [T/G genotype: Adjusted odds ratio (AOR), 1.30; 95% confidence interval (CI), 0.88-1.93; and G/G genotype: AOR, 1.18; 95% CI, 0.78-1.80]. The subgroup analysis of gender, histology, smoking status and epidermal growth factor receptor mutation status also indicated that there was no association with lung cancer. Additionally, the genotypes did not have an effect on the age at the time of diagnosis of lung cancer (P=0.25). In conclusion, the G allele frequency in the lung cancer cases was 0.551, which was similar to other studies. The results of the present study suggest that the c.309T>G is not significantly associated with lung cancer.
Collapse
Affiliation(s)
- Yasuaki Enokida
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Kimihiro Shimizu
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Seiichi Kakegawa
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Jun Atsumi
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Yoshiaki Takase
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Yohei Miyamae
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Toshiteru Nagashima
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Yoichi Ohtaki
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Kyoichi Kaira
- Department of Oncology Clinical Development, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Noriaki Sunaga
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Noriko Yanagitani
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Reiko Yoshino
- Department of Internal Medicine, National Hospital Organization Nishi-Gunma Hospital, Shibukawa, Gunma 377-8511, Japan
| | - Katsuhiko Tsunekawa
- Department of Clinical Laboratory Medicine, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Hitoshi Igai
- Department of General Thoracic Surgery, Maebashi Red Cross Hospital, Maebashi, Gunma 371-0014, Japan
| | - Mitsuhiro Kamiyoshihara
- Department of General Thoracic Surgery, Maebashi Red Cross Hospital, Maebashi, Gunma 371-0014, Japan
| | - Kengo Usui
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Alexander Lezhava
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshio Tomizawa
- Department of Internal Medicine, National Hospital Organization Nishi-Gunma Hospital, Shibukawa, Gunma 377-8511, Japan
| | - Toshihisa Ishikawa
- NGO Personalized Medicine and Healthcare, Yokohama, Kanagawa 226-0016, Japan
| | - Masami Murakami
- Department of Clinical Laboratory Medicine, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa 230-0045, Japan
| | - Izumi Takeyoshi
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| |
Collapse
|
6
|
Okano Y, Nezu U, Enokida Y, Lee MTM, Kinoshita H, Lezhava A, Hayashizaki Y, Morita S, Taguri M, Ichikawa Y, Kaneko T, Natsumeda Y, Yokose T, Nakayama H, Miyagi Y, Ishikawa T. SNP (-617C>A) in ARE-like loci of the NRF2 gene: a new biomarker for prognosis of lung adenocarcinoma in Japanese non-smoking women. PLoS One 2013; 8:e73794. [PMID: 24040073 PMCID: PMC3770684 DOI: 10.1371/journal.pone.0073794] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 07/26/2013] [Indexed: 12/30/2022] Open
Abstract
Purpose The transcription factor NRF2 plays a pivotal role in protecting normal cells from external toxic challenges and oxidative stress, whereas it can also endow cancer cells resistance to anticancer drugs. At present little information is available about the genetic polymorphisms of the NRF2 gene and their clinical relevance. We aimed to investigate the single nucleotide polymorphisms in the NRF2 gene as a prognostic biomarker in lung cancer. Experimental Design We prepared genomic DNA samples from 387 Japanese patients with primary lung cancer and detected SNP (c.–617C>A; rs6721961) in the ARE-like loci of the human NRF2 gene by the rapid genetic testing method we developed in this study. We then analyzed the association between the SNP in the NRF2 gene and patients’ overall survival. Results Patients harboring wild-type (WT) homozygous (c.–617C/C), SNP heterozygous (c.–617C/A), and SNP homozygous (c.–617A/A) alleles numbered 216 (55.8%), 147 (38.0%), and 24 (6.2%), respectively. Multivariate logistic regression models revealed that SNP homozygote (c.–617A/A) was significantly related to gender. Its frequency was four-fold higher in female patients than in males (10.8% female vs 2.7% male) and was associated with female non-smokers with adenocarcinoma. Interestingly, lung cancer patients carrying NRF2 SNP homozygous alleles (c.–617A/A) and the 309T (WT) allele in the MDM2 gene exhibited remarkable survival over 1,700 days after surgical operation (log-rank p = 0.021). Conclusion SNP homozygous (c.–617A/A) alleles in the NRF2 gene are associated with female non-smokers with adenocarcinoma and regarded as a prognostic biomarker for assessing overall survival of patients with lung adenocarcinoma.
Collapse
Affiliation(s)
- Yasuko Okano
- Omics Science Center, RIKEN Yokohama Institute, Yokohama, Japan
- Department of Clinical Oncology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Uru Nezu
- Omics Science Center, RIKEN Yokohama Institute, Yokohama, Japan
- Department of Clinical Pharmacology and Therapeutics, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Yasuaki Enokida
- Omics Science Center, RIKEN Yokohama Institute, Yokohama, Japan
- Division of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maehashi, Japan
| | - Ming Ta Michael Lee
- Laboratory for International Alliance on Genomic Research, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | | | | | | | - Satoshi Morita
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Masataka Taguri
- Department of Biostatistics and Epidemiology, Yokohama City University Medical Center, Yokohama, Japan
| | - Yasushi Ichikawa
- Department of Clinical Oncology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Kaneko
- Omics Science Center, RIKEN Yokohama Institute, Yokohama, Japan
- Respiratory Disease Center, Yokohama City University Medical Center, Yokohama, Japan
| | - Yutaka Natsumeda
- Department of Clinical Research, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tomoyuki Yokose
- Department of Pathology, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Haruhiko Nakayama
- Department of Thoracic Surgery, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Yohei Miyagi
- Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Toshihisa Ishikawa
- Omics Science Center, RIKEN Yokohama Institute, Yokohama, Japan
- * E-mail:
| |
Collapse
|