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Ramos-Díaz R, Escuela-Escobar A, Díaz-Usera A, Hernández Pérez JM, González-Carracedo MA, Pérez-Pérez JA. Real-time PCR detection of PI*S and PI*Z alleles of SERPINA1 gene using SYBR green. Gene 2024; 921:148540. [PMID: 38723785 DOI: 10.1016/j.gene.2024.148540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/14/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Alpha-1 antitrypsin deficiency is an underdiagnosed genetic condition that predisposes to pulmonary complications and is mainly caused by rs28929474 (PI*Z allele) and rs17580 (PI*S allele) mutations in the SERPINA1 gene. OBJECTIVE Development of a homogeneous genotyping test for detection of PI*S and PI*Z alleles based on the principles of allele-specific PCR and amplicon melting analysis with a fluorescent dye. METHODS Sixty individuals, which included all possible genotypes that result from combinations of rs28929474 and rs17580 single nucleotide variants, were assayed with tailed allele-specific primers and SYBR Green dye in a real-time PCR machine. RESULTS A clear discrimination of mutant and wild-type variants was achieved in the genetic loci that define PI*S and PI*Z alleles. Specific amplicons showed a difference of 2.0 °C in melting temperature for non-S and S variants and of 2.9 °C for non-Z and Z variants. CONCLUSIONS The developed genotyping method is robust, fast, and easily scalable on a standard real-time PCR platform. While it overcomes the handicaps of non-homogeneous approaches, it greatly reduces genotyping costs compared with other homogeneous approaches.
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Affiliation(s)
- Ruth Ramos-Díaz
- Fundación Canaria Instituto de Investigación Sanitaria de Canarias (FIISC) - Unidad de Investigación Complejo Hospitalario Universitario de Canarias, Servicio de Farmacia, Tenerife, Spain
| | - Ainhoa Escuela-Escobar
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands (IUETSPC), Universidad de La Laguna (ULL), Tenerife, Spain; Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), Tenerife, Spain
| | - Ana Díaz-Usera
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), Tenerife, Spain
| | | | - Mario Andrés González-Carracedo
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands (IUETSPC), Universidad de La Laguna (ULL), Tenerife, Spain; Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), Tenerife, Spain.
| | - José Antonio Pérez-Pérez
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands (IUETSPC), Universidad de La Laguna (ULL), Tenerife, Spain; Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), Tenerife, Spain
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Wittwer CT, Hemmert AC, Kent JO, Rejali NA. DNA melting analysis. Mol Aspects Med 2024; 97:101268. [PMID: 38489863 DOI: 10.1016/j.mam.2024.101268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/19/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Melting is a fundamental property of DNA that can be monitored by absorbance or fluorescence. PCR conveniently produces enough DNA to be directly monitored on real-time instruments with fluorescently labeled probes or dyes. Dyes monitor the entire PCR product, while probes focus on a specific locus within the amplicon. Advances in amplicon melting include high resolution instruments, saturating DNA dyes that better reveal multiple products, prediction programs for domain melting, barcode taxonomic identification, high speed microfluidic melting, and highly parallel digital melting. Most single base variants and small insertions or deletions can be genotyped by high resolution amplicon melting. High resolution melting also enables heterozygote scanning for any variant within a PCR product. A web application (uMelt, http://www.dna-utah.org) predicts amplicon melting curves with multiple domains, a useful tool for verifying intended products. Additional applications include methylation assessment, copy number determination and verification of sequence identity. When amplicon melting does not provide sufficient detail, unlabeled probes or snapback primers can be used instead of covalently labeled probes. DNA melting is a simple, inexpensive, and powerful tool with many research applications that is beginning to make its mark in clinical diagnostics.
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Affiliation(s)
- Carl T Wittwer
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.
| | | | - Jana O Kent
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Nick A Rejali
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
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Santhanam P, Labbé C, Tremblay V, Bélanger RR. A rapid molecular diagnostic tool to discriminate alleles of avirulence genes and haplotypes of Phytophthora sojae using high-resolution melting analysis. MOLECULAR PLANT PATHOLOGY 2024; 25:e13406. [PMID: 38009407 PMCID: PMC10799203 DOI: 10.1111/mpp.13406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 10/02/2023] [Accepted: 11/03/2023] [Indexed: 11/28/2023]
Abstract
Effectors encoded by avirulence genes (Avr) interact with the Phytophthora sojae resistance gene (Rps) products to generate incompatible interactions. The virulence profile of P. sojae is rapidly evolving as a result of the large-scale deployment of Rps genes in soybean. For a successful exploitation of Rps genes, it is recommended that soybean growers use cultivars containing the Rps genes corresponding to Avr genes present in P. sojae populations present in their fields. Determination of the virulence profile of P. sojae isolates is critical for the selection of soybean cultivars. High-resolution melting curve (HRM) analysis is a powerful tool, first applied in medicine, for detecting mutations with potential applications in different biological fields. Here, we report the development of an HRM protocol, as an original approach to discriminate effectors, to differentiate P. sojae haplotypes for six Avr genes. An HRM assay was performed on 24 P. sojae isolates with different haplotypes collected from soybean fields across Canada. The results clearly confirmed that the HRM assay discriminated different virulence genotypes. Moreover, the HRM assay was able to differentiate multiple haplotypes representing small allelic variations. HRM-based prediction was validated by phenotyping assays. This HRM assay provides a unique, cost-effective and efficient tool to predict virulence pathotypes associated with six different Avr (1b, 1c, 1d, 1k, 3a and 6) genes from P. sojae, which can be applied in the deployment of appropriate Rps genes in soybean fields.
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Affiliation(s)
- Parthasarathy Santhanam
- Département de PhytologieUniversité LavalQuebecQuebecCanada
- Present address:
Agriculture Agri‐Food Canada, MRDCMordenManitobaCanada
| | - Caroline Labbé
- Département de PhytologieUniversité LavalQuebecQuebecCanada
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Ginart S, Garrigos Calivares L, Caputo M, Corach D, Sala A. Improving the efficiency of Y-chromosome detection and the quality of STR typing in forensic casework with an in-house made qPCR and HRM system based on SYTO™ 9 chemistry. Forensic Sci Int 2024; 354:111893. [PMID: 38064775 DOI: 10.1016/j.forsciint.2023.111893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024]
Abstract
DNA quantification prior to STR amplification is a crucial step in forensic casework. Obtaining good-quality genetic STR profiles depends mainly on the amount and integrity of the DNA input in the PCR. In addition, the detection of male trace DNA provides key information for forensic investigation. AIM To evaluate the correlation between the quantification results obtained with the previously developed Amel-Y system, and its ability to detect Y-chromosome DNA by HRM, with the resulting STR profiles, and to ultimately show that Amel-Y can be routinely used in forensic casework to improve STR and Y-STR results. MATERIAL & METHODS Biological samples derived from forensic casework (85 reference and 391 evidence samples) were quantified by the Amel-Y system (a duplex qPCR/HRM based on SYTO™ 9 chemistry) using Rotor-Gene 6000. STRs were amplified and analyzed with GeneAmp™ PCR System 9700 or Veriti™ Thermal Cyclers and ABI 3500 Genetic Analyzer, respectively. RESULTS After DNA normalization, a total of 386 STR profiles were obtained (305 full and 81 partial). Sex typing by HRM was 100% successful in reference samples. Male DNA was detected by HRM in 210 evidence samples. 80/201 were mixed with an excess of female DNA. In addition, Amel-Y was able to detect Y-chromosome DNA in mixed samples that did not amplify the Y-variant of Amelogenin marker with commercial STR kits. The reproducibility and precision of the Amel-Y system were demonstrated (CVCt% ≤ 9.55) within the dynamic range analyzed (0.016-50 ng/µL; 41 independent runs). Amel-Y also proved to be compatible with other real-time PCR platforms. CONCLUSION We demonstrated that Amel-Y is a robust quantification system that can be routinely used in forensic casework to obtain reliable autosomal STR profiles and can be suitable as a predictor for Y-STR typing success when male DNA is detected. HRM can be used as a rapid screening tool for male DNA detection in mixed samples. Alternative designs like Amel-Y offer independence from commercial quantification kits in forensic labs.
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Affiliation(s)
- S Ginart
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina.
| | - L Garrigos Calivares
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
| | - M Caputo
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
| | - D Corach
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
| | - A Sala
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
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Kovalchuk SN, Arkhipova AL. Development of TaqMan PCR assay for genotyping SNP rs211250281 of the bovine agpat6 gene. Anim Biotechnol 2023; 34:3250-3255. [PMID: 35635030 DOI: 10.1080/10495398.2022.2077742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Milk fat percentage is an important production trait of dairy cattle and is one of the goals of breeding programs. Over 95% of the milk fat accounts for triacylglycerols. AGPAT6 (1-acylglycerol-3-phosphate O-acyltransferase 6) catalyzes an intermediary step of triglyceride synthesis in the mammary cells. Genome-wide association studies identified SNP rs211250281 (g27: 36520069 G/T) in the agpat6 gene associated with milk fat content and fat-to-protein ratio in dairy cattle. The article presents data on the development of TaqMan PCR assay for genotyping SNP rs211250281 of the bovine agpat6 gene. In this method, a primer pair, initiating amplification of 75-bp fragments of the agpat6 gene, and two allele-specific TaqMan probes are used. Identification of the G and T alleles is based on a comparison of the final fluorescence intensity of FAM and VIC dyes, respectively. The developed TaqMan PCR assay was validated by Sanger sequencing method. The results of both methods fully coincided, that confirmed high accuracy of the developed TaqMan PCR assay. This reliable, simple, rapid, and high-throughput method could be a suitable tool for studying the distribution of the SNP rs211250281 among different cattle breeds and its association with milk fat content.
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Affiliation(s)
- Svetlana N Kovalchuk
- Department of Molecular Biotechnology, Institute of Innovative Biotechnologies in Animal Husbandry - the branch of L.K. Ernst Federal Research Center for Animal Husbandry, Moscow, Russia
| | - Anna L Arkhipova
- Department of Molecular Biotechnology, Institute of Innovative Biotechnologies in Animal Husbandry - the branch of L.K. Ernst Federal Research Center for Animal Husbandry, Moscow, Russia
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Jenks JD, White PL, Kidd SE, Goshia T, Fraley SI, Hoenigl M, Thompson GR. An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections. Expert Rev Mol Diagn 2023; 23:1135-1152. [PMID: 37801397 PMCID: PMC10842420 DOI: 10.1080/14737159.2023.2267977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens. AREAS COVERED We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS). EXPERT OPINION PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings.
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Affiliation(s)
- Jeffrey D Jenks
- Durham County Department of Public Health, Durham, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - P Lewis White
- Public Health Wales Microbiology Cardiff, UHW, United Kingdom and Centre for trials research/Division of Infection/Immunity, Cardiff University, Cardiff, UK
| | - Sarah E Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, Australia
| | - Tyler Goshia
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - George R Thompson
- University of California Davis Center for Valley Fever, Sacramento, CA, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Sacramento, CA, USA
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
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7
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Nan W, Gong M, Lu Y, Li J, Li L, Qu H, Liu C, Wang Y, Wu F, Wu X, Wang Z, Chen Y, Peng D. A novel triplex real-time PCR assay for the differentiation of lumpy skin disease virus, goatpox virus, and sheeppox virus. Front Vet Sci 2023; 10:1175391. [PMID: 37448583 PMCID: PMC10336199 DOI: 10.3389/fvets.2023.1175391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/07/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction Three members of Capripoxvirus (CaPV) genus, including lumpy skin disease virus (LSDV), goatpox virus (GTPV), and sheeppox virus (SPPV), are mentioned as notifiable forms by World Organization for Animal Health. These viruses have negatively impacted ruminant farming industry worldwide, causing great economic losses. Although SPPV and GTPV cause more severe clinical disease in only one animal species, they can transfer between sheep and goats. Both homologous and heterologous immunization strategies are used to protect animals against CaPVs. However, development of accurate and rapid methods to distinguish these three viruses is helpful for the early detection, disease surveillance, and control of CaPV infection. Therefore, we developed a novel triplex real-time PCR (qPCR) for the differentiation of LSDV, GTPV, and SPPV. Methods Universal primers were designed to detect pan-CaPV sequences. Species-specific minor groove binder (MGB)-based probes were designed, which were labeled with FAM for LSDV, HEX for GTPV, and ROX for SPPV. The sensitivity, specificity, reproducibility, and ability of detecting mixed infections were evaluated for the triplex qPCR. Further, 226 clinical samples of the infection and negative controls were subjected to the triplex qPCR, and the results were verified using PCR-restriction fragment length polymorphism (PCR-RFLP) and sequencing methods for PRO30 gene. Results The triplex qPCR could successfully distinguish LSDV, GTPV, and SPPV in one reaction, and the assay sensitivity was 5.41, 27.70, and 17.28 copies/μL, respectively. No cross-reactivity was observed with other viruses causing common ruminant diseases, including des petits ruminants virus, foot-and-mouth disease virus, bluetongue virus, ovine contagious pustular dermatitis virus, infectious bovine rhinotracheitis virus, and bovine viral diarrhea-mucosal disease virus. Inter-and intra-assay variabilities were < 2.5%. The results indicated that the triplex qPCR was highly specific, sensitive, and reproducible. Simulation experiments revealed that this assay could successfully distinguish two or three viruses in case of mixed infections without any cross-reaction. For clinical samples, the results were completely consistent with the results of PCR-RFLP and sequencing. This demonstrated that the assay was reliable for clinical application. Discussion The triplex qPCR is a robust, rapid, and simple tool for identifying various types of CaPV as it can successfully distinguish LSDV, GTPV, and SPPV in one reaction. Furthermore, the assay can facilitate more accurate disease diagnosis and surveillance for better control of CaPV infection.
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Affiliation(s)
- Wenlong Nan
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Mingxia Gong
- China Animal Health and Epidemiology Center, Qingdao, China
| | - You Lu
- China Animal Health and Epidemiology Center, Qingdao, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jinming Li
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Lin Li
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Hailong Qu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Chunju Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Ying Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Faxing Wu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Xiaodong Wu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Zhiliang Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Yiping Chen
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Daxin Peng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
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Chen S, Yin X, Han J, Sun W, Yao H, Song J, Li X. DNA barcoding in herbal medicine: Retrospective and prospective. J Pharm Anal 2023; 13:431-441. [PMID: 37305789 PMCID: PMC10257146 DOI: 10.1016/j.jpha.2023.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/07/2023] [Accepted: 03/25/2023] [Indexed: 06/13/2023] Open
Abstract
DNA barcoding has been widely used for herb identification in recent decades, enabling safety and innovation in the field of herbal medicine. In this article, we summarize recent progress in DNA barcoding for herbal medicine to provide ideas for the further development and application of this technology. Most importantly, the standard DNA barcode has been extended in two ways. First, while conventional DNA barcodes have been widely promoted for their versatility in the identification of fresh or well-preserved samples, super-barcodes based on plastid genomes have rapidly developed and have shown advantages in species identification at low taxonomic levels. Second, mini-barcodes are attractive because they perform better in cases of degraded DNA from herbal materials. In addition, some molecular techniques, such as high-throughput sequencing and isothermal amplification, are combined with DNA barcodes for species identification, which has expanded the applications of herb identification based on DNA barcoding and brought about the post-DNA-barcoding era. Furthermore, standard and high-species coverage DNA barcode reference libraries have been constructed to provide reference sequences for species identification, which increases the accuracy and credibility of species discrimination based on DNA barcodes. In summary, DNA barcoding should play a key role in the quality control of traditional herbal medicine and in the international herb trade.
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Affiliation(s)
- Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xianmei Yin
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xiwen Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
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Hussein EM, Muhammad MAA, Hussein AM, Elzagawy SM, Zaki WM, Temsah AG, Badr MS, Alabbassy MM. Levels of Genetic Variants Among Symptomatic Blastocystis Subtypes and their Relationship to Mucosal Immune Surveillance in the Precancerous Colons of Experimentally Infected Rats. Acta Parasitol 2023; 68:70-83. [PMID: 36380160 PMCID: PMC10011339 DOI: 10.1007/s11686-022-00628-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE The relationship between the genetic diversity of Blastocystis and immune surveillance in precancerous colons with blastocystosis is still under investigation. This study aimed to identify the genetic Blastocystis variants among 54 symptomatic human isolates and their relationship to mucosal immune surveillance in the precancerous polyps of experimentally infected rats. METHODS Polymerase chain reaction and high-resolution melting (PCR/HRM) curves discriminated human symptomatic Blastocystis isolates into subtypes (STs)/intrasubtypes, which were orally administered to rats to induce experimental infection. Then, the mucosal immune responses of the infected colons were evaluated in relation to polyp formation through immunostaining to identify mucus MUC2 and determine mucosal immune cell (goblet, lymphocyte and mast) counts, secretory IgA levels and parasitic intestinal invasion. RESULTS ST1, ST3, and ST4 were found in 18.5% (10/54), 54.7% (29/54), and 27.8% (15/54) of the samples, respectively. Then, the HRM curve discriminated ST3 into the wild, mutant, and heterozygous [17/54 (31.5%), 5/54 (9.3%), and 7/54 (12.9%)] intrasubtypes. ST1 and ST4 had no genetic variations. Precancerous polyps were detected in the colons of 40.5% of the infected rats. ST1 constituted 14.7% of these cases, while the wild, mutant, and heterozygous intrasubtypes of ST3 showed polyps in 12.9%, 5.5%, and 5.5% of cases, respectively. Only 1.9% of the polyps were related to ST4. MUC2 showed weak immunostaining in 44.5% of the infected colons, and 38.9% were polyp inducers. Low goblet cell numbers and high interepithelial lymphocyte counts were significantly associated with polyp formation, particularly with ST1 and wild ST3. Among the polyp inducers, high numbers of mast cells were detected in wild ST3 and ST4, while a low number was found with heterozygous ST3. The level of secretory IgA was low in polyp-inducing STs. Most of the results were statistically significant. CONCLUSION Immunosurveillance showed a potential relationship between ST1 and the ST3 intrasubtypes and precancerous polyps. This relationship may provide insight into the prevention and/or development of new immunotherapeutic strategies to combat colorectal cancer.
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Affiliation(s)
- Eman M Hussein
- Medical Parasitology Department, Faculty of Medicine, Suez Canal University, Ismailia, 41522, Egypt.
| | - Muhammad A A Muhammad
- Pathology Department, Faculty of Medicine, Suez Canal, University, Ismailia, 41522, Egypt
| | - Abdalla M Hussein
- Bio-Physics Department, Faculty of Science, Al-Azhar University, Cairo, 11652, Egypt
| | - Sherine M Elzagawy
- Medical Parasitology Department, Faculty of Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Wafaa M Zaki
- Medical Parasitology Department, Faculty of Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Ashraf G Temsah
- Medical Parasitology Department, Faculty of Medicine, Damietta Branch, AL Azhar University, Damietta, Egypt
| | - Mohamed S Badr
- Medical Genetic Centre, Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Maha M Alabbassy
- Medical Parasitology Department, Faculty of Medicine, Suez Canal University, Ismailia, 41522, Egypt
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10
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Emerging biotechnology applications in natural product and synthetic pharmaceutical analyses. Acta Pharm Sin B 2022; 12:4075-4097. [DOI: 10.1016/j.apsb.2022.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/15/2022] Open
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11
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Ruengdit C, Punyamung M, Khamphikham P, Pongpunyayuen P, Intasai N, Pornprasert S. Multiplex Quantitative Real-Time Polymerase Chain Reaction and High-Resolution Melting Analysis for Identification of a Couple At-Risk of Having a Newborn with Severe Thalassemia. Hemoglobin 2022; 45:309-313. [PMID: 35139748 DOI: 10.1080/03630269.2022.2028634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Many polymerase chain reaction (PCR)-based techniques have been used for routine diagnosis of α- and β-thalassemias. However, most require a multi step of post-PCR processes that are time-consuming and labor-intensive procedures. This study reported the successful use of multiplex quantitative real-time PCR (qPCR), with high-resolution melting (HRM) analysis for diagnosis of two common deletional α0-thalassemia (α0-thal) and 15 common β-thalassemia (β-thal) mutations, in order to identify a couple at-risk of having a newborn with severe thalassemia in the northern region of Thailand. With this approach, 22 (7.2%) of 306 couples were diagnosed as being at-risk for having a child with severe thalassemia, including three homozygous α0-thal, five homozygous β-thal and 14 Hb E (HBB: c.79G>A)/β0-thal disease. Our findings indicated that multiplex qPCR with HRM is applicable for routine molecular diagnosis in order to identify a couple at-risk of having a newborn with severe thalassemia, especially in an endemic region.
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Affiliation(s)
- Chedtapak Ruengdit
- Division of Clinical Microscopy, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Manoo Punyamung
- Associated Medical Sciences Clinical Service Center, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Pinyaphat Khamphikham
- Division of Clinical Microscopy, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Panida Pongpunyayuen
- Associated Medical Sciences Clinical Service Center, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Nutjeera Intasai
- Division of Clinical Microscopy, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Sakorn Pornprasert
- Division of Clinical Microscopy, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
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12
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Azizi MMF, Lau HY, Abu-Bakar N. Integration of advanced technologies for plant variety and cultivar identification. J Biosci 2021. [DOI: 10.1007/s12038-021-00214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Wan J, Zheng L, Kong L, Lu Z, Tao Y, Feng Z, Lv F, Meng F, Bie X. Development of a rapid detection method for real-time fluorescent quantitative PCR of Salmonella spp. and Salmonella Enteritidis in ready-to-eat fruits and vegetables. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Kovalchuk SN, Arkhipova AL. Development of TaqMan PCR assay for detection of A and B variants of the bovine β-lactoglobulin. Anim Biotechnol 2020; 33:997-1001. [PMID: 33174805 DOI: 10.1080/10495398.2020.1844221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
β-Lactoglobulin (BLG) is one of the prevalent whey protein in cattle. To date, several variants of bovine BLG have been found, but the most common are A and B, which differ from each other by SNPs rs109625649 and rs110066229. Numerous studies showed effects of A and B variants of BLG on milk yield, fat and protein content and cheese-making properties. To date, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), allele-specific polymerase chain reaction (ASPCR), PCR single-strand conformation polymorphism (PCR-SSCP) and high resolution melting (HRM) methods have been proposed for detection of A and B variants of bovine BLG. These methods involve multistep sample processing, which is an essential disadvantage in conducting large-scale cattle genotyping projects. This article describes a development of TaqMan PCR assay for detection of A and B variants (rs109625649) of bovine BLG. In this method a primer pair, initiating amplification of 101-bp fragment of BLG gene, and two allele-specific TaqMan probes are used. Identification of B and A variants of BLG is based on comparison of final fluorescence intensity of FAM and VIC dyes, respectively. The developed one-step method requires less time and is more suitable for large-scale genotyping of cattle compared to the commonly used PCR-RFLP.
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Affiliation(s)
- Svetlana N Kovalchuk
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Russia
| | - Anna L Arkhipova
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Russia
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Zhang W, Ming Z, Chen N, Liu L, Liao Y, Xiao X, Wang H. An interlocked DNA cascade system for universal probe-based melting curve analysis. NANOSCALE 2020; 12:20449-20455. [PMID: 33026003 DOI: 10.1039/d0nr04691d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-base mutations are the most common type of mutation in human diseases. Melting curve analysis is currently one of the most commonly used methods to detect single base mutations. However, the existing melting curve analysis cannot possess universality and robust detection performance simultaneously. Therefore, herein, we invented an interlocked DNA cascade system based universal melting curve analysis (ICU-MCA). The strategy is based on the probe dissolution curve method by designing a bridge strand to achieve an ideal distinction between mutant-type DNA and wild-type DNA. What is more, this method can complete multiplexed detection only by changing the bridge sequence, replacing the specific and expensive probe in a traditional probe based melting curve analysis. We performed 6-plex detection on 6 single-base point mutations in BRAC1/2 genes on synthetic single stranded DNA and verified the compatibility of ICU-MCA and PCR and detected BRCA1/c.2082C>T and BRCA2/c.7397T>C mutations in peripheral blood DNA of ovarian cancer patients. Overall, ICU-MCA is one of the best methods in the field of melting curve analysis for detecting single-base mutations.
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Affiliation(s)
- Wei Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Zhihao Ming
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China. and Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Na Chen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liquan Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuheng Liao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xianjin Xiao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China. and Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hongbo Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
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Rojas MF, König GA, Vagnozzi AE, Vera FS, Scolaro LA, Craig MI. Optimization and application of a high-resolution melting protocol in the characterization of avian infectious laryngotracheitis virus. Rev Argent Microbiol 2020; 53:89-97. [PMID: 32921516 DOI: 10.1016/j.ram.2020.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/21/2020] [Accepted: 04/06/2020] [Indexed: 10/23/2022] Open
Abstract
A previous sequence analysis of a US5 gene fragment of infectious laryngotracheitis virus (ILTV) performed in an Argentinian epidemiological study allowed to differentiate between wild and vaccine strains. This analysis also defined five ILTV haplotypes with specific variations at positions 461, 484, 832, 878 and 894 of the US5 gene. This characterization of viral strains may also be accomplished using the High-Resolution Melting Analysis (HRMA), which has been described as an effective, fast and sensitive method to detect mutations in PCR products. In the present study, an HRM protocol was developed with the aim of characterizing the circulating ILTV strains in Argentina. The specificity of this tool was confirmed in different DNA diluents, without interference from heterologous DNA or other cellular metabolites. Additionally, the salt concentration in the elution buffer used for DNA extraction did not alter the curve profiles. Higher concentrations of DNA (Ct≅26.0) displayed well-defined curve profiles, whereas lower concentrations (Ct≅32.5) exhibited more heterogeneous curves. The HRMA showed 97.49% concordance with the reference technique, i.e., sequencing. The HRM protocol has the capability to perform DNA amplification prior to its characterization. Thus, eventually this technique may be used simultaneously as a diagnostic tool. This advantage implies a significant reduction in the time and effort involved in sample processing.
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Affiliation(s)
- M Florencia Rojas
- Laboratorio de Sanidad Aviar, INTA EEA Concepción del Uruguay, Ruta 39 Km 143,5 (3260) Concepción del Uruguay, Entre Ríos, Argentina
| | - Guido A König
- Instituto de Biotecnología, CICVyA, INTA Hurlingham, CC 25 (1712) Hurlingham, Buenos Aires, Argentina; Consejo de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Ariel E Vagnozzi
- Instituto de Virología, CICVyA, INTA Hurlingham, CC 25 (1712) Hurlingham, Buenos Aires, Argentina
| | - Federico S Vera
- Laboratorio de Sanidad Aviar, INTA EEA Concepción del Uruguay, Ruta 39 Km 143,5 (3260) Concepción del Uruguay, Entre Ríos, Argentina
| | - Luis A Scolaro
- Departamento de Química Biológica, FCEN, Universidad de Buenos Aires, (1428), Buenos Aires, Argentina
| | - M Isabel Craig
- Instituto de Virología, CICVyA, INTA Hurlingham, CC 25 (1712) Hurlingham, Buenos Aires, Argentina.
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Improving Quantitative Power in Digital PCR through Digital High-Resolution Melting. J Clin Microbiol 2020; 58:JCM.00325-20. [PMID: 32295887 DOI: 10.1128/jcm.00325-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/05/2020] [Indexed: 12/23/2022] Open
Abstract
Applying digital PCR (dPCR) technology to challenging clinical and industrial detection tasks has become more prevalent because of its capability for absolute quantification and rare target detection. However, practices learned from quantitative PCR (qPCR) that promote assay robustness and wide-ranging utility are not readily applied in dPCR. These include internal amplification controls to account for false-negative reactions and amplicon high-resolution melt (HRM) analysis to distinguish true positives from false positives. Incorporation of internal amplification controls in dPCR is challenging because of the limited fluorescence channels available on most machines, and the application of HRM analysis is hindered by the separation of heating and imaging functions on most dPCR systems. We use a custom digital HRM platform to assess the utility of HRM-based approaches for mitigation of false positives and false negatives in dPCR. We show that detection of an exogenous internal control using dHRM analysis reduces the inclusion of false-negative partitions, changing the calculated DNA concentration up to 52%. The integration of dHRM analysis enables classification of partitions that would otherwise be considered ambiguous "rain," which accounts for up to ∼3% and ∼10% of partitions in intercalating dye and hydrolysis probe dPCR, respectively. We focused on developing an internal control method that would be compatible with broad-based microbial detection in dPCR-dHRM. Our approach can be applied to a number of DNA detection methods including microbial profiling and may advance the utility of dPCR in clinical applications where accurate quantification is imperative.
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18
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Martínez-Saucedo M, Ornelas-Fuentes C, Dedden M, Sánchez-Urbina R, Díaz-García H, Aquino-Jarquin G, Moreno-Salgado R, Granados-Riveron JT. Implementation of high-resolution melting analysis of the porcupine (PORCN) gene for molecular diagnosis of focal dermal hypoplasia: Identification of a novel mutation. J Gene Med 2020; 22:e3165. [PMID: 31984575 DOI: 10.1002/jgm.3165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/18/2020] [Accepted: 01/19/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Focal dermal hypoplasia (FDH) is rare X-linked dominant disease characterized by atrophy and linear pigmentation of the skin, split hand/foot deformities and ocular anomalies. FDH is caused by mutations of the Porcupine (PORCN) gene, which encodes an enzyme that catalyzes the palmitoylation of Wnt ligands required for their secretion. High resolution melting analysis (HRM) is a technique that allows rapid, labor-efficient, low-cost detection of genomic variants. In the present study, we report the successful implementation of HRM in the molecular diagnosis of FDH. METHODS Polymerase chain reaction and HRM assays were designed and optimized for each of the coding exons of the PORCN gene, processing genomic DNA samples form a non-affected control and a patient complying with the FDH diagnostic criteria. The causal mutation was characterized by Sanger sequencing from an amplicon showing a HRM trace suggesting heterozygous variation and was validated using an amplification-refractory mutation system (ARMS) assay. RESULTS The melting profiles suggested the presence of a variant in the patient within exon 1. Sanger sequencing revealed a previously unknown C to T transition replacing a glutamine codon for a premature stop codon at position 28, which was validated using ARMS. CONCLUSIONS Next-generation sequencing facilitates the molecular diagnosis of monogenic disorders; however, its cost-benefit ratio is not optimal when a single, small or medium size causal gene is already identified and the clinical diagnostic presumption is strong. Under those conditions, as it is the case for FDH, HRM represents a cost- and labor-effective approach.
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Affiliation(s)
- Mirna Martínez-Saucedo
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Carolina Ornelas-Fuentes
- Department of Medical Genetics and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Mark Dedden
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Rocío Sánchez-Urbina
- Laboratory of Developmental Biology and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez,, Mexico City, México
| | - Héctor Díaz-García
- Laboratory of Developmental Biology and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez,, Mexico City, México
| | - Guillermo Aquino-Jarquin
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Rodrigo Moreno-Salgado
- Department of Medical Genetics and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Javier T Granados-Riveron
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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Shevelev GY, Kabilov MR, Lomzov AA, Dovydenko IS, Pyshnyi DV. Features of Determining Thermodynamic Parameters of Formation of Nucleic Acid Complexes Using Thermal Denaturation with Fluorimetric Signal Detection. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019060359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Herrmann MG, Durtschi JD, Wittwer CT, Voelkerding KV. Expanded Instrument Comparison of Amplicon DNA Melting Analysis for Mutation Scanning and Genotyping. Clin Chem 2020; 53:1544-8. [PMID: 17556647 DOI: 10.1373/clinchem.2007.088120] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: Additional instruments have become available since instruments for DNA melting analysis of PCR products for genotyping and mutation scanning were compared. We assessed the performance of these new instruments for genotyping and scanning for mutations.
Methods: A 110-bp fragment of the β-globin gene including the sickle cell anemia locus (HBB c. 20A>T) was amplified by PCR in the presence of LCGreen Plus or SYBR Green I. Amplicons of 4 different genotypes [wild-type, homozygous, and heterozygous HBB c. 20A>T and double-heterozygote HBB c. (9C>T; 20A>T)] were melted on 7 different instruments [Applied Biosystems 7300, Corbett Life Sciences Rotor-Gene 6500HRM, Eppendorf Mastercycler RealPlex4S, Idaho Technology LightScanner (384 well), Roche LightCycler 480 (96 and 384 well) and Stratagene Mx3005p] at a rate of 0.61 °C/s or when this was not possible, at 0.50 °C steps. We evaluated the ability of each instrument to genotype by melting temperature (Tm) and to scan for heterozygotes by curve shape.
Results: The ability of most instruments to accurately genotype single-base changes by amplicon melting was limited by spatial temperature variation across the plate (SD of Tm = 0.020 to 0.264 °C). Other variables such as data density, signal-to-noise ratio, and melting rate also affected heterozygote scanning.
Conclusions: Different instruments vary widely in their ability to genotype homozygous variants and scan for heterozygotes by whole amplicon melting analysis. Instruments specifically designed for high-resolution melting, however, displayed the least variation, suggesting better genotyping accuracy and scanning sensitivity and specificity.
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Affiliation(s)
- Mark G Herrmann
- Institute for Clinical and Experimental Pathology, ARUP, Salt Lake City, UT 84108, USA.
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21
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Yang P, Song Y, Xia X, Zhang AM. Rapid screening mutations of first-line-drug-resistant genes in Mycobacterium tuberculosis strains by allele-specific real-time quantitative PCR. PeerJ 2019; 7:e6696. [PMID: 30972260 PMCID: PMC6448557 DOI: 10.7717/peerj.6696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/27/2019] [Indexed: 12/27/2022] Open
Abstract
Tuberculosis (TB) is a worldwide health, economic, and social burden, especially in developing countries. Drug-resistant TB is the most serious type of this burden. Thus, it is necessary to screen drug-resistant mutations by using a simple and rapid detection method. A total of 32 pairs of allele-specific PCR (AS-PCR) primers were designed to screen mutation and/or wild-type alleles of 16 variations in four first-line drug-resistant genes (katG, rpoB, rpsL, and embB) of TB strains. A pair of primers was designed to amplify 16S rRNA gene and to verify successful amplification. Subsequently, we tested the specificity and sensitivity of these AS-PCR primers. The optimized condition of these AS-PCR primers was first confirmed. All mutations could be screened in general AS-PCR, but only 13 of 16 variations were intuitively investigated by using real-time quantitative PCR (qPCR) and AS-PCR primers. The results of specificity assay suggested that the AS-PCR primers with mutation and/or wildtype alleles could successfully amplify the corresponding allele under optimized PCR conditions. The sensitivity of nine pairs of primers was 500 copy numbers, and the other seven pairs of primers could successfully amplify correct fragments with a template comprising 103 or 104 copy numbers template. An optimized AS-qPCR was established to screen drug-resistant mutations in TB strains with high specificity and sensitivity.
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Affiliation(s)
- Pengpeng Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yuzhu Song
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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Application of high-resolution melting curve analysis for identification of Muscovy duck parvovirus and goose parvovirus. J Virol Methods 2019; 266:121-125. [DOI: 10.1016/j.jviromet.2018.12.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 12/19/2018] [Accepted: 12/26/2018] [Indexed: 01/21/2023]
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23
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Gao Z, Liu Y, Wang X, Wei X, Han J. DNA Mini-Barcoding: A Derived Barcoding Method for Herbal Molecular Identification. FRONTIERS IN PLANT SCIENCE 2019; 10:987. [PMID: 31555305 PMCID: PMC6724574 DOI: 10.3389/fpls.2019.00987] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 07/12/2019] [Indexed: 05/06/2023]
Abstract
In recent years, the demand for natural herbal products (NHP) has increased; however, the quality of these products is difficult to confirm due to the lack of a comprehensive quality control system. Traditional methods are not effective in detecting processed ingredients. DNA barcoding is an established technique that has been used for more than 10 years. This technique uses short standard sequences (generally 200-600 bp) to identify species. While a complete DNA barcode is difficult to obtain from NHP due to DNA degradation, mini-barcoding is a complementary tool to identify species in NHP. DNA mini-barcoding uses smaller DNA segments for polymerase chain reaction amplification and can be applied to identify species rapidly. The present review summarizes the development and application of DNA mini-barcodes over recent years and discusses the limitations of this technique. This review also compares mini-barcoding and meta-barcoding, a technique using universal polymerase chain reaction primers to simultaneously amplify multiple DNA barcodes and identify many species in a single environmental sample. Additionally, other detection methods that can be combined with mini-barcodes, such as nucleotide signatures, high-resolution DNA melting analysis, and gold nanoparticles, are discussed. DNA mini-barcoding can fill the gaps left by other methods in the field of herbal molecular identification.
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Fitarelli-Kiehl M, Yu F, Ashtaputre R, Leong KW, Ladas I, Supplee J, Paweletz C, Mitra D, Schoenfeld JD, Parangi S, Makrigiorgos GM. Denaturation-Enhanced Droplet Digital PCR for Liquid Biopsies. Clin Chem 2018; 64:1762-1771. [PMID: 30274976 DOI: 10.1373/clinchem.2018.293845] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/04/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Although interest in droplet-digital PCR technology (ddPCR) for cell-free circulating DNA (cfDNA) analysis is burgeoning, the technology is compromised by subsampling errors and the few clinical targets that can be analyzed from limited input DNA. The paucity of starting material acts as a "glass ceiling" in liquid biopsies because, irrespective how analytically sensitive ddPCR techniques are, detection limits cannot be improved past DNA input limitations. METHODS We applied denaturation-enhanced ddPCR (dddPCR) using fragmented genomic DNA (gDNA) with defined mutations. We then tested dddPCR on cfDNA from volunteers and patients with cancer for commonly-used mutations. gDNA and cfDNA were tested with and without end repair before denaturation and digital PCR. RESULTS By applying complete denaturation of double-stranded DNA before ddPCR droplet formation the number of positive droplets increased. dddPCR using gDNA resulted in a 1.9-2.0-fold increase in data-positive droplets, whereas dddPCR applied on highly-fragmented cfDNA resulted in a 1.6-1.7-fold increase. End repair of cfDNA before denaturation enabled cfDNA to display a 1.9-2.0-fold increase in data-positive signals, similar to gDNA. Doubling of data-positive droplets doubled the number of potential ddPCR assays that could be conducted from a given DNA input and improved ddPCR precision for cfDNA mutation detection. CONCLUSIONS dddPCR is a simple and useful modification in ddPCR that enables extraction of more information from low-input clinical samples with minor change in protocols. It should be applicable to all ddPCR platforms for mutation detection and, potentially, for gene copy-number analysis in cancer and prenatal screening.
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Affiliation(s)
- Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ravina Ashtaputre
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Julianna Supplee
- Department of Medical Oncology and Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Cloud Paweletz
- Department of Medical Oncology and Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Devarati Mitra
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jonathan D Schoenfeld
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sareh Parangi
- Department of General & Gastrointestinal Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA;
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Hou M, Liang X, Zhang T, Qiu C, Chen J, Liu S, Wang W, Fan X. DNA Melting Analysis with Optofluidic Lasers Based on Fabry-Pérot Microcavity. ACS Sens 2018; 3:1750-1755. [PMID: 30141331 DOI: 10.1021/acssensors.8b00481] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We conduct DNA high-resolution melting (HRM) analysis using optofluidic lasers based on a Fabry-Pérot microcavity. Compared to the fluorescence-based HRM, the laser-based HRM has advantages of higher emission intensity for better signal-to-noise ratio and sharper transition for better temperature resolution. In addition, the melting temperature can be lowered by optimizing the laser conditions such as external pump and cavity Q-factor. In this work, we first theoretically analyze the laser-based HRM. Then experiments are performed on three long DNA sequences as model systems, one being 99 bases and the other two being 130 bases long but with different GC contents. We show that the laser-based HRM is able to distinguish the target and the single-base mismatched DNA as long as 130 bases and with nearly 50% GC content. The dependence of laser threshold on the temperature for each DNA sample is first experimentally investigated and by optimizing the external pump, the melting temperature is reduced by more than 10 °C, compared to the fluorescence-based HRM for long DNA sequences up to 130 bases. Finally, we demonstrate an alternative method of using the laser-based HRM for rapid DNA screening that does not exist for the fluorescence-based HRM, in which laser excitation is scanned at a fixed temperature to distinguish the target and the base-mismatched DNA sequences. It is shown that the 130-bases-long DNA with nearly 50% GC content can have as much as 20% difference in the laser threshold and 40% difference in the laser output slope between the target and the single-base mismatched sequences, despite only 0.5 °C difference in their melting temperature, indicating that the laser-excitation-scanning method can also be suitable for long DNA sequences with higher GC content.
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Affiliation(s)
- Mengdi Hou
- Key Lab of Advanced Transducers and Intelligent Control System of Ministry of Education, Taiyuan University of Technology, 79 Yingze Street, Taiyuan 030024, P. R. China
| | - Xiyue Liang
- Key Lab of Advanced Transducers and Intelligent Control System of Ministry of Education, Taiyuan University of Technology, 79 Yingze Street, Taiyuan 030024, P. R. China
| | - Tingting Zhang
- Key Lab of Advanced Transducers and Intelligent Control System of Ministry of Education, Taiyuan University of Technology, 79 Yingze Street, Taiyuan 030024, P. R. China
| | - Chengyu Qiu
- Key Lab of Advanced Transducers and Intelligent Control System of Ministry of Education, Taiyuan University of Technology, 79 Yingze Street, Taiyuan 030024, P. R. China
| | - Jingdong Chen
- Key Lab of Advanced Transducers and Intelligent Control System of Ministry of Education, Taiyuan University of Technology, 79 Yingze Street, Taiyuan 030024, P. R. China
| | - Shaoding Liu
- Key Lab of Advanced Transducers and Intelligent Control System of Ministry of Education, Taiyuan University of Technology, 79 Yingze Street, Taiyuan 030024, P. R. China
| | - Wenjie Wang
- Key Lab of Advanced Transducers and Intelligent Control System of Ministry of Education, Taiyuan University of Technology, 79 Yingze Street, Taiyuan 030024, P. R. China
| | - Xudong Fan
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109, United States
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Sinha M, Mack H, Coleman TP, Fraley SI. A High-Resolution Digital DNA Melting Platform for Robust Sequence Profiling and Enhanced Genotype Discrimination. SLAS Technol 2018; 23:580-591. [DOI: 10.1177/2472630318769846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA melting analysis provides a rapid method for genotyping a target amplicon directly after PCR amplification. To transform melt genotyping into a broad-based profiling approach for heterogeneous samples, we previously proposed the integration of universal PCR and melt analysis with digital PCR. Here, we advanced this concept by developing a high-resolution digital melt platform with precise thermal control to accomplish reliable, high-throughput heat ramping of microfluidic chip digital PCR reactions. Using synthetic DNA oligos with defined melting temperatures, we characterized sources of melting variability and minimized run-to-run variations. Within-run comparisons throughout a 20,000-reaction chip revealed that high-melting-temperature sequences were significantly less prone to melt variation. Further optimization using bacterial 16S amplicons revealed a strong dependence of the number of melting transitions on the heating rate during curve generation. These studies show that reliable high-resolution melt curve genotyping can be achieved in digital, picoliter-scale reactions and demonstrate that rate-dependent melt signatures may be useful for enhancing automated melt genotyping.
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Affiliation(s)
- Mridu Sinha
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Clinical Translational Research Institute, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Hannah Mack
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Clinical Translational Research Institute, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Todd P. Coleman
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Stephanie I. Fraley
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Clinical Translational Research Institute, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
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Abstract
High-resolution melting analysis (HRMA) is a simple, quick, and effective method to scan and screen PCR amplicons for sequence variants. HRMA is a nondestructive closed tube assay; after PCR, DNA melting can directly be performed on the amplified samples without any purification or separation steps. For single SNP genotyping, HRMA is an attractive alternative to Sanger sequencing, restriction enzyme analysis, and hydrolysis probes.
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Affiliation(s)
- Rolf H A M Vossen
- Department of Human Genetics, Leiden Genome Technology Center, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
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Li M, Palais R, Zhou L, Wittwer C. Quantifying variant differences in DNA melting curves: Effects of length, melting rate, and curve overlay. Anal Biochem 2017; 539:90-95. [DOI: 10.1016/j.ab.2017.10.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 10/12/2017] [Accepted: 10/19/2017] [Indexed: 11/30/2022]
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Słomka M, Sobalska-Kwapis M, Wachulec M, Bartosz G, Strapagiel D. High Resolution Melting (HRM) for High-Throughput Genotyping-Limitations and Caveats in Practical Case Studies. Int J Mol Sci 2017; 18:ijms18112316. [PMID: 29099791 PMCID: PMC5713285 DOI: 10.3390/ijms18112316] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/06/2017] [Accepted: 10/31/2017] [Indexed: 01/02/2023] Open
Abstract
High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup.
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Affiliation(s)
- Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
| | - Monika Wachulec
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236 Łódź, Poland.
| | - Grzegorz Bartosz
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236 Łódź, Poland.
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
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Pryor RJ, Myrick JT, Palais RA, Sundberg SO, Paek JY, Wittwer CT, Knight IT. High-Speed Melting Analysis: The Effect of Melting Rate on Small Amplicon Microfluidic Genotyping. Clin Chem 2017; 63:1624-1632. [PMID: 28818830 DOI: 10.1373/clinchem.2017.276147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 07/06/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND High-resolution DNA melting analysis of small amplicons is a simple and inexpensive technique for genotyping. Microfluidics allows precise and rapid control of temperature during melting. METHODS Using a microfluidic platform for serial PCR and melting analysis, 4 targets containing single nucleotide variants were amplified and then melted at different rates over a 250-fold range from 0.13 to 32 °C/s. Genotypes (n = 1728) were determined manually by visual inspection after background removal, normalization, and conversion to negative derivative plots. Differences between genotypes were quantified by a genotype discrimination ratio on the basis of inter- and intragenotype differences using the absolute value of the maximum vertical difference between curves as a metric. RESULTS Different homozygous curves were genotyped by melting temperature and heterozygous curves were identified by shape. Technical artifacts preventing analysis (0.3%), incorrect (0.06%), and indeterminate (0.4%) results were minimal, occurring mostly at slow melting rates (0.13-0.5 °C/s). Genotype discrimination was maximal at around 8 °C/s (2-8 °C/s for homozygotes and 8-16 °C/s for heterozygotes), and no genotyping errors were made at rates >0.5 °C/s. PCR was completed in 10-12.2 min, followed by melting curve acquisition in 4 min down to <1 s. CONCLUSIONS Microfluidics enables genotyping by melting analysis at rates up to 32 °C/s, requiring <1 s to acquire an entire melting curve. High-speed melting reduces the time for melting analysis, decreases errors, and improves genotype discrimination of small amplicons. Combined with extreme PCR, high-speed melting promises nucleic acid amplification and genotyping in < 1 min.
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Affiliation(s)
- Robert J Pryor
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
| | | | - Robert A Palais
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT.,Department of Mathematics, Utah Valley University, Orem, UT
| | - Scott O Sundberg
- Canon Virginia, Inc., Newport News, VA.,Canon U.S. Life Sciences, Inc., Rockville, MD
| | | | - Carl T Wittwer
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT;
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Moghadam AAS, Mahjoubi F, Reisi N, Vosough P. Investigation of FANCA gene in Fanconi anaemia patients in Iran. Indian J Med Res 2017; 143:184-96. [PMID: 27121516 PMCID: PMC4859127 DOI: 10.4103/0971-5916.180206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND & OBJECTIVES Fanconi anaemia (FA) is a syndrome with a predisposition to bone marrow failure, congenital anomalies and malignancies. It is characterized by cellular hypersensitivity to cross-linking agents such as mitomycin C (MMC). In the present study, a new approach was selected to investigate FANCA (Fanconi anaemia complementation group A) gene in patients clinically diagnosed with cellular hypersensitivity to DNA cross-linking agent MMC. METHODS Chromosomal breakage analysis was performed to prove the diagnosis of Fanconi anaemia in 318 families. Of these, 70 families had a positive result. Forty families agreed to molecular genetic testing. In total, there were 27 patients with unknown complementary types. Genomic DNA was extracted and total RNA was isolated from fresh whole blood of the patients. The first-strand cDNA was synthesized and the cDNA of each patient was then tested with 21 pairs of overlapping primers. High resolution melting curve analysis was used to screen FANCA, and LinReg software version 1.7 was utilized for analysis of expression. RESULTS In total, six sequence alterations were identified, which included two stop codons, two frames-shift mutations, one large deletion and one amino acid exchange. FANCA expression was downregulated in patients who had sequence alterations. INTERPRETATION & CONCLUSIONS The results of the present study show that high resolution melting (HRM) curve analysis may be useful in the detection of sequence alteration. It is simpler and more cost-effective than the multiplex ligation-dependent probe amplification (MLPA) procedure.
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Affiliation(s)
| | - Frouzandeh Mahjoubi
- Medical Biotechnology Institute, National Institute of Genetic Engineering & Biotechnology (NIGEB), Tehran, Iran
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Graziano S, Gullì M, Marmiroli N. Development and validation of a SYBR-Green I Real-Time PCR test to detect bivalves includingMytilusspecies in foods. Int J Food Sci Technol 2017. [DOI: 10.1111/ijfs.13429] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sara Graziano
- Dipartimento di Bioscienze; Università degli Studi di Parma; Parco Area delle Scienze 11a Parma 43124 Italy
| | - Mariolina Gullì
- Dipartimento di Bioscienze; Università degli Studi di Parma; Parco Area delle Scienze 11a Parma 43124 Italy
- Centro Interdipartimentale SITEIA.PARMA; Università degli Studi di Parma; Parco Area delle Scienze 181/A Parma 43124 Italy
| | - Nelson Marmiroli
- Dipartimento di Bioscienze; Università degli Studi di Parma; Parco Area delle Scienze 11a Parma 43124 Italy
- Centro Interdipartimentale SITEIA.PARMA; Università degli Studi di Parma; Parco Area delle Scienze 181/A Parma 43124 Italy
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Hurtado-Gonzales O, Aragon-Caballero L, Flores-Torres J, Veld WMI’, Lamour K. Molecular comparison of natural hybrids ofPhytophthora nicotianaeandP. cactoruminfecting loquat trees in Peru and Taiwan. Mycologia 2017; 101:496-502. [DOI: 10.3852/08-079] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- O.P. Hurtado-Gonzales
- Entomology and Plant Pathology Department, University of Tennessee, Knoxville, Tennessee 37996
| | | | - J.G. Flores-Torres
- Departamento de Fitopatologia, Universidad Nacional Agraria La Molina, Lima 12, Peru
| | - Willem Man in ’t Veld
- Department of Mycology, Plant Protection Service, P.O. Box 9102, 6700, HC, Wageningen, the Netherlands
| | - K.H. Lamour
- Entomology and Plant Pathology Department, University of Tennessee, Knoxville, Tennessee 37996
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Xu JJ, Yao FR, Jiang M, Zhang YT, Guo F. High-resolution melting analysis for rapid and sensitive NOTCH1 screening in chronic lymphocytic leukemia. Int J Mol Med 2017; 39:415-422. [PMID: 28075457 DOI: 10.3892/ijmm.2017.2849] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 12/14/2016] [Indexed: 11/05/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a biological and clinical heterogeneous disease. Activating mutations of NOTCH1 have been implicated to be associated with adverse prognosis in CLL. The objective of the present study was to develop an effective high-resolution melting (HRM) assay for detecting NOTCH1 mutations. Genomic DNA (gDNA) extracted from 133 CLL patients was screened by HRM assay, and the results were compared with the data obtained using direct sequencing. The relative sensitivity of the HRM assay and direct sequencing was evaluated using diluted gDNA with different NOTCH1 mutational frequencies. The HRM assay was able to detect and discriminate samples with NOTCH1 mutations from the wild-type template in CLL. Eight of the 133 CLL patients (6.02%) were scored positively for NOTCH1 mutations in the HRM assay. The results of the NOTCH1 mutations detected by HRM analysis achieved 100% concordance with those determined from direct sequencing. HRM had a higher sensitivity (1%) and shorter turn-around time (TAT), compared to direct sequencing. In conclusion, the HRM assay developed by us was confirmed to be a rapid, sensitive, and promising approach for high-throughput prognostic NOTCH1 screening in CLL. It enables real-time NOTCH1 evaluation, which is of great significance in clinical practice and may facilitate the decision-making of clinicians in CLL.
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Affiliation(s)
- Jing-Jing Xu
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Fei-Rong Yao
- Department of Radiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Min Jiang
- Department of Blood Transfusion, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - You-Tao Zhang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Feng Guo
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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Abstract
DNA melting analysis for the identification of sequence is increasingly used in molecular diagnostics. Recent advances in DNA melting analysis, including high-resolution instrumentation and specialized fluorescent DNA-binding dyes, allow genotyping by whole amplicon melting without probes. With the popularity of melting analysis as a diagnostic tool, there is a need to characterize the ability of commercially available real-time PCR instruments to perform high-resolution amplicon melting analyses. Four real-time instruments varying in sample format, throughput, and heat transfer (Cepheid's SmartCycler, Idaho Technology's HR-1, and Roche's LightCycler 1.2 and LightCycler 2.0) were evaluated for their ability to differentiate homozygous genotypes at the human β-globin sickle cell locus. The melting transition was monitored by including the dye LCGreen Plus in the PCR, and the data were uniformly analyzed with custom in-house software. The wild-type and mutant homozygous genotypes differed by a theoretical Tm of 0.09°C and were best discriminated by the high-resolution HR-1 instrument. All instruments could identify a double single nucleotide polymorphism heterozygote by the heteroduplexes formed. However, signal-to-noise ratios varied from 260 to 3500, suggesting that melting instrument design (data acquisition, data density, thermal control) determines the accuracy of genotyping by amplicon melting. (JALA 2006;11:273-7)
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36
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Lin CY, Ho CM, Tamamyan G, Yang SF, Peng CT, Chang JG. Validating the Sensitivity of High-Resolution Melting Analysis for JAK2 V617F Mutation in the Clinical Setting. J Clin Lab Anal 2016; 30:838-844. [PMID: 27169616 DOI: 10.1002/jcla.21945] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/05/2016] [Accepted: 01/13/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Janus kinase 2 (JAK2) plays an important role in normal hematopoietic growth factor signaling. The detection of the JAK2 V617F mutation (c.1849GNT, GTC → TTC) is crucial for the diagnosis of myeloproliferative neoplasm (MPN) and has become the essential criteria for diagnosis of MPN by the WHO. High-resolution melt (HRM) curve analysis is a nongel-based, closed-tube method, in which PCR amplification and subsequent analysis are sequentially performed in the well, making it more convenient than other scanning methodologies. METHODS We evaluated JAK2 V617F mutation by HRM. Twenty-nine patients diagnosed with MPN were examined. We studied the analytical sensitivity of the HRM analysis using real-time polymerase chain reaction (PCR) for identifying the JAK2 V617F mutation. Additionally, the sensitivity of HRM analysis and allele-specific PCR (AS-PCR) assay was compared. RESULTS The JAK2 V617F mutation was successfully discriminated at an abundance of 6% or above in HRM analysis. Both HRM analysis and AS-PCR showed 100% accuracy with detection limits of 6% and 2.5%, respectively. CONCLUSION HRM analysis is a fast, simple, reliable, and nonexpensive method for the detection of the JAK2 V617F mutation. However, more validation of the detection limits of HRM analysis should be performed before declaration of the analytic sensitivity of the method.
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Affiliation(s)
- Chien-Yu Lin
- Graduate Institute of Clinical Medical Sciences, China Medical University, Taichung, Taiwan.,Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Cheng-Mao Ho
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Department of Nursing, Hungkuang University, Taichung, Taiwan
| | - Gevorg Tamamyan
- Department of Pediatric Hemato/Oncology, Complex Clinic of Chemotherapy, Yerevan State Medical University "Muratsan" Hospital, Yerevan, Armenia
| | - Shu-Fen Yang
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Ching-Tien Peng
- Division of Pediatric Hemato/Oncology, China Medical University Children's Hospital, Taichung, Taiwan. .,Department of Biotechnology, Asia University, Taichung, Taiwan.
| | - Jan-Gowth Chang
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan. .,Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan. .,College of Medicine, China Medical University, Taichung, Taiwan.
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Precise Detection of IDH1/2 and BRAF Hotspot Mutations in Clinical Glioma Tissues by a Differential Calculus Analysis of High-Resolution Melting Data. PLoS One 2016; 11:e0160489. [PMID: 27529619 PMCID: PMC4987040 DOI: 10.1371/journal.pone.0160489] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/20/2016] [Indexed: 01/08/2023] Open
Abstract
High resolution melting (HRM) is a simple and rapid method for screening mutations. It offers various advantages for clinical diagnostic applications. Conventional HRM analysis often yields equivocal results, especially for surgically obtained tissues. We attempted to improve HRM analyses for more effective applications to clinical diagnostics. HRM analyses were performed for IDH1R132 and IDH2R172 mutations in 192 clinical glioma samples in duplicate and these results were compared with sequencing results. BRAFV600E mutations were analyzed in 52 additional brain tumor samples. The melting profiles were used for differential calculus analyses. Negative second derivative plots revealed additional peaks derived from heteroduplexes in PCR products that contained mutations; this enabled unequivocal visual discrimination of the mutations. We further developed a numerical expression, the HRM-mutation index (MI), to quantify the heteroduplex-derived peak of the mutational curves. Using this expression, all IDH1 mutation statuses matched those ascertained by sequencing, with the exception of three samples. These discordant results were all derived from the misinterpretation of sequencing data. The effectiveness of our approach was further validated by analyses of IDH2R172 and BRAFV600E mutations. The present analytical method enabled an unequivocal and objective HRM analysis and is suitable for reliable mutation scanning in surgically obtained glioma tissues. This approach could facilitate molecular diagnostics in clinical environments.
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Zhang J, Zhao K, Hou D, Cai J, Zhang Q, Cheng T, Pan H, Yang W. Genome-Wide Discovery of DNA Polymorphisms in Mei ( Prunus mume Sieb. et Zucc.), an Ornamental Woody Plant, with Contrasting Tree Architecture and their Functional Relevance for Weeping Trait. PLANT MOLECULAR BIOLOGY REPORTER 2016; 35:37-46. [PMID: 28239231 PMCID: PMC5306074 DOI: 10.1007/s11105-016-1000-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Next-generation sequencing technologies provide opportunities to ascertain the genetic basis of phenotypic differences, even in the closely related cultivars via detection of large amount of DNA polymorphisms. In this study, we performed whole-genome re-sequencing of two mei cultivars with contrasting tree architecture. 75.87 million 100 bp pair-end reads were generated, with 92 % coverage of the genome. Re-sequencing data of two former upright mei cultivars were applied for detecting DNA polymorphisms, since we were more interested in variations conferring weeping trait. Applying stringent parameters, 157,317 mutual single nucleotide polymorphisms (SNPs) and 15,064 mutual insertions-deletions (InDels) were detected and found unevenly distributed within and among the mei chromosomes, which lead to the discovery of 220 high-density, 463 low-density SNP regions together with 80 high-density InDel regions. Additionally, 322 large-effect SNPs and 433 large-effect InDels were detected, and 10.09 % of the SNPs were observed in coding regions. 5.25 % SNPs in coding regions resulted in non-synonymous changes. Ninety SNPs were chosen randomly for validation using high-resolution melt analysis. 93.3 % of the candidate SNPs contained the predicted SNPs. Pfam analysis was further conducted to better understand SNP effects on gene functions. DNA polymorphisms of two known QTL loci conferring weeping trait and their functional effect were also analyzed thoroughly. This study highlights promising functional markers for molecular breeding and a whole-genome genetic basis of weeping trait in mei.
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Affiliation(s)
- Jie Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Kai Zhao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Dan Hou
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Junhuo Cai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Weiru Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
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Sun W, Li JJ, Xiong C, Zhao B, Chen SL. The Potential Power of Bar-HRM Technology in Herbal Medicine Identification. FRONTIERS IN PLANT SCIENCE 2016; 7:367. [PMID: 27066026 PMCID: PMC4811891 DOI: 10.3389/fpls.2016.00367] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/09/2016] [Indexed: 05/06/2023]
Abstract
The substitution of low-cost or adulterated herbal products for high-priced herbs makes it important to be able to identify and trace herbal plant species and their processed products in the drug supply chain. PCR-based methods play an increasing role in monitoring the safety of herbal medicines by detecting adulteration. Recent studies have shown the potential of DNA barcoding combined with high resolution melting (Bar-HRM) analysis in herbal medicine identification. This method involves precisely monitoring the change in fluorescence caused by the release of an intercalating DNA dye from a DNA duplex as it is denatured by a gradual increase in temperature. Since the melting profile depends on the GC content, length, and strand complementarity of the amplification product, Bar-HRM analysis opens up the possibility of detecting single-base variants or species-specific differences in a short region of DNA. This review summarizes key factors affecting Bar-HRM analysis and describes how Bar-HRM is performed. We then discuss advances in Bar-HRM analysis of medicinal plant ingredients (herbal materia medica) as a contribution toward safe and effective herbal medicines.
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Affiliation(s)
- Wei Sun
- Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing, China
| | - Jing-jian Li
- Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing, China
- College of Forestry and Landscape Architecture South China Agricultural UniversityGuangzhou, China
| | - Chao Xiong
- Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing, China
| | - Bo Zhao
- Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing, China
- Zhuhai College of Jilin UniversityZhuhai, China
| | - Shi-lin Chen
- Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing, China
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Chen T, Jia Y, Dong C, Gao J, Mak PI, Martins RP. Sub-7-second genotyping of single-nucleotide polymorphism by high-resolution melting curve analysis on a thermal digital microfluidic device. LAB ON A CHIP 2016; 16:743-752. [PMID: 26781669 DOI: 10.1039/c5lc01533b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We developed a thermal digital microfluidic (T-DMF) device enabling ultrafast DNA melting curve analysis (MCA). Within 7 seconds, the T-DMF device succeeded in differentiating a melting point difference down to 1.6 °C with a variation of 0.3 °C in a tiny droplet sample (1.2 μL), which was 300 times faster and with 20 times less sample spending than the standard MCA (35 minutes, 25 μL) run in a commercial qPCR machine. Such a performance makes it possible for a rapid discrimination of single-nucleotide mutation relevant to prompt clinical decision-making. Also, aided by electronic intelligent control, the T-DMF device facilitates sample handling and pipelining in an automatic serial manner. An optimized oval-shaped thermal electrode is introduced to achieve high thermal uniformity. A device-sealing technique averts sample contamination and permits uninterrupted chemical/biological reactions. Simple fabrication using a single chromium layer fulfills both the thermal and typical transport electrode requirements. Capable of thermally modulating DNA samples with ultrafast MCA, this T-DMF device has the potential for a wide variety of life science analyses, especially for disease diagnosis and prognosis.
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Affiliation(s)
- Tianlan Chen
- State-Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao, China.
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Benitez AJ, Winchell JM. Rapid detection and typing of pathogenic nonpneumophila Legionella spp. isolates using a multiplex real-time PCR assay. Diagn Microbiol Infect Dis 2016; 84:298-303. [PMID: 26867966 DOI: 10.1016/j.diagmicrobio.2016.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/05/2016] [Accepted: 01/09/2016] [Indexed: 11/26/2022]
Abstract
We developed a single tube multiplex real-time PCR assay that allows for the rapid detection and typing of 9 nonpneumophila Legionella spp. isolates that are clinically relevant. The multiplex assay is capable of simultaneously detecting and discriminating L. micdadei, L. bozemanii, L. dumoffii, L. longbeachae, L. feeleii, L. anisa, L. parisiensis, L. tucsonensis serogroup (sg) 1 and 3, and L. sainthelensis sg 1 and 2 isolates. Evaluation of the assay with nucleic acid from each of these species derived from both clinical and environmental isolates and typing strains demonstrated 100% sensitivity and 100% specificity when tested against 43 other Legionella spp. Typing of L. anisa, L. parisiensis, and L. tucsonensis sg 1 and 3 isolates was accomplished by developing a real-time PCR assay followed by high-resolution melt (HRM) analysis targeting the ssrA gene. Further typing of L. bozemanii, L. longbeachae, and L. feeleii isolates to the serogroup level was accomplished by developing a real-time PCR assay followed by HRM analysis targeting the mip gene. When used in conjunction with other currently available diagnostic tests, these assays may aid in rapidly identifying specific etiologies associated with Legionella outbreaks, clusters, sporadic cases, and potential environmental sources.
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Affiliation(s)
- Alvaro J Benitez
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jonas M Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Safa AH, Harandi MF, Tajaddini M, Rostami-Nejad M, Mohtashami-Pour M, Pestehchian N. Rapid Identification of Echinococcus granulosus and E. canadensis Using High-Resolution Melting (HRM) Analysis by Focusing on a Single Nucleotide Polymorphism. Jpn J Infect Dis 2016; 69:300-5. [DOI: 10.7883/yoken.jjid.2015.161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Ahmad Hosseini Safa
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences
| | | | - Mohammad Rostami-Nejad
- Gastroenterology and Liver Disease Research Center, Shahid Beheshti University of Medical Sciences
| | - Mehdi Mohtashami-Pour
- Department of Medical Parasitology and Mycology, Tabriz University of Medical Sciences
| | - Nader Pestehchian
- Department of Medical Parasitology and Mycology, Isfahan University of Medical Sciences
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Lombal AJ, Wenner TJ, Burridge CP. Assessment of high-resolution melting (HRM) profiles as predictors of microsatellite variation: an example in Providence Petrel (Pterodroma solandri). Genes Genomics 2015. [DOI: 10.1007/s13258-015-0327-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Botezatu IV, Nechaeva IO, Stroganova АМ, Senderovich AI, Kondratova VN, Shelepov VP, Lichtenstein AV. Optimization of melting analysis with TaqMan probes for detection of KRAS, NRAS, and BRAF mutations. Anal Biochem 2015; 491:75-83. [DOI: 10.1016/j.ab.2015.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/06/2015] [Accepted: 09/07/2015] [Indexed: 01/04/2023]
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Kanderian S, Jiang L, Knight I. Automated Classification and Cluster Visualization of Genotypes Derived from High Resolution Melt Curves. PLoS One 2015; 10:e0143295. [PMID: 26605797 PMCID: PMC4659556 DOI: 10.1371/journal.pone.0143295] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/03/2015] [Indexed: 11/19/2022] Open
Abstract
Introduction High Resolution Melting (HRM) following PCR has been used to identify DNA genotypes. Fluorescent dyes bounded to double strand DNA lose their fluorescence with increasing temperature, yielding different signatures for different genotypes. Recent software tools have been made available to aid in the distinction of different genotypes, but they are not fully automated, used only for research purposes, or require some level of interaction or confirmation from an analyst. Materials and Methods We describe a fully automated machine learning software algorithm that classifies unknown genotypes. Dynamic melt curves are transformed to multidimensional clusters of points whereby a training set is used to establish the distribution of genotype clusters. Subsequently, probabilistic and statistical methods were used to classify the genotypes of unknown DNA samples on 4 different assays (40 VKORC1, CYP2C9*2, CYP2C9*3 samples in triplicate, and 49 MTHFR c.665C>T samples in triplicate) run on the Roche LC480. Melt curves of each of the triplicates were genotyped separately. Results Automated genotyping called 100% of VKORC1, CYP2C9*3 and MTHFR c.665C>T samples correctly. 97.5% of CYP2C9*2 melt curves were genotyped correctly with the remaining 2.5% given a no call due to the inability to decipher 3 melt curves in close proximity as either homozygous mutant or wild-type with greater than 99.5% posterior probability. Conclusions We demonstrate the ability to fully automate DNA genotyping from HRM curves systematically and accurately without requiring any user interpretation or interaction with the data. Visualization of genotype clusters and quantification of the expected misclassification rate is also available to provide feedback to assay scientists and engineers as changes are made to the assay or instrument.
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Affiliation(s)
- Sami Kanderian
- Canon U.S. Life Sciences, Rockville, MD, United States of America
- * E-mail:
| | - Lingxia Jiang
- Canon U.S. Life Sciences, Rockville, MD, United States of America
| | - Ivor Knight
- Canon U.S. Life Sciences, Rockville, MD, United States of America
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Sanjuan-Jimenez R, Toro-Peinado I, Bermudez P, Colmenero JD, Morata P. Comparative Study of a Real-Time PCR Assay Targeting senX3-regX3 versus Other Molecular Strategies Commonly Used in the Diagnosis of Tuberculosis. PLoS One 2015; 10:e0143025. [PMID: 26600434 PMCID: PMC4658205 DOI: 10.1371/journal.pone.0143025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/29/2015] [Indexed: 11/19/2022] Open
Abstract
Background Nucleic acid amplification tests are increasingly used for the rapid diagnosis of tuberculosis. We undertook a comparative study of the efficiency and diagnostic yield of a real-time PCR senX3-regX3 based assay versus the classical IS6110 target and the new commercial methods. Methods This single-blind prospective comparative study included 145 consecutive samples: 76 from patients with culture-confirmed tuberculosis (86.8% pulmonary and 13.2% extrapulmonary tuberculosis: 48.7% smear-positive and 51.3% smear-negative) and 69 control samples (24 from patients diagnosed with non-tuberculous mycobacteria infections and 45 from patients with suspected tuberculosis which was eventually ruled out). All samples were tested by two CE-marked assays (Xpert®MTB/RIF and AnyplexTM plus MTB/NTM) and two in-house assays targeting senX3-regX3 and the IS6110 gene. Results The detection limit ranged from 1.00E+01 fg for Anyplex, senX3-regX3 and IS6110 to 1.00E+04 fg for Xpert. All three Xpert, senX3-regX3 and IS6110 assays detected all 37 smear-positive cases. Conversely, Anyplex was positive in 34 (91.9%) smear-positive cases. In patients with smear-negative tuberculosis, differences were observed between the assays; Xpert detected 22 (56.41%) of the 39 smear-negative samples, Anyplex 24 (61.53%), senX3-regX3 28 (71.79%) and IS6110 35 (89.74%). Xpert and senX3-regX3 were negative in all control samples; however, the false positive rate was 8.7% and 13% for Anyplex and IS6110, respectively. The overall sensitivity was 77.6%, 85.7%, 77.3% and 94.7% and the specificity was 100%, 100%, 90.8% and 87.0% for the Xpert, senX3-regX3, Anyplex and IS6110 assays, respectively. Conclusion Real-time PCR assays targeting IS6110 lack the desired specificity. The Xpert MTB/RIF and in-house senX3-regX3 assays are both sensitive and specific for the detection of MTBC in both pulmonary and extrapulmonary samples. Therefore, the real time PCR senX3-regX3 based assay could be a useful and complementary tool in the diagnosis of tuberculosis.
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Affiliation(s)
- Rocio Sanjuan-Jimenez
- Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Malaga, Malaga, Spain
- * E-mail:
| | | | - Pilar Bermudez
- Microbiology Service, Regional University Hospital, Malaga, Spain
| | - Juan D. Colmenero
- Infectious Diseases Service, Regional University Hospital, Malaga, Spain
| | - Pilar Morata
- Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Malaga, Malaga, Spain
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Kho SL, Chua KH, George E, Tan JAMA. A novel gap-PCR with high resolution melting analysis for the detection of α-thalassaemia Southeast Asian and Filipino β°-thalassaemia deletion. Sci Rep 2015; 5:13937. [PMID: 26365497 PMCID: PMC4568469 DOI: 10.1038/srep13937] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/31/2015] [Indexed: 11/11/2022] Open
Abstract
Homozygosity for the α-thalassaemia Southeast Asian (α-SEA) and Filipino β0-thalassaemia (β-FIL) deletions can cause serious complications leading to foetal death or life-long blood transfusions. A rapid and accurate molecular detection assay is essential in populations where the deletions are common. In this study, gap-polymerase chain reaction (PCR) with high resolution melting (HRM) analysis was developed to detect both the large deletions. Melting curves at 86.9 ± 0.1 °C were generated by normal individuals without the α-SEA deletion, 84.7 ± 0.1 °C by homozygous α-SEA deletion individuals and two melting curves at 84.7 ± 0.1 °C and 86.9 ± 0.1 °C by α-SEA deletion carriers. Normal individuals without the β-FIL deletion produce amplicons with a melting temperature (Tm) at 74.6 ± 0.1 °C, homozygous β-FIL individuals produce amplicons with Tm at 73.6 ± 0.1 °C and heterozygous β-FIL individuals generate two amplicons with Tm at 73.6 ± 0.1 °C and 74.6 ± 0.1 °C. Evaluation using blinded tests on 220 DNA samples showed 100% sensitivity and specificity. The developed assays are sensitive and specific for rapid molecular and prenatal diagnosis for the α-SEA and β-FIL deletions.
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Affiliation(s)
- Siew Leng Kho
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Jin Ai Mary Anne Tan
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Balboni A, Dondi F, Prosperi S, Battilani M. Development of a SYBR Green real-time PCR assay with melting curve analysis for simultaneous detection and differentiation of canine adenovirus type 1 and type 2. J Virol Methods 2015; 222:34-40. [PMID: 26028428 DOI: 10.1016/j.jviromet.2015.05.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/11/2015] [Accepted: 05/21/2015] [Indexed: 11/29/2022]
Abstract
Canine adenovirus type 1 (CAdV-1) and canine adenovirus type 2 (CAdV-2) cause infectious canine hepatitis (ICH) and infectious tracheobronchitis (ITB) in dogs, respectively. Cases of ICH have been documented in recent years and recent surveys have demonstrated a wide percentage of asymptomatic CAdV-1 infection in the canine population. Since both CAdV types are detectable in the same biological matrices, and viral coinfection with CAdV-1 and CAdV-2 are reported with high frequency, it is urgent to have available a rapid, highly sensitive and specific assay for the diagnosis of CAdV infection and distinction between CAdV-1 and CAdV-2. In order to detect canine adenovirus in biological samples and to rapidly distinguish the two viral types, a SYBR Green real-time PCR assay was optimized to discriminate CAdV-1 and CAdV-2 via a melting curve analysis. The developed assay showed high sensitivity and reproducibility and was highly efficient and specific in discriminating the two CAdV types. This reliable and rapid technique may represent a simple, useful and economic option for simultaneous CAdV types detection, which would be feasible and attractive for all diagnostic laboratories, both for clinical purposes and for epidemiological investigations.
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Affiliation(s)
- Andrea Balboni
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia (BO), Italy
| | - Francesco Dondi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia (BO), Italy
| | - Santino Prosperi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia (BO), Italy
| | - Mara Battilani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia (BO), Italy.
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Ebili HO, Ilyas M. Cancer mutation screening: Comparison of high-resolution melt analysis between two platforms. Ecancermedicalscience 2015; 9:522. [PMID: 25932046 PMCID: PMC4406528 DOI: 10.3332/ecancer.2015.522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Indexed: 11/18/2022] Open
Abstract
High-resolution melt analysis (HRMA) is a cheap and reliable post-polymerase chain reaction (PCR) cancer mutation screening technique, which is fast gaining clinical relevance. The HRMA capabilities of the LightScanner (Idaho Technology) have been severally studied. However, the ABI 7500 HRM has not been tested against the purpose-built HRM instrument such as the LightScanner. DNA from formalin-fixed, paraffin-embedded gastric cancer, colorectal cancer, and normal tissue as well as from colorectal cancer cell lines were amplified at exons 2, 3, and 4 of KRAS, and at exons 11 and 15 of BRAF in the ABI 7500 fast real-time PCR machine and subjected to melting both on the ABI and on the LightScanner. HRMA data were analysed with the ABI HRM software v2.0.1 and the LightScanner Call-IT 2.5. We tested the ABI 7500 HRM for internal precision, accuracy, sensitivity, and specificity at mutation screening relative to the LightScanner, using crude percentage concordance, kappa statistics, and the area under the receiver operator characteristics (AUROC) curve on SPSS version 19. The results show that the ABI 7500 HRMA has a high internal precision, and excellent concordance, sensitivity, and specificity at mutation screening compared with the LightScanner. However, in contrast to the LightScanner HRM software analysis, the ABI HRM software v.2.0.1, cannot distinguish real from certain pseudovariations in PCR amplicons that are sometimes brought about by the artefacts of the melting process. In conclusion, the ABI HRM has a comparable performance level with the LightScanner, although in certain respects mentioned previously, the LightScanner has an edge over the ABI.
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Affiliation(s)
- Henry O Ebili
- Morbid Anatomy and Histopathology Department, Olabisi Onabanjo University, Ago-Iwoye, Nigeria ; University College Hospital, Ibadan, Nigeria
| | - Mohammad Ilyas
- Division of Pathology, University of Nottingham, Queen's Medical Centre Campus, Nottingham, UK
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Enhanced ratio of signals enables digital mutation scanning for rare allele detection. J Mol Diagn 2015; 17:284-92. [PMID: 25772705 DOI: 10.1016/j.jmoldx.2014.12.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 12/12/2014] [Accepted: 12/19/2014] [Indexed: 12/23/2022] Open
Abstract
The use of droplet digital PCR (ddPCR) for low-level DNA mutation detection in cancer, prenatal diagnosis, and infectious diseases is growing rapidly. However, although ddPCR has been implemented successfully for detection of rare mutations at pre-determined positions, no ddPCR adaptation for mutation scanning exists. Yet, frequently, clinically relevant mutations reside on multiple sequence positions in tumor suppressor genes or complex hotspot mutations in oncogenes. Here, we describe a combination of coamplification at lower denaturation temperature PCR (COLD-PCR) with ddPCR that enables digital mutation scanning within approximately 50-bp sections of a target amplicon. Two FAM/HEX-labeled hydrolysis probes matching the wild-type sequence are used during ddPCR. The ratio of FAM/HEX-positive droplets is constant when wild-type amplicons are amplified but deviates when mutations anywhere under the FAM or HEX probes are present. To enhance the change in FAM/HEX ratio, we employed COLD-PCR cycling conditions that enrich mutation-containing amplicons anywhere on the sequence. We validated COLD-ddPCR on multiple mutations in TP53 and in EGFR using serial mutation dilutions and cell-free circulating DNA samples, and demonstrate detection down to approximately 0.2% to 1.2% mutation abundance. COLD-ddPCR enables a simple, rapid, and robust two-fluorophore detection method for the identification of multiple mutations during ddPCR and potentially can identify unknown DNA variants present in the target sequence.
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