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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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2
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Syahrani L, Asih PBS, Bowolaksono A, Dwiranti A, Zubaidah S, Rozi IE, Permana DH, Bøgh C, Bangs MJ, Grieco JP, Achee NL, Lobo NF, Syafruddin D. Impact of a spatial repellent intervention on Anopheles kdr insecticide resistance allele in Sumba, Indonesia. Malar J 2024; 23:31. [PMID: 38254131 PMCID: PMC10802001 DOI: 10.1186/s12936-024-04841-1] [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: 10/15/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND The emergence of insecticide resistance and outdoor transmission in malaria-endemic areas underlines the urgent need to develop innovative tools, such as spatial repellents (SR), that may circumvent this residual transmission. With limited options for effective insecticides, regular resistance monitoring is warranted for selecting and using appropriate tools. This study evaluates the pyrethroid knockdown resistance (kdr) allele before and after implementing a transfluthrin-based spatial repellent (SR) intervention in placebo-treated clusters. METHODS This study looks at the frequency distribution of the kdr allele in Sumba Island from June 2015 to August 2018. Insecticide susceptibility tests were carried out on female Anopheles sp. aged 3-5 days against permethrin 21.5 μg/ml, deltamethrin 12.5 μg/ml, and transfluthrin 10 μg/ml using CDC bottle assay. PCR sequencing of representative samples from adult mosquito collections and insecticide tests revealed the presence of kdr mutations (L1014F and L1014S) in the VGSC gene. RESULTS A total of 12 Anopheles species, Anopheles tesselatus, Anopheles. aconitus, Anopheles barbirostris, Anopheles kochi, Anopheles annularis, Anopheles maculatus, Anopheles sundaicus, Anopheles flavirostris, Anopheles balabacensis, Anopheles indefinitus, Anopheles subpictus, and Anopheles vagus were analysed. Anopheles vagus and An. sundaicus predominated in the larval populations. Susceptibility assays for all insecticides identified fully susceptible phenotypes in all species examined. Anopheles increasing frequency of kdr mutant alleles during the 3 year SR deployment was observed in both SR-treated and placebo areas, a statistically significant increase occurred in each arm. However, it is unclear how significant SR is in causing the increase in mutant alleles. The L1014S, knockdown resistance east type (kdr-e) allele was detected for the first time among the mosquito samples in this study. The L1014F, knockdown resistance west type (kdr-w) allele and heteroduplex form (wild-type-mutant) were found in almost all Anopheles species examined, including An. vagus, An. aconitus, An. subpictus, An. tesselatus, An. annularis, An. flavirostris and An. sundaicus. CONCLUSION The presence of fully susceptible phenotypes over time, along with an increase in the frequency distribution of the L1014F/S mutations post-intervention, suggest drivers of resistance external to the study, including pyrethroid use in agriculture and long-lasting insecticidal nets (LLINs). However, this does not negate possible SR impacts that support resistance. More studies that enable the comprehension of possible SR-based drivers of resistance in mosquitoes need to be conducted.
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Affiliation(s)
- Lepa Syahrani
- Doctoral Program, Department of Biology, Faculty of Mathematics and Natural Sciences, University of Indonesia, Depok, Indonesia
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Puji B S Asih
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency (BRIN), Cibinong, Indonesia.
| | - Anom Bowolaksono
- Department of Biology, Faculty of Mathematics and Natural Sciences, University of Indonesia, Depok, Indonesia
| | - Astari Dwiranti
- Department of Biology, Faculty of Mathematics and Natural Sciences, University of Indonesia, Depok, Indonesia
| | - Siti Zubaidah
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Ismail E Rozi
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
- Doctoral Program, Faculty of Medicine, University of Hasanuddin, Makassar, Indonesia
| | - Dendi H Permana
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
- Doctoral Program of Biomedical Sciences, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Claus Bøgh
- The Sumba Foundation, Public Health and Malaria Control, Sumba, Indonesia
| | - Michael J Bangs
- Public Health and Malaria Control, PT Freeport Indonesia, International SOS, Mimika, Indonesia
| | - John P Grieco
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, USA
| | - Nicole L Achee
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, USA
| | - Neil F Lobo
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, USA
| | - Din Syafruddin
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
- Department of Parasitology, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
- Hasanuddin University Medical Research Center (HUMRC), Makassar, Indonesia
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3
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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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Divanoglou N, Komninou D, Stea EA, Argiriou A, Papatzikas G, Tsakalof A, Pazaitou-Panayiotou K, Georgakis MK, Petridou E. Association of Vitamin D Receptor Gene Polymorphisms with Serum Vitamin D Levels in a Greek Rural Population (Velestino Study). Lifestyle Genom 2021; 14:81-90. [PMID: 34139712 DOI: 10.1159/000514338] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/06/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIM An alarming increase in vitamin D deficiency even in sunny regions highlights the need for a better understanding of the genetic background of the vitamin D endocrine system and the molecular mechanisms of gene polymorphisms of the vitamin D receptor (VDR). In this study, the serum levels of 25(OH)D3 were correlated with common VDR polymorphisms (ApaI, BsmI, FokI, and TaqI) in 98 subjects of a Greek homogeneous rural population. METHODS 25(OH)D3 concentration was measured by ultra-HPLC, and the VDR gene polymorphisms were identified by quantitative real-time PCR followed by amplicon high-resolution melting analysis. RESULTS Subjects carrying either the B BsmI (OR: 0.52, 95% CI: 0.27-0.99) or t TaqI (OR: 2.06, 95%: 1.06-3.99) allele presented twice the risk for developing vitamin D deficiency compared to the reference allele. Moreover, subjects carrying 1, 2, or all 3 of these genotypes (BB/Bb, Tt/tt, and FF) demonstrated 2-fold (OR: 2.04, 95% CI: 0.42-9.92), 3.6-fold (OR: 3.62, 95% CI: 1.07-12.2), and 7-fold (OR: 6.92, 95% CI: 1.68-28.5) increased risk for low 25(OH)D3 levels, respectively. CONCLUSIONS Our findings reveal a cumulative effect of specific VDR gene polymorphisms that may regulate vitamin D concentrations explaining, in part, the paradox of vitamin D deficiency in sunny regions, with important implications for precision medicine.
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Affiliation(s)
- Natalia Divanoglou
- Department of Nutritional Sciences and Dietetics, School of Health Sciences, International Hellenic University, Thessaloniki, Greece
| | - Despina Komninou
- Department of Nutritional Sciences and Dietetics, School of Health Sciences, International Hellenic University, Thessaloniki, Greece
| | - Eleni A Stea
- Institute of Applied Biosciences, CERTH-ΙΝAΒ Centre for Research & Technology Hellas, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, CERTH-ΙΝAΒ Centre for Research & Technology Hellas, Thessaloniki, Greece
| | - Grigorios Papatzikas
- Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | - Andreas Tsakalof
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Larisa, Greece
| | | | - Marios K Georgakis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Institute for Stroke and Dementia Research (ISD), University Hospital of Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Eleni Petridou
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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Felde O, Kreizinger Z, Sulyok KM, Wehmann E, Gyuranecz M. Development of molecular biological tools for the rapid determination of antibiotic susceptibility of Mycoplasma hyopneumoniae isolates. Vet Microbiol 2020; 245:108697. [PMID: 32456809 DOI: 10.1016/j.vetmic.2020.108697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 11/17/2022]
Abstract
Mycoplasma hyopneumoniae is the etiologic agent of porcine enzootic pneumonia, a contagious respiratory disease, causing significant economic losses worldwide. Antibiotic treatment is commonly utilised in the pig industry to control M. hyopneumoniae infection. Since the conventional antibiotic susceptibility test is time-consuming, taking up to weeks' period, antibiotics are usually empirically chosen. Certain single nucleotide polymorphisms in the parC (C239A/T, G250A) and gyrA (G242C, C247 T, A260 G) genes show correlation with decreased fluoroquinolone susceptibility by the change of the target site. Furthermore, the nucleotide alteration A2059 G in the 23S rRNA sequence correlates with significantly decreased macrolide and lincosamide susceptibility of M. hyopneumoniae. Mismatch amplification mutation assays (MAMA) and high resolution melt (HRM) analysis, capable to detect the mentioned resistance markers, were developed in the present study, in order to provide susceptibility data in a considerably shorter time than the conventional methods. The results of the MAMA and HRM assays were congruent with the results of the conventional antibiotic susceptibility method of the tested M. hyopneumoniae field isolates. The sensitivity of the MAMAs was 103-104 copy numbers, while that of the HRM assay was 105-106 copy numbers. To the best of our knowledge this was the first time that MAMA and HRM assays were developed for the rapid detection of decreased fluoroquinolone, macrolide or lincosamide susceptibility in M. hyopneumoniae strains.
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Affiliation(s)
- Orsolya Felde
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Zsuzsa Kreizinger
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Kinga Maria Sulyok
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Eniko Wehmann
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Miklos Gyuranecz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary; Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary.
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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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Rapid detection and genotyping of ALK fusion variants by adapter multiplex PCR and high-resolution melting analysis. J Transl Med 2020; 100:110-119. [PMID: 31641223 DOI: 10.1038/s41374-019-0330-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/08/2019] [Accepted: 09/07/2019] [Indexed: 11/08/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) fusion is a promising predictive biomarker of ALK-tyrosine kinase inhibitor (ALK-TKI) treatment. Furthermore, different fusion variants correlate to different ALK-TKIs responses. Although variant identification assists in treatment direction, most ALK detection assays do not genotype different fusion variants. We developed a high-resolution melting (HRM) assay to rapidly detect ALK fusions and automatically distinguish at least 20 fusion variants in one tube. Adapter multiplex PCR was designed to amplify ALK fusion variants and the reference gene GAPDH. After HRM, negative derivative curves showed a low temperature GAPDH peak, and if an ALK fusion was present, a high temperature peak from the ALK segment and variably a middle temperature part associated with the fusion partner. Selected regions of the second derivative curves were analyzed to extract features (∆Tm, PTS/ITS, H1/H2) that define two curve types (monotonic and non-monotonic). Synthetic samples of 20 ALK fusion variants were used to train a quadratic discriminate analysis model, and the accuracy was 97.06% (66/68) and 85.71% (144/162) for monotonic and non-monotonic variants, respectively. The limit of detection of the assay was 1%. The analytical sensitivity of genotyping was 1 and 5% for monotonic and non-monotonic variants, respectively. In a blinded study, we detected ALK fusion from formalin-fixed paraffin-embedded lung cancer samples with a 100% 47) and genotyping /47) and genotyping (7/7). Multiplex adapter HRM is a simple, fast, and sensitive way of ALK fusion detection and genotyping. Automatic genotyping with parameters extracted from second derivative curves is a promising method that may be applicable to other types of gene variants detected by HRM.
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Wang J, Liu A, Zhang S, Gao S, Rashid M, Li Y, Liu J, Ma Q, Li Z, Liu Z, Luo J, Guan G, Yin H. High resolution melting analysis of the 18S rRNA gene for the rapid diagnosis of bovine babesiosis. Parasit Vectors 2019; 12:523. [PMID: 31694676 PMCID: PMC6833191 DOI: 10.1186/s13071-019-3781-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023] Open
Abstract
Background Bovine babesiosis is caused by protozoan parasites of the genus Babesia and presents a wide spectrum of clinical manifestations. Disease severity depends on the type of Babesia species infection. Generally, B. bovis and B. bigemina are considered as the causative agents of bovine babesiosis; in addition, Babesia ovata and B. major are a group of benign bovine piroplasms. Therefore, species identification is important for diagnosis, epidemiological investigations and follow-up management. Methods Real-time PCR combined with high resolution melting (RT-PCR-HRM) analysis was used to detect and discriminate four Babesia species infective to cattle, including Babesia bovis, B. bigemina, B. major and B. ovata. The melting profiles and melting temperatures (Tm) of the amplicon targeting 18S rRNA revealed differences that can discriminate the four Babesia spp. Sensitivity and specificity of the analytical method were evaluated using 50 blood samples collected from experimentally infected cattle and 240 blood samples from areas where bovine babesiosis is an issue. Results RT-PCR-HRM analysis allowed to detect and discriminate four Babesia spp. (B. bovis, B. bigemina, B. major and B. ovata), which were responsible for bovine babesiosis in China. The protocol was validated with DNA samples from experimentally infected cattle and field infection in cattle. Conclusions Our results indicate that RT-PCR-HRM is a fast and robust tool for the simultaneous detection and discrimination of four Babesia species that are responsible for bovine babesiosis in China. This approach is applicable for both field and experimental samples, thus it could be useful in epidemiological investigations and diagnoses of bovine babesiosis.
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Affiliation(s)
- Jinming Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Aihong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Shangdi Zhang
- Department of Clinical Laboratory, The Second Hospital of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Shandian Gao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Muhammad Rashid
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Youquan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Quanying Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Zhi Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Zhijie Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China.
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China. .,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, People's Republic of China.
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Bowes C, Redd M, Yousfi M, Tauzin M, Murayama E, Herbomel P. Coronin 1A depletion restores the nuclear stability and viability of Aip1/Wdr1-deficient neutrophils. J Cell Biol 2019; 218:3258-3271. [PMID: 31471458 PMCID: PMC6781450 DOI: 10.1083/jcb.201901024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 06/20/2019] [Accepted: 07/01/2019] [Indexed: 12/21/2022] Open
Abstract
Bowes et al. show that in zebrafish embryos deficient in the cofilin cofactor AIP1/Wdr1, neutrophils display F-actin as cytoplasmic aggregates, spatially uncoupled from active myosin, then undergo a progressive unwinding of their nucleus followed by eruptive cell death. This adverse phenotype is fully rescued by depletion of another cofilin cofactor, coronin 1A. Actin dynamics is central for cells, and especially for the fast-moving leukocytes. The severing of actin filaments is mainly achieved by cofilin, assisted by Aip1/Wdr1 and coronins. We found that in Wdr1-deficient zebrafish embryos, neutrophils display F-actin cytoplasmic aggregates and a complete spatial uncoupling of phospho-myosin from F-actin. They then undergo an unprecedented gradual disorganization of their nucleus followed by eruptive cell death. Their cofilin is mostly unphosphorylated and associated with F-actin, thus likely outcompeting myosin for F-actin binding. Myosin inhibition reproduces in WT embryos the nuclear instability and eruptive death of neutrophils seen in Wdr1-deficient embryos. Strikingly, depletion of the main coronin of leukocytes, coronin 1A, fully restores the cortical location of F-actin, nuclear integrity, viability, and mobility of Wdr1-deficient neutrophils in vivo. Our study points to an essential role of actomyosin contractility in maintaining the integrity of the nucleus of neutrophils and a new twist in the interplay of cofilin, Wdr1, and coronin in regulating F-actin dynamics.
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Affiliation(s)
- Charnese Bowes
- Institut Pasteur, Department of Developmental and Stem Cell Biology, Paris, France.,Centre National de la Recherche Scientifique, UMR3738, Paris, France
| | - Michael Redd
- University of Utah, Huntsman Cancer Institute, Salt Lake City, UT
| | - Malika Yousfi
- Institut Pasteur, Department of Developmental and Stem Cell Biology, Paris, France.,Centre National de la Recherche Scientifique, UMR3738, Paris, France
| | - Muriel Tauzin
- Institut Pasteur, Department of Developmental and Stem Cell Biology, Paris, France.,Centre National de la Recherche Scientifique, UMR3738, Paris, France
| | - Emi Murayama
- Institut Pasteur, Department of Developmental and Stem Cell Biology, Paris, France.,Centre National de la Recherche Scientifique, UMR3738, Paris, France
| | - Philippe Herbomel
- Institut Pasteur, Department of Developmental and Stem Cell Biology, Paris, France .,Centre National de la Recherche Scientifique, UMR3738, Paris, France
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10
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Bindel-PCR: a novel and convenient method for identifying CRISPR/Cas9-induced biallelic mutants through modified PCR using Thermus aquaticus DNA polymerase. Sci Rep 2019; 9:9923. [PMID: 31289302 PMCID: PMC6617447 DOI: 10.1038/s41598-019-46357-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 06/26/2019] [Indexed: 11/08/2022] Open
Abstract
We developed a novel and convenient method for rapidly identifying CRISPR/Cas9-based genome-edited biallelic knockout (KO) cells/individuals carrying insertions or deletions of a few nucleotides (indels) by performing PCR on genomic DNA samples under stringent conditions and low MgCl2 concentrations. The biallelic KO samples can be judged as 'negative' under these conditions. The sense primer corresponds to the sequence recognised by guide RNA and subsequently cleaved by Cas9 immediately upstream of a target gene's proto-spacer adjacent motif (PAM), and the reverse primer corresponds to the sequence ~200 bp downstream from the PAM. PCR performed using this primer set under standard MgCl2 concentrations (1.5-2.5 mM) should generate PCR products derived from both mutated and unedited alleles, whereas PCR performed using lower MgCl2 concentrations (0.8-2 mM) should yield products derived from unedited alleles. This enables high-throughput screening of biallelic mutants among cells/embryos having ≥1 indels at a region within 5 bp upstream of the PAM (where more than 94% of indels are known to appear). We performed proof-of-principle analyses of this novel approach using genome-edited Et1, Tyr, Ramp1, Ramp3, and Rosa26 mouse samples carrying various types of indels, and demonstrate that this new technique allows rapid identification of biallelic KO mutants among samples carrying various types of indels and mosaic mutations with 100% accuracy. We name this system detection of biallelic KO mutants harbouring indels using PCR (Bindel-PCR).
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Xanthopoulou A, Ganopoulos I, Tryfinopoulou P, Panagou EZ, Osanthanunkul M, Madesis P, Kizis D. Rapid and accurate identification of black aspergilli from grapes using high-resolution melting (HRM) analysis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:309-314. [PMID: 29876941 DOI: 10.1002/jsfa.9189] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Aspergillus is a diverse genus of fungi with high economic and social impact. Various species that belong to section Nigri (black aspergilli) are common agents of grape spoilage and potent producers of ochratoxin A (OTA), a mycotoxin associated with various nephrotoxic and immunotoxic effects in humans. Black aspergilli are difficult to classify following only phenotypic criteria; thus chemotaxonomic and molecular methods are employed in parallel with phenotypic ones for species characterization. These approaches, though accurate and replicable, require more than one individual step and are to a certain extent laborious when a rapid identification of these species is required. RESULTS The aim of this study was to develop a high-resolution melting polymerase chain reaction (HRM-PCR) assay as a rapid method for identification of Aspergillus spp. section Nigri isolates and their detection in grape samples. Melt curve analysis of amplicons originating from the internal transcribed spacer 2 (ITS2) ribosomal region generated species-specific HRM curve profiles, enabling the accurate differentiation of the analyzed genotypes. Furthermore, the assay was able to identify A. carbonarius, A. tubingensis, A. niger, A. ibericus and A. japonicus in grape samples artificially inoculated with conidia of these fungi. CONCLUSION To our knowledge this is the first report on the development of an HRM-PCR assay for the identification of black Aspergillus species in grape samples. © 2018 Society of Chemical Industry.
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Affiliation(s)
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER, Thessaloniki, Greece
| | - Paschalitsa Tryfinopoulou
- Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Efstathios Z Panagou
- Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Maslin Osanthanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | - Dimosthenis Kizis
- Laboratory of Mycology, Department of Phytopathology, Benaki Phytopathological Institute, Athens, Greece
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Agrimonti C, Sanangelantoni AM, Marmiroli N. Simultaneous enumeration of Campylobacter jejuni and Salmonella enterica genome equivalents by melting curve analysis following duplex real time PCR in the presence of SYBR Green. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.03.077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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13
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Liu Y, Xiang L, Zhang Y, Lai X, Xiong C, Li J, Su Y, Sun W, Chen S. DNA barcoding based identification of Hippophae species and authentication of commercial products by high resolution melting analysis. Food Chem 2018; 242:62-67. [DOI: 10.1016/j.foodchem.2017.09.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 09/02/2017] [Accepted: 09/08/2017] [Indexed: 10/18/2022]
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14
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Mishra P, Shukla AK, Sundaresan V. Candidate DNA Barcode Tags Combined With High Resolution Melting (Bar-HRM) Curve Analysis for Authentication of Senna alexandrina Mill. With Validation in Crude Drugs. FRONTIERS IN PLANT SCIENCE 2018; 9:283. [PMID: 29593755 PMCID: PMC5859231 DOI: 10.3389/fpls.2018.00283] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/19/2018] [Indexed: 05/07/2023]
Abstract
Senna alexandrina (Fabaceae) is a globally recognized medicinal plant for its laxative properties as well as the only source of sennosides, and is highly exported bulk herb from India. Its major procurement is exclusively from limited cultivation, which leads to risks of deliberate or unintended adulteration. The market raw materials are in powdered or finished product form, which lead to difficulties in authentication. Here, DNA barcode tags based on chloroplast genes (rbcL and matK) and intergenic spacers (psbA-trnH and ITS) were developed for S. alexandrina along with the allied species. The ability and performance of the ITS1 region to discriminate among the Senna species resulted in the present proposal of the ITS1 tags as successful barcode. Further, these tags were coupled with high-resolution melting (HRM) curve analysis in a real-time PCR genotyping method to derive Bar-HRM (Barcoding-HRM) assays. Suitable HRM primer sets were designed through SNP detection and mutation scanning in genomic signatures of Senna species. The melting profiles of S. alexandrina and S. italica subsp. micrantha were almost identical and the remaining five species were clearly separated so that they can be differentiated by HRM method. The sensitivity of the method was utilized to authenticate market samples [Herbal Sample Assays (HSAs)]. HSA01 (S. alexandrina crude drug sample from Bangalore) and HSA06 (S. alexandrina crude drug sample from Tuticorin, Tamil Nadu, India) were found to be highly contaminated with S. italica subsp. micrantha. Species admixture samples mixed in varying percentage was identified sensitively with detection of contamination as low as 1%. The melting profiles of PCR amplicons are clearly distinct, which enables the authentic differentiation of species by the HRM method. This study reveals that DNA barcoding coupled with HRM is an efficient molecular tool to authenticate Senna herbal products in the market for quality control in the drug supply chain. CIMAP Communication Number: CIMAP/PUB/2017/31.
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Affiliation(s)
- Priyanka Mishra
- Plant Biology and Systematics, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, India
| | - Ashutosh K. Shukla
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Velusamy Sundaresan
- Plant Biology and Systematics, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, India
- *Correspondence: Velusamy Sundaresan, ;
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Sulyok KM, Bekő K, Kreizinger Z, Wehmann E, Jerzsele Á, Rónai Z, Turcsányi I, Makrai L, Szeredi L, Jánosi S, Nagy SÁ, Gyuranecz M. Development of molecular methods for the rapid detection of antibiotic susceptibility of Mycoplasma bovis. Vet Microbiol 2017; 213:47-57. [PMID: 29292003 DOI: 10.1016/j.vetmic.2017.11.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/12/2017] [Accepted: 11/17/2017] [Indexed: 10/18/2022]
Abstract
Determining the antibiotic susceptibility profile of Mycoplasma bovis isolates in vitro provides the basis for the appropriate choice of antibiotics in the therapy. Traditionally, the antibiotic susceptibility examination of mycoplasmas is technically demanding, time-consuming and rarely performed in diagnostic laboratories. The aim of the present study was to develop rapid molecular assays to determine mutations responsible for elevated minimal inhibitory concentrations (MICs) to fluoroquinolones, tetracyclines, aminocyclitols, macrolides, lincosamides, phenicols and pleuromutilins in M. bovis. The nine mismatch amplification mutation assays (MAMA) and seven high resolution melt (HRM) tests designed in the present study enable the simultaneous detection of these genetic markers. The sensitivity of the assays varied between 102-105 copy numbers/reaction. Cross-reactions with other mycoplasmas occurring in cattle were detected in assays targeting universal regions (e.g. 16S rRNA). Nevertheless, results of the novel method were in accordance with sequence and MICs data of the M. bovis pure cultures. Also, the tests of clinical samples containing high amount of M. bovis DNA were congruent even in the presence of other Mycoplasma spp. The presented method is highly cost-effective and can provide an antibiogram to 12 antibiotics in approximately 3-4 days when previous isolation of M. bovis is applied. In order to assure the proper identification of the genetic markers at issue, the regions examined by the MAMA and HRM tests are overlapping. In conclusion, the developed assays have potential to be used in routine diagnostics for the detection of antibiotic susceptibility in M. bovis.
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Affiliation(s)
- Kinga M Sulyok
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1143, Hungária körút 21, Hungary
| | - Katinka Bekő
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1143, Hungária körút 21, Hungary
| | - Zsuzsa Kreizinger
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1143, Hungária körút 21, Hungary
| | - Enikő Wehmann
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1143, Hungária körút 21, Hungary
| | - Ákos Jerzsele
- University of Veterinary Medicine, Budapest, István utca 2, Hungary
| | - Zsuzsanna Rónai
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, 1143, Tábornok utca 2, Hungary
| | - Ibolya Turcsányi
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, 1143, Tábornok utca 2, Hungary
| | - László Makrai
- University of Veterinary Medicine, Budapest, István utca 2, Hungary
| | - Levente Szeredi
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, 1143, Tábornok utca 2, Hungary
| | - Szilárd Jánosi
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, 1143, Tábornok utca 2, Hungary
| | - Sára Ágnes Nagy
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1143, Hungária körút 21, Hungary
| | - Miklós Gyuranecz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1143, Hungária körút 21, Hungary.
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Xu A, Lv T, Zhang B, Zhang W, Ou X, Huang J. Development and evaluation of an unlabeled probe high-resolution melting assay for detection of ATP7B mutations in Wilson's disease. J Clin Lab Anal 2017; 31:e22064. [PMID: 27638368 PMCID: PMC6817005 DOI: 10.1002/jcla.22064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/16/2016] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Wilson's disease (WD) is a rare autosomal recessive disorder characterized by the deposition of copper mainly in the liver or nerve system that leads to their dysfunction. Mutations in the gene encoding ATPase, Cu+ transporting, beta polypeptide (ATP7B) are causative for WD. The aim of this study was to develop a rapid and convenient assay for detection of the three most common causative ATP7B mutations, p.R778L, p.P992L, and p.V1106I. METHODS Plasmids containing DNA fragments harboring each of the three ATP7B mutations were constructed. High-resolution melting (HRM) analysis was conducted by asymmetric polymerase chain reaction (PCR) amplification with paired primer and unlabeled probe, performed in a 96-well plate formatted LightCycler 480 Real-Time PCR System. The assay was evaluated for accuracy and reproducibility by genotyping of 41 WD cases. RESULTS The unlabeled probe HRM assays performed on constructs with the p.R778L, p.P992L, and p.V1106I mutations in the ATP7B gene resulted in additional melting peaks. According to the unlabeled probe HRM molecular signature, we could differentiate homozygous mutations from wild-type with the ΔTm (difference between melting temperatures) >4°C, and the coefficient of variation in repeatability tests was <5%. In the validation assay using our method to examine clinical samples, a 100% accuracy rate was achieved. CONCLUSIONS The newly developed assay to rapidly genotype the ATP7B mutations is convenient, accurate, and reproducible, and represents a favorable alternative to Sanger sequencing in the identification of specific ATP7B mutations.
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Affiliation(s)
- Anjian Xu
- Experimental CenterBeijing Friendship HospitalCapital Medical UniversityBeijingChina
- National Clinical Research Center for Digestive DiseaseBeijing Friendship HospitalCapital Medical UniversityBeijingChina
| | - Tingxia Lv
- Experimental CenterBeijing Friendship HospitalCapital Medical UniversityBeijingChina
- National Clinical Research Center for Digestive DiseaseBeijing Friendship HospitalCapital Medical UniversityBeijingChina
| | - Bei Zhang
- Experimental CenterBeijing Friendship HospitalCapital Medical UniversityBeijingChina
- National Clinical Research Center for Digestive DiseaseBeijing Friendship HospitalCapital Medical UniversityBeijingChina
| | - Wei Zhang
- National Clinical Research Center for Digestive DiseaseBeijing Friendship HospitalCapital Medical UniversityBeijingChina
- Liver Research CenterBeijing Friendship HospitalCapital Medical UniversityBeijingChina
| | - Xiaojuan Ou
- National Clinical Research Center for Digestive DiseaseBeijing Friendship HospitalCapital Medical UniversityBeijingChina
- Liver Research CenterBeijing Friendship HospitalCapital Medical UniversityBeijingChina
| | - Jian Huang
- Experimental CenterBeijing Friendship HospitalCapital Medical UniversityBeijingChina
- National Clinical Research Center for Digestive DiseaseBeijing Friendship HospitalCapital Medical UniversityBeijingChina
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17
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Sun W, Yan S, Li J, Xiong C, Shi Y, Wu L, Xiang L, Deng B, Ma W, Chen S. Study of Commercially Available Lobelia chinensis Products Using Bar-HRM Technology. FRONTIERS IN PLANT SCIENCE 2017; 8:351. [PMID: 28360920 PMCID: PMC5352710 DOI: 10.3389/fpls.2017.00351] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/28/2017] [Indexed: 05/23/2023]
Abstract
There is an unmet need for herbal medicine identification using a fast, sensitive, and easy-to-use method that does not require complex infrastructure and well-trained technicians. For instance, the detection of adulterants in Lobelia chinensis herbal product has been challenging, since current detection technologies are not effective due to their own limits. High Resolution Melting (HRM) has emerged as a powerful new technology for clinical diagnosis, research in the food industry and in plant molecular biology, and this method has already highlighted the complexity of species identification. In this study, we developed a method of species specific detection of L. chinensis using HRM analysis combined with internal transcribed spacer 2. We then applied this method to commercial products purporting to contain L. chinensis. Our results demonstrated that HRM can differentiate L. chinensis from six common adulterants. HRM was proven to be a fast and accurate technique for testing the authenticity of L. chinensis in herbal products. Based on these results, a HRM approach for herbal authentication is provided.
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Affiliation(s)
- Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Song Yan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- Pharmacy College, Heilongjiang University of Chinese MedicineHarbin, China
| | - Jingjian Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural UniversityGuangzhou, China
| | - Chao Xiong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- College of Pharmacy, Hubei University of Chinese MedicineWuhan, China
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Li Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Bo Deng
- Department of Oncology of Integrative Chinese and Western Medicine, China-Japan Friendship HospitalBeijing, China
| | - Wei Ma
- Pharmacy College, Heilongjiang University of Chinese MedicineHarbin, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
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18
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Andini N, Wang B, Athamanolap P, Hardick J, Masek BJ, Thair S, Hu A, Avornu G, Peterson S, Cogill S, Rothman RE, Carroll KC, Gaydos CA, Wang JTH, Batzoglou S, Yang S. Microbial Typing by Machine Learned DNA Melt Signatures. Sci Rep 2017; 7:42097. [PMID: 28165067 PMCID: PMC5292719 DOI: 10.1038/srep42097] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/05/2017] [Indexed: 11/09/2022] Open
Abstract
There is still an ongoing demand for a simple broad-spectrum molecular diagnostic assay for pathogenic bacteria. For this purpose, we developed a single-plex High Resolution Melt (HRM) assay that generates complex melt curves for bacterial identification. Using internal transcribed spacer (ITS) region as the phylogenetic marker for HRM, we observed complex melt curve signatures as compared to 16S rDNA amplicons with enhanced interspecies discrimination. We also developed a novel Naïve Bayes curve classification algorithm with statistical interpretation and achieved 95% accuracy in differentiating 89 bacterial species in our library using leave-one-out cross-validation. Pilot clinical validation of our method correctly identified the etiologic organisms at the species-level in 59 culture-positive mono-bacterial blood culture samples with 90% accuracy. Our findings suggest that broad bacterial sequences may be simply, reliably and automatically profiled by ITS HRM assay for clinical adoption.
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Affiliation(s)
- Nadya Andini
- Emergency Medicine, Stanford University, Stanford, California, 94305, USA
| | - Bo Wang
- Computer Science, Stanford University, Stanford, California, 94305, USA
| | - Pornpat Athamanolap
- Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Justin Hardick
- Infectious Disease, Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Billie J Masek
- Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Simone Thair
- Emergency Medicine, Stanford University, Stanford, California, 94305, USA
| | - Anne Hu
- Emergency Medicine, Stanford University, Stanford, California, 94305, USA
| | - Gideon Avornu
- Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Stephen Peterson
- Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Steven Cogill
- Emergency Medicine, Stanford University, Stanford, California, 94305, USA
| | - Richard E Rothman
- Infectious Disease, Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.,Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Karen C Carroll
- Medical Microbiology, Pathology, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Charlotte A Gaydos
- Infectious Disease, Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.,Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Jeff Tza-Huei Wang
- Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.,Mechanical Engineering, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Serafim Batzoglou
- Computer Science, Stanford University, Stanford, California, 94305, USA
| | - Samuel Yang
- Emergency Medicine, Stanford University, Stanford, California, 94305, USA
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Song M, Li J, Xiong C, Liu H, Liang J. Applying high-resolution melting (HRM) technology to identify five commonly used Artemisia species. Sci Rep 2016; 6:34133. [PMID: 27698485 PMCID: PMC5048426 DOI: 10.1038/srep34133] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/07/2016] [Indexed: 12/19/2022] Open
Abstract
Many members of the genus Artemisia are important for medicinal purposes with multiple pharmacological properties. Often, these herbal plants sold on the markets are in processed forms so it is difficult to authenticate. Routine testing and identification of these herbal materials should be performed to ensure that the raw materials used in pharmaceutical products are suitable for their intended use. In this study, five commonly used Artemisia species included Artemisia argyi, Artemisia annua, Artemisia lavandulaefolia, Artemisia indica, and Artemisia atrovirens were analyzed using high resolution melting (HRM) analysis based on the internal transcribed spacer 2 (ITS2) sequences. The melting profiles of the ITS2 amplicons of the five closely related herbal species are clearly separated so that they can be differentiated by HRM method. The method was further applied to authenticate commercial products in powdered. HRM curves of all the commercial samples tested are similar to the botanical species as labeled. These congeneric medicinal products were also clearly separated using the neighbor-joining (NJ) tree. Therefore, HRM method could provide an efficient and reliable authentication system to distinguish these commonly used Artemisia herbal products on the markets and offer a technical reference for medicines quality control in the drug supply chain.
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Affiliation(s)
- Ming Song
- School of Chemical Engineering, Wuhan University of Technology, Wuhan 430070, China
| | - Jingjian Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Chao Xiong
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Hexia Liu
- Guangxi Institute of Botany, The Chinese Academy of Sciences, Guilin 541006, China
| | - Junsong Liang
- College of Life Science &Technology, Yulin Normal University, Yulin 537000, China
- Cultivation Base for Key Laboratory of Conservation and Utilization of Rare and Economic Species at Southeast Guangxi, Yulin Normal University, Yulin 537000, China
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Simko I. High-Resolution DNA Melting Analysis in Plant Research. TRENDS IN PLANT SCIENCE 2016; 21:528-537. [PMID: 26827247 DOI: 10.1016/j.tplants.2016.01.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/05/2015] [Accepted: 01/05/2016] [Indexed: 05/22/2023]
Abstract
Genetic and genomic studies provide valuable insight into the inheritance, structure, organization, and function of genes. The knowledge gained from the analysis of plant genes is beneficial to all aspects of plant research, including crop improvement. New methods and tools are continually being developed to facilitate rapid and accurate mapping, sequencing, and analyzing of genes. Here, I review the recent progress in the application of high-resolution melting (HRM) analysis of DNA, a method that allows detecting polymorphism in double-stranded DNA by comparing profiles of melting curves. Use of HRM has expanded considerably in the past few years as the method was successfully applied for high-throughput genotyping, mapping genes, testing food products and seeds, and other areas of plant research.
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Affiliation(s)
- Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA 93905, USA.
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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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Capper RL, Jin YK, Lundgren PB, Peplow LM, Matz MV, van Oppen MJH. Quantitative high resolution melting: two methods to determine SNP allele frequencies from pooled samples. BMC Genet 2015; 16:62. [PMID: 26070466 PMCID: PMC4465018 DOI: 10.1186/s12863-015-0222-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 05/27/2015] [Indexed: 01/06/2023] Open
Abstract
Background The advent of next-generation sequencing has brought about an explosion of single nucleotide polymorphism (SNP) data in non-model organisms; however, profiling these SNPs across multiple natural populations still requires substantial time and resources. Results Here, we introduce two cost-efficient quantitative High Resolution Melting (qHRM) methods for measuring allele frequencies at known SNP loci in pooled DNA samples: the “peaks” method, which can be applied to large numbers of SNPs, and the “curves” method, which is more labor intensive but also slightly more accurate. Using the reef-building coral Acropora millepora, we show that both qHRM methods can recover the allele proportions from mixtures prepared using two or more individuals of known genotype. We further demonstrate advantages of each method over previously published methods; specifically, the “peaks” method can be rapidly scaled to screen several hundred SNPs at once, whereas the “curves” method is better suited for smaller numbers of SNPs. Conclusions Compared to genotyping individual samples, these methods can save considerable effort and genotyping costs when relatively few candidate SNPs must be profiled across a large number of populations. One of the main applications of this method could be validation of SNPs of interest identified in population genomic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0222-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roxana L Capper
- Department of Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Young K Jin
- School of Marine and Tropical Biology, James Cook University, Townsville, Qld, 4811, Australia. .,Australian Institute of Marine Science, PMB3, Townsville MC, Qld, 4810, Australia.
| | - Petra B Lundgren
- Department of Anatomy and Developmental Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, 3800, Australia.
| | - Lesa M Peplow
- Australian Institute of Marine Science, PMB3, Townsville MC, Qld, 4810, Australia.
| | - Mikhail V Matz
- Department of Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
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González S, Mannise N, Repetto L, Maldonado JE. Sex determination of three Neotropical canids by high resolution melting analysis. CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-015-0466-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Improved protocol for rapid identification of certain spa types using high resolution melting curve analysis. PLoS One 2015; 10:e0116713. [PMID: 25768007 PMCID: PMC4358892 DOI: 10.1371/journal.pone.0116713] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 12/12/2014] [Indexed: 11/24/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus is one of the most significant pathogens associated with health care. For efficient surveillance, control and outbreak investigation, S. aureus typing is essential. A high resolution melting curve analysis was developed and evaluated for rapid identification of the most frequent spa types found in an Austrian hospital consortium covering 2,435 beds. Among 557 methicillin-resistant Staphylococcus aureus isolates 38 different spa types were identified by sequence analysis of the hypervariable region X of the protein A gene (spa). Identification of spa types through their characteristic high resolution melting curve profiles was considerably improved by double spiking with genomic DNA from spa type t030 and spa type t003 and allowed unambiguous and fast identification of the ten most frequent spa types t001 (58%), t003 (12%), t190 (9%), t041 (5%), t022 (2%), t032 (2%), t008 (2%), t002 (1%), t5712 (1%) and t2203 (1%), representing 93% of all isolates within this hospital consortium. The performance of the assay was evaluated by testing samples with unknown spa types from the daily routine and by testing three different high resolution melting curve analysis real-time PCR instruments. The ten most frequent spa types were identified from all samples and on all instruments with 100% specificity and 100% sensitivity. Compared to classical spa typing by sequence analysis, this gene scanning assay is faster, cheaper and can be performed in a single closed tube assay format. Therefore it is an optimal screening tool to detect the most frequent endemic spa types and to exclude non-endemic spa types within a hospital.
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Pomeroy RS, Balamurugan K, Wong H, Duncan G. High-resolution melt analysis of the minisatellite D1S80: A potential forensic screening tool. Electrophoresis 2014; 35:3020-7. [DOI: 10.1002/elps.201400143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 07/24/2014] [Accepted: 08/20/2014] [Indexed: 01/11/2023]
Affiliation(s)
- Robert S. Pomeroy
- Department of Chemistry and Biochemistry; University of California; San Diego CA USA
| | | | - Helena Wong
- Department of Chemistry and Biochemistry; University of California; San Diego CA USA
| | - George Duncan
- Oceanographic Institute; Nova Southeastern University; Fort Lauderdale FL USA
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Handt M, Epplen A, Hoffjan S, Mese K, Epplen JT, Dekomien G. Point mutation frequency in the FMR1 gene as revealed by fragile X syndrome screening. Mol Cell Probes 2014; 28:279-83. [PMID: 25171808 DOI: 10.1016/j.mcp.2014.08.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 01/05/2023]
Abstract
Fragile X syndrome (FXS) is a common cause of intellectual disability, developmental delay and autism spectrum disorders. This syndrome is due to a functional loss of the FMR1 gene product FMRP, and, in most cases, it is caused by CGG repeat expansion in the FMR1 promoter. Yet, also other FMR1 mutations may cause a FXS-like phenotype. Since standard molecular testing does not include the analysis of the FMR1 coding region, the prevalence of point mutations causing FXS is not well known. Here, high resolution melting (HRM) was used to screen for FMR1 gene mutations in 508 males with clinical signs of mental retardation and developmental delay, but without CGG and GCC repeat expansions in the FMR1 gene and AFF2 genes, respectively. Sequence variations were identified by HRM analysis and verified by direct DNA sequencing. Two novel missense mutations (p.Gly482Ser in one patient and p.Arg534His in two unrelated patients), one intronic and two 3'-untranslated region (UTR) variations were identified in the FMR1 gene. Missense mutations in the FMR1 gene might account for a considerable proportion of cases in male patients with FXS-related symptoms, such as those linked to mental retardation and developmental delay.
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Affiliation(s)
- Maximilian Handt
- Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Straße 50, 58448 Witten, Germany
| | - Andrea Epplen
- Human Genetics, Ruhr-University, Universitätsstraße 150, 44801 Bochum, Germany
| | - Sabine Hoffjan
- Human Genetics, Ruhr-University, Universitätsstraße 150, 44801 Bochum, Germany
| | - Kemal Mese
- Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Straße 50, 58448 Witten, Germany
| | - Jörg T Epplen
- Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Straße 50, 58448 Witten, Germany; Human Genetics, Ruhr-University, Universitätsstraße 150, 44801 Bochum, Germany
| | - Gabriele Dekomien
- Human Genetics, Ruhr-University, Universitätsstraße 150, 44801 Bochum, Germany.
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Li M, Zhou L, Palais RA, Wittwer CT. Genotyping Accuracy of High-Resolution DNA Melting Instruments. Clin Chem 2014; 60:864-72. [DOI: 10.1373/clinchem.2013.220160] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
High-resolution DNA melting is a closed-tube method for genotyping and variant scanning that depends on the thermal stability of PCR-generated products. Instruments vary in thermal precision, sample format, melting rates, acquisition, and software. Instrument genotyping accuracy has not been assessed.
METHODS
Each genotype of the single nucleotide variant (SNV) (c.3405–29A>T) of CPS1 (carbamoyl-phosphate synthase 1, mitochondrial) was amplified by PCR in the presence of LCGreen Plus with 4 PCR product lengths. After blinding and genotype randomization, samples were melted in 10 instrument configurations under conditions recommended by the manufacturer. For each configuration and PCR product length, we analyzed 32–96 samples (depending on batch size) with both commercial and custom software. We assessed the accuracy of heterozygote detection and homozygote differentiation of a difficult, nearest-neighbor symmetric, class 4 variant with predicted ΔTm of 0.00 °C.
RESULTS
Overall, the heterozygote accuracy was 99.7% (n = 2141), whereas homozygote accuracy was 70.3% (n = 4441). Instruments with single sample detection as opposed to full-plate imaging better distinguished homozygotes (78.1% and 61.8%, respectively, χ2P < 0.0005). Custom software improved accuracy over commercial software (P < 0.002), although melting protocols recommended by manufacturers were better than a constant ramp rate of 0.1 °C with an oil overlay. PCR products of 51, 100, 272, and 547 bp had accuracies of 72.3%, 83.1%, 59.8%, and 65.9%, respectively (P < 0.0005).
CONCLUSIONS
High-resolution melting detects heterozygotes with excellent accuracy, but homozygote accuracy is dependent on detection mode, analysis software, and PCR product size, as well as melting temperature differences between, and variation within, homozygotes.
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Affiliation(s)
- Mei Li
- Department of Pathology, University of Utah Medical School, Salt Lake City, UT
- current address: Laboratory Center, the Second Hospital of Dalian Medical University, Dalian, China
| | - Luming Zhou
- Department of Pathology, University of Utah Medical School, Salt Lake City, UT
| | | | - Carl T Wittwer
- Department of Pathology, University of Utah Medical School, Salt Lake City, UT
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Kurdyukov I, Rodionov G, Radilov A, Babakov V. Genotyping single-nucleotide polymorphisms of human genes involved in organophosphate detoxification by high-resolution melting. Anal Bioanal Chem 2014; 406:5087-92. [PMID: 24705954 DOI: 10.1007/s00216-014-7734-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 02/21/2014] [Accepted: 02/27/2014] [Indexed: 10/25/2022]
Abstract
Paraoxonase-1 (PON1) and butyrylcholinesterase (BCHE) are natural bioscavengers of organophosphate acetylcholinesterase inhibitors in the human body, which can determine individual sensitivity to organophosphate toxicity. Interindividual differences in activity of PON1 (catalytic bioscavenger) and substrate specificity are strongly associated with the substitution of two amino acids: Leu/Met (L/M) at position 55 (rs854560) and Gln/Arg (Q/R) at position 192 (rs662). In the case of BCHE (stoichiometric bioscavenger) substitution, Ala/Thr (A/T) at position 539 produces the so-called "K-variant" of the enzyme (rs1803274). Threonine allele is often co-inherited with an atypical BCHE allele (rs1799807). The atypical variant of BCHE displays a lower affinity for cholinesterase inhibitors. Genotyping rs662 and rs1803274 single-nucleotide polymorphisms (SNP) by high-resolution melting (HRM) is facilitated by the nucleotide substitution A>G (G>A), which resulted in a changed number of hydrogen bonds in the PCR product and, consequently, shifted T m. In the case of rs854560, genotyping is complicated by the nucleotide substitution T>A, which has no significant effect on the T m of the PCR product. An addition of a small quantity of LL homozygote DNA into the reaction mixture before PCR discriminates the three genotypes by the melt curves due to different amounts of heteroduplexes formed in the LM and MM samples. HRM analysis can be applied for genotyping human rs854560, rs662, and rs1803274 SNPs.
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Affiliation(s)
- Ivan Kurdyukov
- Research Institute of Hygiene, Occupational Pathology and Human Ecology (RIHOPHE), Russian Federal Medical Biological Agency, g/p Kuzmolovsky, St. Petersburg, Russia, 188663,
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29
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High resolution melting analysis of deletion/insertion polymorphisms: A new method for the detection and quantification of mixed chimerism in allogeneic stem cell transplantation. Mol Cell Probes 2014; 28:19-24. [DOI: 10.1016/j.mcp.2013.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 09/11/2013] [Accepted: 09/11/2013] [Indexed: 11/23/2022]
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30
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Dwight ZL, Palais R, Kent J, Wittwer CT. Heterozygote PCR Product Melting Curve Prediction. Hum Mutat 2014; 35:278-82. [DOI: 10.1002/humu.22494] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 12/02/2013] [Indexed: 11/09/2022]
Affiliation(s)
| | - Robert Palais
- Department of Mathematics; Utah Valley University; Orem Utah
| | - Jana Kent
- Department of Pathology; University of Utah; Salt Lake City Utah
| | - Carl T. Wittwer
- Department of Pathology; University of Utah; Salt Lake City Utah
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31
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Furtado LV, Weigelin HC, Elenitoba-Johnson KS, Betz BL. A Multiplexed Fragment Analysis-Based Assay for Detection of JAK2 Exon 12 Mutations. J Mol Diagn 2013; 15:592-9. [DOI: 10.1016/j.jmoldx.2013.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 03/27/2013] [Accepted: 04/15/2013] [Indexed: 12/15/2022] Open
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Illson ML, Dempsey-Nunez L, Kent J, Huang Q, Brebner A, Raff ML, Watkins D, Gilfix BM, Wittwer CT, Rosenblatt DS. High resolution melting analysis of the MMAB gene in cblB patients and in those with undiagnosed methylmalonic aciduria. Mol Genet Metab 2013; 110:86-9. [PMID: 23707710 DOI: 10.1016/j.ymgme.2013.04.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 04/29/2013] [Indexed: 11/24/2022]
Abstract
Isolated methylmalonic aciduria (MMA) results either from a defect in the mitochondrial enzyme methylmalonylCoA mutase (MCM), or in the intracellular conversion of vitamin B12 (cobalamin) into its active coenzyme adenosylcobalamin (AdoCbl). Mutations in the MMAB gene affect the function of the enzyme ATP:cob(I)alamin adenosyltransferase (ATR) and the production of AdoCbl. Measurement of MCM function in cultured patient fibroblasts, followed by somatic cell complementation analysis in cases where MCM function is decreased, has classically been used to diagnose the cblB cobalamin disorder. A patient with persistent MMA, who could not be diagnosed using traditional somatic cell studies, was subsequently shown by sequencing in a clinical laboratory to contain two variants in the MMAB gene. This observation brings into question whether somatic cell studies have failed to diagnose other cblB patients with mild cellular phenotypes. A high resolution melting analysis (HRMA) assay was developed for the MMAB gene. It was used to scan 96 reference samples and two cohorts of patients: 42 patients diagnosed with cblB by complementation studies; and 181 patients with undiagnosed MMA. MMAB mutations, including one novel nonsense mutation (c.12 C>A [p.C4X]), were identified in all members of the cblB cohort. Four patients with undiagnosed MMA, including the index case described above, were found to contain variants in the MMAB gene: c.185C>T (p.T62M), c.394T>C (p.C132R), c.398C>T (p.S133F), c.521C>T (p.S174L), c.572G>A (p.R191Q). Only the index case was found to have two variants, suggesting that somatic cell studies diagnose almost all cblB patients.
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Affiliation(s)
- Margaret L Illson
- Department of Human Genetics, McGill University, Montreal, QC, Canada
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33
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Pindurová E, Zourková A, Zrůstová J, Juřica J, Pavelka A. Alternative reliable method for cytochrome P450 2D6 poor metabolizers genotyping. Mol Biotechnol 2013; 53:29-40. [PMID: 22367691 DOI: 10.1007/s12033-012-9510-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
High-resolution melting curve analysis (HRM) of polymerase chain reaction (PCR) amplicons has been described as a fast, cheap, and reliable closed-tube method of genotyping with no need for labeled primers or labeled probes. We adapted this melting analysis assay for the detection of the most common nonfunctional alleles of cytochrome P-450 (CYP) 2D6 in the Caucasian population that affect the metabolism of many commonly used drugs. We used this method to genotype 91 patients under paroxetine therapy. The presence and the constitution of the most common single-nucleotide polymorphisms (1846G>A, 2988G>A, 100C>T, 2549delA, 2615_2617delAAG, and 1707delT) in poor and intermediate metabolizers from the Caucasian population were detected in short amplicons (≤148 bp). After fluorescence normalization, the wild-type, homozygous, and heterozygous samples were easily distinguishable from each other by their specific melting curve shape. A total of 92.6% of the 1846G>A heterozygotes, 96% of the 100C>T heterozygotes, and 100% of the 2988G>A, 2549delA, 2615_2617delAAG, and 1707delT heterozygotes have been correctly distinguished from the wild types. One hundred percent of all the homozygotes in this group of patients have been detected without any error. HRM of short amplicons is a simple tool for effective, rapid, and reliable CYP2D6 genotyping that does not require real-time PCR, labeled probes, processing or any separations after PCR. The reaction is performed in a closed-tube system and is highly specific and sensitive. We proved that this technique is highly reliable for use in routine diagnostics.
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Affiliation(s)
- E Pindurová
- Department of Applied Neuroscience, Faculty of Medicine, Central European Institute of Technology (CEITEC), Brno, Czech Republic.
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Cui G, Zhang L, Xu Y, Cianflone K, Ding H, Wang DW. Development of a high resolution melting method for genotyping of risk HLA-DQA1 and PLA2R1 alleles and ethnic distribution of these risk alleles. Gene 2013. [DOI: 10.1016/j.gene.2012.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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35
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Kuster CJ, Von Elert E. High-resolution melting analysis: a genotyping tool for population studies on Daphnia. Mol Ecol Resour 2012; 12:1048-57. [PMID: 22925691 DOI: 10.1111/j.1755-0998.2012.03177.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/05/2012] [Accepted: 07/17/2012] [Indexed: 11/27/2022]
Abstract
Determining genetic variation at the DNA level within and between natural populations is important for understanding the role of natural selection on phenotypic traits, but many techniques of screening for genetic variation are either cost intensive, not sensitive enough or too labour- and time-consuming. Here, we demonstrate high-resolution melting analysis (HRMA) as a cost-effective and powerful tool for screening variable target genes in natural populations. HRMA is based on monitoring the melting of PCR amplicons. Owing to saturating concentrations of a dye that binds at high concentrations to double-stranded DNA, it is possible to genotype high numbers of samples rapidly and accurately. We analysed digestive trypsins of two Daphnia magna populations as an application example for HRMA. One population originated from a pond containing toxic cyanobacteria that possibly produce protease inhibitors and the other from a pond without such cyanobacteria. The hypothesis was that D. magna clones from ponds with cyanobacteria have undergone selection by these inhibitors, which has led to different trypsin alleles. We first sequenced pooled genomic PCR products of trypsins from both populations to identify variable DNA sequences of active trypsins. Second, we screened variable DNA sequences of each D. magna clone from both populations for single nucleotide polymorphisms via HRMA. The HRMA results revealed that both populations exhibited phenotypic differences in the analysed trypsins. Our results indicate that HRMA is a powerful genotyping tool for studying the variation of target genes in response to selection within and between natural Daphnia populations.
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Affiliation(s)
- C J Kuster
- Zoological Institute, Aquatic Chemical Ecology, University of Cologne, Cologne, Germany.
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36
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Feldkamp ML, Bowles NE, Botto LD. AEBP1gene variants in infants with gastroschisis. ACTA ACUST UNITED AC 2012; 94:738-42. [DOI: 10.1002/bdra.23041] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 05/09/2012] [Accepted: 05/10/2012] [Indexed: 01/16/2023]
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Determination of RET Sequence Variation in an MEN2 Unaffected Cohort Using Multiple-Sample Pooling and Next-Generation Sequencing. J Thyroid Res 2012; 2012:318232. [PMID: 22545224 PMCID: PMC3321559 DOI: 10.1155/2012/318232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 01/23/2012] [Indexed: 11/30/2022] Open
Abstract
Multisample, nonindexed pooling combined with next-generation sequencing (NGS) was used to discover RET proto-oncogene sequence variation within a cohort known to be unaffected by multiple endocrine neoplasia type 2 (MEN2). DNA samples (113 Caucasians, 23 persons of other ethnicities) were amplified for RET intron 9 to intron 16 and then divided into 5 pools of <30 samples each before library prep and NGS. Two controls were included in this study, a single sample and a pool of 50 samples that had been previously sequenced by the same NGS methods. All 59 variants previously detected in the 50-pool control were present. Of the 61 variants detected in the unaffected cohort, 20 variants were novel changes. Several variants were validated by high-resolution melting analysis and Sanger sequencing, and their allelic frequencies correlated well with those determined by NGS. The results from this unaffected cohort will be added to the RET MEN2 database.
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Li H, Shu C, He X, Gao J, Liu R, Huang D. Detection and identification of vegetative insecticidal proteins vip3 genes of Bacillus thuringiensis strains using polymerase chain reaction-high resolution melt analysis. Curr Microbiol 2012; 64:463-8. [PMID: 22350000 DOI: 10.1007/s00284-012-0092-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 01/23/2012] [Indexed: 10/28/2022]
Abstract
In this study, vegetative insecticidal proteins vip3 genes from Bacillus thuringiensis strains were detected based on polymerase chain reaction-high resolution melt (PCR-HRM) analysis. A pair of primers was designed according to the conservative sequences in 150 bp region of the known vip3 subfamily. The 150 bp regions of difference vip3 genes have only a few nucleotide difference vip3 genes were detected in 8 of 11 standard B. thuringiensis strains, and vip3Aa genes, vip3Af genes and vip3Ba gene can be distinguished as different melting curves by this method. The results demonstrate the utility of the HRM assay for mutant screening using vip3 gene. The PCR-HRM method may be a valuable and reliable tool for specific detection and identification of vip3 genes.
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Affiliation(s)
- Haitao Li
- Northeast Agricultural University, Harbin 150030, People's Republic of China.
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Differential high-resolution melting analysis for the detection of K-ras codons 12 and 13 mutations in pancreatic cancer. Pancreas 2011; 40:1283-8. [PMID: 21989023 DOI: 10.1097/mpa.0b013e318220af91] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
OBJECTIVE The aim of this study was to establish a differential high-resolution melting analysis for the detection of K-ras codons 12 and 13 mutations in pancreatic cancer tissue. METHODS We tested the sensitivity of this genotyping approach in cell lines with known K-ras mutations using 163- and 59-base pair (bp) amplicons spanning codons 12 and 13. We then screened 50 pancreatic cancer tissues, which were subsequently sequenced to confirm mutations discovered in K-ras codons 12 and 13. RESULTS High-resolution melting analysis was more sensitive in detecting mutations than standard sequencing and was able to reliably detect as little as 10% of mutant cell line DNA diluted in wild-type cell line DNA. Compared with the 163-bp amplicons, the shorter 59-bp amplicons displayed a higher sensitivity, even at 3% to 5% dilution. CONCLUSIONS High-resolution melting analysis is a sensitive and accurate screening methodology for K-ras codons 12 and 13 mutations in clinical samples. The accuracy and sensitivity of high-resolution melting analysis can provide appropriate and cost-effective therapeutic choices for physicians.
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Carillo S, Henry L, Lippert E, Girodon F, Guiraud I, Richard C, Dubois Galopin F, Cleyrat C, Jourdan E, Kralovics R, Hermouet S, Lavabre-Bertrand T. Nested high-resolution melting curve analysis a highly sensitive, reliable, and simple method for detection of JAK2 exon 12 mutations--clinical relevance in the monitoring of polycythemia. J Mol Diagn 2011; 13:263-70. [PMID: 21497288 DOI: 10.1016/j.jmoldx.2010.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 11/08/2010] [Accepted: 12/10/2010] [Indexed: 10/18/2022] Open
Abstract
JAK2 exon 12 mutations are found in myeloproliferative disorders characterized by erythrocytosis. Lying in a 33-bp region and conserving the open reading frame, they often present a low allelic burden (<10%), which excludes screening with techniques such as allele-specific PCR or different sequencing protocols. High-resolution melting (HRM), a fast in-tube method, seems the most accurate routine technique for that. We describe a reliable and powerful nested HRM technique, independent of DNA preparation and with technical sensitivity of 100% (95% CI, 93% to 100%) and specificity of 96.7% (95% CI, 89.7% to 96.7%). Screening a cohort of 10 idiopathic erythrocytosis, 28 polycythemia vera, and 7 secondary erythrocytosis cases allowed the detection of 15 mutants, including 9 different mutations, of which 3 were unreported, all in the polycythemia vera group, and presented a characteristic profile: pure erythrocytosis associated with low serum erythropoietin. Threshold detection level ranged from 1% to 3% allelic burden, depending on the mutation. All of the HRM positive signals were found mutated by sequencing. Six of them (40%), however, required cloning before sequencing, because of low allelic burden. Classic techniques such as genomic sequencing may therefore miss patients with mutations. Given its sensitivity, HRM (and nested HRM) can be used in routine diagnosis and seems to be the most efficient of current techniques for detection of JAK2 exon 12 mutations.
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Affiliation(s)
- Serge Carillo
- Laboratory of Clinical Cytology, CHU Caremeau, Nîmes, France
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Tricarico R, Crucianelli F, Alvau A, Orlando C, Sestini R, Tonelli F, Valanzano R, Genuardi M. High resolution melting analysis for a rapid identification of heterozygous and homozygous sequence changes in the MUTYH gene. BMC Cancer 2011; 11:305. [PMID: 21777424 PMCID: PMC3156810 DOI: 10.1186/1471-2407-11-305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 07/21/2011] [Indexed: 11/29/2022] Open
Abstract
Background MUTYH-associated polyposis (MAP) is an autosomal recessive form of intestinal polyposis predisposing to colorectal carcinoma. High resolution melting analysis (HRMA) is a mutation scanning method that allows detection of heterozygous sequence changes with high sensitivity, whereas homozygosity for a nucleotide change may not lead to significant curve shape or melting temperature changes compared to homozygous wild-type samples. Therefore, HRMA has been mainly applied to the detection of mutations associated with autosomal dominant or X-linked disorders, while applications to autosomal recessive conditions are less common. Methods MUTYH coding sequence and UTRs were analyzed by both HRMA and sequencing on 88 leukocyte genomic DNA samples. Twenty-six samples were also examined by SSCP. Experiments were performed both with and without mixing the test samples with wild-type DNA. Results The results show that all MUTYH sequence variations, including G > C and A > T homozygous changes, can be reliably identified by HRMA when a condition of artificial heterozygosity is created by mixing test and reference DNA. HRMA had a sensitivity comparable to sequencing and higher than SSCP. Conclusions The availability of a rapid and inexpensive method for the identification of MUTYH sequence variants is relevant for the diagnosis of colorectal cancer susceptibility, since the MAP phenotype is highly variable.
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Affiliation(s)
- Rossella Tricarico
- Department of Clinical Pathophysiology, Medical Genetics Unit, University of Florence, Florence, Italy
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Alonso M, Navarro Y, Barletta F, Martínez Lirola M, Gotuzzo E, Bouza E, García de Viedma D. A novel method for the rapid and prospective identification of Beijing Mycobacterium tuberculosis strains by high-resolution melting analysis. Clin Microbiol Infect 2011; 17:349-57. [PMID: 20384709 DOI: 10.1111/j.1469-0691.2010.03234.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genotypic analysis of Mycobacterium tuberculosis (MTB) has enabled the definition of several lineages. The Beijing family, which is considered highly virulent and transmissible, has been associated with resistance in certain settings and involved in severe outbreaks, making it one of the most closely-monitored lineages. Therefore, rapid prospective identification of Beijing MTB strains could be relevant. In the present study, we evaluate a real-time PCR followed by high-resolution melting (HRM) based on the identification of a single nucleotide polymorphism (SNP) in the Rv2629 gene which defines Beijing lineage (A191C for Beijing genotype and A191A for non-Beijing genotype). This combined methodology efficiently differentiated Beijing and non-Beijing strains in 100% of the isolates from a collection of reference strains without requiring specific DNA probes. Additionally, HRM was able to assign a Beijing/non-Beijing genotype in 90.9% of the respiratory specimens assayed. Its applicability was tested on a Peruvian sample of circulating MTB strains, in which it identified 10.7% as belonging to the Beijing genotype; this proportion reached 20% in the North Lima area. HRM analysis of the A191C SNP is a rapid, reliable, and sensitive method for the efficient prospective survey of high-risk Beijing MTB strains, even in developing settings where MTB culture is often not available.
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Affiliation(s)
- M Alonso
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorìo Marañón, Madrid, Spain
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Zhou ZW, Yan JB, Li H, Ren ZR. Application of high-resolution melting for genotyping bovine mitochondrial DNA. Biotechnol Prog 2011; 27:592-5. [DOI: 10.1002/btpr.548] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 09/03/2010] [Indexed: 11/12/2022]
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Svensson AM, Chou LS, Meadows C, Miller CE, Palais R, Sumner K, Wayman TC, Mao R, Lyon E. Implementation of a cost-effective unlabeled probe high-resolution melt assay for genotyping of Factor V Leiden. Genet Test Mol Biomarkers 2011; 15:207-13. [PMID: 21254846 DOI: 10.1089/gtmb.2010.0137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Factor V Leiden mutation (FVL; c.1601G>A, p.Arg534Gln), the most common aberration underlying activated Protein C resistance, results in disruption of a major anticoagulation pathway and is a leading cause of inherited thrombophilia. A high-throughput assay for FVL mutation detection was developed using a single unlabeled probe on a high-resolution platform, the 96-well Roche 480 LightCycler (LC480) instrument. This method replaced the U.S. Food and Drug Administration-approved Roche Factor V Leiden kit assay on the LightCycler PCR instrument, decreasing total cost by 48%. The analytical sensitivity and specificity of the LC480 high-resolution assay approached 100% for the FVL mutation. Factor V mutations in proximity to the FVL locus may influence probe binding efficiency and melt characteristics. One out of three very rare variants tested in a separate study, 1600delC, was not distinguishable from FVL using the described high-resolution assay. However, a c.1598G>A variant, which changes the amino acid sequence from arginine to lysine at position 533, was detected by this high-resolution assay and confirmed by bidirectional sequencing. In the labeled probe LightCycler assay, the c.1598G>A variant was indistinguishable from the heterozygous FVL control. The c.1598G>A variant has not been described previously and its clinical significance is uncertain. In conclusion, the LC480 FVL assay is cost effective in a high-throughput setting, with capability to detect both previously described and novel FV variants.
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Affiliation(s)
- Annika M Svensson
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.
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Pietzka AT, Stöger A, Huhulescu S, Allerberger F, Ruppitsch W. Gene Scanning of an Internalin B Gene Fragment Using High-Resolution Melting Curve Analysis as a Tool for Rapid Typing of Listeria monocytogenes. J Mol Diagn 2010; 13:57-63. [PMID: 21227395 DOI: 10.1016/j.jmoldx.2010.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/27/2010] [Accepted: 08/10/2010] [Indexed: 11/28/2022] Open
Abstract
The ability to accurately track Listeria monocytogenes strains involved in outbreaks is essential for control and prevention of listeriosis. Because current typing techniques are time-consuming, cost-intensive, technically demanding, and difficult to standardize, we developed a rapid and cost-effective method for typing of L. monocytogenes. In all, 172 clinical L. monocytogenes isolates and 20 isolates from culture collections were typed by high-resolution melting (HRM) curve analysis of a specific locus of the internalin B gene (inlB). All obtained HRM curve profiles were verified by sequence analysis. The 192 tested L. monocytogenes isolates yielded 15 specific HRM curve profiles. Sequence analysis revealed that these 15 HRM curve profiles correspond to 18 distinct inlB sequence types. The HRM curve profiles obtained correlated with the five phylogenetic groups I.1, I.2, II.1, II.2, and III. Thus, HRM curve analysis constitutes an inexpensive assay and represents an improvement in typing relative to classical serotyping or multiplex PCR typing protocols. This method provides a rapid and powerful screening tool for simultaneous preliminary typing of up to 384 samples in approximately 2 hours.
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Affiliation(s)
- Ariane T Pietzka
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
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Cheng J, Yim OS, Low PS, Tay SKH, Yap EPH, Lai PS. Detection of hemi/homozygotes through heteroduplex formation in high-resolution melting analysis. Anal Biochem 2010; 410:158-60. [PMID: 21111703 DOI: 10.1016/j.ab.2010.11.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 11/07/2010] [Accepted: 11/17/2010] [Indexed: 01/06/2023]
Abstract
Heteroduplex formation, required for the complete detection of hemi/homozygotes using high-resolution melting analysis, can be induced either by pre-PCR mixing of genomic DNAs or by post-PCR mixing of PCR products from unknown and reference samples. This study investigates the effects of both methods using two single nucleotide polymorphisms in X-linked DMD gene. The results show that both methods resulted in the same effect when mixing samples with the same gene copy number. Mixing samples with different gene copy numbers has not been previously explored and we show that post-PCR mixing is insensitive to gene copy number differences as compared to pre-PCR mixing.
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Affiliation(s)
- Jinting Cheng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore
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Mader E, Ruzicka J, Schmiderer C, Novak J. Quantitative high-resolution melting analysis for detecting adulterations. Anal Biochem 2010; 409:153-5. [PMID: 20946863 DOI: 10.1016/j.ab.2010.10.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Revised: 10/01/2010] [Accepted: 10/01/2010] [Indexed: 11/17/2022]
Abstract
Admixtures of different plant species are a common problem in raw materials for medicinal use. Two exemplary assays were developed to admixtures in Helleborus niger with high-resolution melting analysis. HRM proved to be a very sensitive tool in detecting admixtures, able to detect a ratio of 1:1000 with unknown species, and of 1:200,000 with Veratrum nigrum. The example proves the ability of HRM for quantification in multiplex PCR. The method is not limited to detecting adulterations. It can also be used to quantify a specific target by integrating a second amplicon in the assay as internal standard.
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Affiliation(s)
- Eduard Mader
- Institute for Applied Botany, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Wien, Austria.
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Liew M, Wittwer C, Voelkerding KV. Nucleotide extension genotyping by high-resolution melting. J Mol Diagn 2010; 12:731-8. [PMID: 20847280 DOI: 10.2353/jmoldx.2010.090149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One limitation of small amplicon melting is the inability to genotype certain nearest-neighbor symmetric variations without manipulating the sample. We have developed a method for these exceptions: a high-resolution melting single nucleotide extension assay. Single nucleotide extension was performed in a new instrument, the LightScanner 32 (LS32), which uses capillary reaction tubes and is capable of real-time PCR and sequential high-resolution melting of 32 samples. Asymmetric PCR used Platinum Taq and LC Green Plus in the master mix for target amplification. Dideoxynucleotides and extension oligonucleotides were sequestered in the tube cap and added post-PCR, maintaining a closed system. One dideoxynucleotides was used per capillary tube. Samples were cycled five times to incorporate dideoxynucleotides into the extension products using ThermoSequenase, followed by high-resolution melting. Single nucleotide polymorphisms from the RET proto-oncogene (n = 7), hemochromatosis (HFE, n = 30), coagulation factor 2 (F2, n = 29), coagulation factor 5 (F5, n = 30), and methylenetetrahydrofolate reductase (MTHFR, n = 60) genes were genotyped. The DNA melting profiles identified the target single nucleotide polymorphisms by the lowest melting temperature transition. All genotypes had a distinctive melting pattern. The method was 100% concordant with samples previously genotyped at HFE, MTHFR, and F2 and 90% concordant with F5. F5 discordants were genotyped correctly by redesigning the assay. Our results demonstrate that although single nucleotide polymorphisms can be successfully differentiated using this methodology, the method requires careful optimization.
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Affiliation(s)
- Michael Liew
- Associated Regional and University Pathologists (ARUP) Institute for Clinical and Experimental Pathology, 500 Chipeta Way, Salt Lake City, UT 84108-1221, USA.
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Ishikawa T, Kamei Y, Otozai S, Kim J, Sato A, Kuwahara Y, Tanaka M, Deguchi T, Inohara H, Tsujimura T, Todo T. High-resolution melting curve analysis for rapid detection of mutations in a Medaka TILLING library. BMC Mol Biol 2010; 11:70. [PMID: 20840787 PMCID: PMC2949603 DOI: 10.1186/1471-2199-11-70] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 09/15/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During the last two decades, DNA sequencing has led to the identification of numerous genes in key species; however, in most cases, their functions are still unknown. In this situation, reverse genetics is the most suitable method to assign function to a gene. TILLING (Targeting Induced Local Lesions IN Genomes) is a reverse-genetic strategy that combines random chemical mutagenesis with high-throughput discovery of the induced mutations in target genes. The method has been applied to a variety of plant and animal species. Screening of the induced mutations is the most important step in TILLING. Currently, direct sequencing or nuclease-mediated screening of heteroduplexes is widely used for detection of mutations in TILLING. Both methods are useful, but the costs are substantial and turnaround times are relatively long. Thus, there is a need for an alternative method that is of higher throughput and more cost effective. RESULTS In this study, we developed a high resolution melting (HRM) assay and evaluated its effectiveness for screening ENU-induced mutations in a medaka TILLING library. We had previously screened mutations in the p53 gene by direct sequencing. Therefore, we first tested the efficiency of the HRM assay by screening mutations in p53, which indicated that the HRM assay is as useful as direct sequencing. Next, we screened mutations in the atr and atm genes with the HRM assay. Nonsense mutations were identified in each gene, and the phenotypes of these nonsense mutants confirmed their loss-of-function nature. CONCLUSIONS These results demonstrate that the HRM assay is useful for screening mutations in TILLING. Furthermore, the phenotype of the obtained mutants indicates that medaka is an excellent animal model for investigating genome stability and gene function, especially when combined with TILLING.
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Affiliation(s)
- Tomoko Ishikawa
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, B4, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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Shirasawa K, Asamizu E, Fukuoka H, Ohyama A, Sato S, Nakamura Y, Tabata S, Sasamoto S, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, Isobe S. An interspecific linkage map of SSR and intronic polymorphism markers in tomato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:731-9. [PMID: 20431859 PMCID: PMC2909429 DOI: 10.1007/s00122-010-1344-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 04/11/2010] [Indexed: 05/20/2023]
Abstract
Despite the collection and availability of abundant tomato genome sequences, PCR-based markers adapted to large scale analysis have not been developed in tomato species. Therefore, using public genome sequence data in tomato, we developed three types of DNA markers: expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers (TES markers), genome-derived SSR markers (TGS markers) and EST-derived intronic polymorphism markers (TEI markers). A total of 2,047 TES, 3,510 TGS and 674 TEI markers were established and used in the polymorphic analysis of a cultivated tomato (Solanum lycopersicum) 'LA925' and its wild relative Solanum pennellii 'LA716', parents of the Tomato-EXPEN 2000 mapping population. The polymorphic ratios between parents revealed by the TES, TGS and TEI markers were 37.3, 22.6 and 80.0%, respectively. Those showing polymorphisms were used to genotype the Tomato-EXPEN 2000 mapping population, and a high-density genetic linkage map composed of 1,433 new and 683 existing marker loci was constructed on 12 chromosomes, covering 1,503.1 cM. In the present map, 48% of the mapped TGS loci were located within heterochromatic regions, while 18 and 21% of TES and TEI loci, respectively, were located in heterochromatin. The large number of SSR and SNP markers developed in this study provide easily handling genomic tools for molecular breeding in tomato. Information on the DNA markers developed in this study is available at http://www.kazusa.or.jp/tomato/.
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Erika Asamizu
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
- Gene Research Center, University of Tsukuba, Ten-no dai 1-1-1, Tsukuba, Ibaraki 305-8572 Japan
| | - Hiroyuki Fukuoka
- National Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392 Japan
| | - Akio Ohyama
- National Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392 Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Yasukazu Nakamura
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540 Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Shigemi Sasamoto
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Tsuyuko Wada
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Yoshie Kishida
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Hisano Tsuruoka
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Tsunakazu Fujishiro
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Manabu Yamada
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
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