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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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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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Shah K, Bentley E, Tyler A, Richards KSR, Wright E, Easterbrook L, Lee D, Cleaver C, Usher L, Burton JE, Pitman JK, Bruce CB, Edge D, Lee M, Nazareth N, Norwood DA, Moschos SA. Field-deployable, quantitative, rapid identification of active Ebola virus infection in unprocessed blood. Chem Sci 2017; 8:7780-7797. [PMID: 29163915 PMCID: PMC5694917 DOI: 10.1039/c7sc03281a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/20/2017] [Indexed: 01/01/2023] Open
Abstract
The West African Ebola virus outbreak underlined the importance of delivering mass diagnostic capability outside the clinical or primary care setting in effectively containing public health emergencies caused by infectious disease. Yet, to date, there is no solution for reliably deploying at the point of need the gold standard diagnostic method, real time quantitative reverse transcription polymerase chain reaction (RT-qPCR), in a laboratory infrastructure-free manner. In this proof of principle work, we demonstrate direct performance of RT-qPCR on fresh blood using far-red fluorophores to resolve fluorogenic signal inhibition and controlled, rapid freeze/thawing to achieve viral genome extraction in a single reaction chamber assay. The resulting process is entirely free of manual or automated sample pre-processing, requires no microfluidics or magnetic/mechanical sample handling and thus utilizes low cost consumables. This enables a fast, laboratory infrastructure-free, minimal risk and simple standard operating procedure suited to frontline, field use. Developing this novel approach on recombinant bacteriophage and recombinant human immunodeficiency virus (HIV; Lentivirus), we demonstrate clinical utility in symptomatic EBOV patient screening using live, infectious Filoviruses and surrogate patient samples. Moreover, we evidence assay co-linearity independent of viral particle structure that may enable viral load quantification through pre-calibration, with no loss of specificity across an 8 log-linear maximum dynamic range. The resulting quantitative rapid identification (QuRapID) molecular diagnostic platform, openly accessible for assay development, meets the requirements of resource-limited countries and provides a fast response solution for mass public health screening against emerging biosecurity threats.
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Affiliation(s)
- Kavit Shah
- Westminster Genomic Services , Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
- BGResearch Ltd. , 6 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - Emma Bentley
- Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
| | - Adam Tyler
- BioGene Ltd. , 8 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - Kevin S R Richards
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - Edward Wright
- Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
| | - Linda Easterbrook
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - Diane Lee
- Fluorogenics LIMITED , Building 227, Tetricus Science Park, Dstl Porton Down , Salisbury , Wiltshire SP4 0JQ , UK
| | - Claire Cleaver
- Fluorogenics LIMITED , Building 227, Tetricus Science Park, Dstl Porton Down , Salisbury , Wiltshire SP4 0JQ , UK
| | - Louise Usher
- Westminster Genomic Services , Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
| | - Jane E Burton
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - James K Pitman
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - Christine B Bruce
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - David Edge
- BioGene Ltd. , 8 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - Martin Lee
- Fluorogenics LIMITED , Building 227, Tetricus Science Park, Dstl Porton Down , Salisbury , Wiltshire SP4 0JQ , UK
| | - Nelson Nazareth
- BioGene Ltd. , 8 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - David A Norwood
- Diagnostic Systems Division and Virology Division , United States Army Medical Research Institute of Infectious Diseases , Fort Detrick , MD 21701-5011 , USA
| | - Sterghios A Moschos
- Westminster Genomic Services , Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
- Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
- Department of Applied Sciences , Faculty of Health and Life Sciences , Northumbria University , C4.03 Ellison Building, Ellison Place , Newcastle Upon Tyne , Tyne and Wear NE1 8ST , UK . ; Tel: +44(0) 191 215 6623
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Ladas I, Fitarelli-Kiehl M, Song C, Adalsteinsson VA, Parsons HA, Lin NU, Wagle N, Makrigiorgos GM. Multiplexed Elimination of Wild-Type DNA and High-Resolution Melting Prior to Targeted Resequencing of Liquid Biopsies. Clin Chem 2017; 63:1605-1613. [PMID: 28679646 PMCID: PMC5914173 DOI: 10.1373/clinchem.2017.272849] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/12/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The use of clinical samples and circulating cell-free DNA (cfDNA) collected from liquid biopsies for diagnostic and prognostic applications in cancer is burgeoning, and improved methods that reduce the influence of excess wild-type (WT) portion of the sample are desirable. Here we present enrichment of mutation-containing sequences using enzymatic degradation of WT DNA. Mutation enrichment is combined with high-resolution melting (HRM) performed in multiplexed closed-tube reactions as a rapid, cost-effective screening tool before targeted resequencing. METHODS We developed a homogeneous, closed-tube approach to use a double-stranded DNA-specific nuclease for degradation of WT DNA at multiple targets simultaneously. The No Denaturation Nuclease-assisted Minor Allele Enrichment with Probe Overlap (ND-NaME-PrO) uses WT oligonucleotides overlapping both strands on putative DNA targets. Under conditions of partial denaturation (DNA breathing), the oligonucleotide probes enhance double-stranded DNA-specific nuclease digestion at the selected targets, with high preference toward WT over mutant DNA. To validate ND-NaME-PrO, we used multiplexed HRM, digital PCR, and MiSeq targeted resequencing of mutated genomic DNA and cfDNA. RESULTS Serial dilution of KRAS mutation-containing DNA shows mutation enrichment by 10- to 120-fold and detection of allelic fractions down to 0.01%. Multiplexed ND-NaME-PrO combined with multiplexed PCR-HRM showed mutation scanning of 10-20 DNA amplicons simultaneously. ND-NaME-PrO applied on cfDNA from clinical samples enables mutation enrichment and HRM scanning over 10 DNA targets. cfDNA mutations were enriched up to approximately 100-fold (average approximately 25-fold) and identified via targeted resequencing. CONCLUSIONS Closed-tube homogeneous ND-NaME-PrO combined with multiplexed HRM is a convenient approach to efficiently enrich for mutations on multiple DNA targets and to enable prescreening before targeted resequencing.
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Affiliation(s)
- Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | | | - Heather A. Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Nancy U. Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - G. Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA,Correspondence: G. Mike Makrigiorgos, Ph.D., Brigham and Women’s Hospital, Level L2, Radiation Therapy, 75 Francis Street, Boston, MA 02115., Tel: 617-525-7122. Fax: 617-582-6037,
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Bogdanov KV, Nikulina TS, Lomaia EG, Slyadnev MN, Zaritskey AY. Identification of oncogene mutations in leukemia patients using microchip-based PCR analysis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017040033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ebili HO, Hassall J, Asiri A, Ham-Karim H, Fadhil W, Agboola AJ, Ilyas M. QMC-PCRx: a novel method for rapid mutation detection. J Clin Pathol 2017; 70:702-711. [PMID: 28153952 DOI: 10.1136/jclinpath-2016-204264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 11/03/2022]
Abstract
AIMS We previously described the quick multiplex consensus PCR (QMC-PCR) as a method for rapid mutation screening in low-quality template. QMC-PCR has two-stages: a prediagnostic multiplex (PDM) reaction followed by a single specific diagnostic reaction with high-resolution melting (HRM) analysis. We aimed to develop QMC-PCRx in which second stage was multiplexed to allow testing of multiple targets. METHODS The PDM reaction was retained without change. For the second stage, in silico design was used to identify targets amenable to a multiplex specific diagnostic reaction and multiplex HRM (mHRM) analysis. Following optimisation, 17 colorectal cancers were tested for mutation in five hotspots. For QMC-PCR, each target was tested individually. For QMC-PCRx, the targets were tested in the following combinations (i) KRAS exon 3/PIK3CA exon 20/PTEN exon 3 in triplex and (ii) PTEN exon 7/NRAS exon 2 in duplex. The degree of agreement between the novel QMC-PCRx and the standard QMC-PCR was tested by the percentage concordance. RESULTS Optimisation of mHRM showed that peaks needed to be separated (without overlap) and the optimal number was three targets per test. Our experimental design produced distinct and widely separated peaks for the individual targets although one of the primers needed a GC-tail. A total of 85 individual targets were tested; this required 85 second-stage PCR/HRM tests by QMC-PCR versus 34 second-stage tests by QMC-PCRx. The percentage concordance between the singleplex and multiplex methodologies was 100%. CONCLUSIONS A multiplexed analysis using HRM is possible without loss of diagnostic accuracy. The novel QMC-PCRx protocol can significantly reduce workload and costs of mutation screening.
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Affiliation(s)
- Henry O Ebili
- Division of Cancer and Stem Cell, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK.,Department of Morbid Anatomy and Histopathology, Olabisi Onabanjo University, Ago-Iwoye, Nigeria
| | - James Hassall
- Division of Cancer and Stem Cell, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK
| | - Abutaleb Asiri
- Division of Cancer and Stem Cell, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK
| | - Hersh Ham-Karim
- Division of Cancer and Stem Cell, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK
| | - Wakkas Fadhil
- Division of Cancer and Stem Cell, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK.,Nottingham Molecular Pathology Node, University of Nottingham, Nottingham, UK
| | - Ayodeji Johnson Agboola
- Department of Morbid Anatomy and Histopathology, Olabisi Onabanjo University, Ago-Iwoye, Nigeria
| | - Mohammad Ilyas
- Division of Cancer and Stem Cell, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK.,Nottingham Molecular Pathology Node, University of Nottingham, Nottingham, UK
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Multiplex Real-Time PCR Assay with High-Resolution Melting Analysis for Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae. J Clin Microbiol 2016; 54:2074-81. [PMID: 27225407 DOI: 10.1128/jcm.03354-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/20/2016] [Indexed: 01/23/2023] Open
Abstract
Resistance to antibiotics used against Neisseria gonorrhoeae infections is a major public health concern. Antimicrobial resistance (AMR) testing relies on time-consuming culture-based methods. Development of rapid molecular tests for detection of AMR determinants could provide valuable tools for surveillance and epidemiological studies and for informing individual case management. We developed a fast (<1.5-h) SYBR green-based real-time PCR method with high-resolution melting (HRM) analysis. One triplex and three duplex reactions included two sequences for N. gonorrhoeae identification and seven determinants of resistance to extended-spectrum cephalosporins (ESCs), azithromycin, ciprofloxacin, and spectinomycin. The method was validated by testing 39 previously fully characterized N. gonorrhoeae strains, 19 commensal Neisseria species strains, and an additional panel of 193 gonococcal isolates. Results were compared with results of culture-based AMR determination. The assay correctly identified N. gonorrhoeae and the presence or absence of the seven AMR determinants. There was some cross-reactivity with nongonococcal Neisseria species, and the detection limit was 10(3) to 10(4) genomic DNA (gDNA) copies/reaction. Overall, the platform accurately detected resistance to ciprofloxacin (sensitivity and specificity, 100%), ceftriaxone (sensitivity, 100%; specificity, 90%), cefixime (sensitivity, 92%; specificity, 94%), azithromycin (sensitivity and specificity, 100%), and spectinomycin (sensitivity and specificity, 100%). In conclusion, our methodology accurately detects mutations that generate resistance to antibiotics used to treat gonorrhea. Low assay sensitivity prevents direct diagnostic testing of clinical specimens, but this method can be used to screen collections of gonococcal isolates for AMR more quickly than current culture-based AMR testing.
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Real-time PCR/DNA melting curve-based assay to identify individual strongylid larvae recovered from ovine faecal cultures. Vet Parasitol 2015; 214:337-41. [DOI: 10.1016/j.vetpar.2015.10.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 10/06/2015] [Accepted: 10/16/2015] [Indexed: 11/20/2022]
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Helsmoortel C, Kooy RF, Vandeweyer G. Multiplexed High Resolution Melting Assay for Versatile Sample Tracking in a Diagnostic and Research Setting. J Mol Diagn 2015; 18:32-8. [PMID: 26614051 DOI: 10.1016/j.jmoldx.2015.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/27/2015] [Accepted: 06/25/2015] [Indexed: 11/30/2022] Open
Abstract
Modern experimental procedures in molecular genetics, such as next-generation sequencing experiments, require that samples are taken along a whole series of wet- and dry-laboratory steps. It generally is accepted that by increasing the complexity and number of steps in the experimental pipeline, the risk of sample swaps increases. It therefore is recommended to confirm the identity of each individual sample at the end of any pipeline. Here, we present a versatile assay to determine the identity of samples rapidly and efficiently by genotyping 21 single-nucleotide polymorphisms (SNPs) using multiplex high resolution melting. The selected SNPs also are present in whole-exome sequencing data, and comparison of the differentially obtained genotypes allows reliable identification of individual samples. In this assay, we combined primers interrogating two to three SNPs per high resolution melting reaction, enabling the generation of the SNP genotype profile in only eight reactions per sample, limiting the hands-on time and minimizing the amount of reagents. This SNP profiling approach also can be used to track samples in custom next-generation sequencing enrichment panels by including these 21 SNPs in the target region, allowing for the often-required independent validation of sample identity in both clinical and research settings.
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Affiliation(s)
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
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Bogdanov KV, Nikitin MM, Slyadnev MN. [Allele polymorphism analysis in coagulation factors F2, F5 and folate metabolism gene MTHFR by using microchip-based multiplex real time PCR]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015. [PMID: 26215413 DOI: 10.18097/pbmc20156103357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Single nucleotide polymorphism (SNP) genotyping methods are widely used for the detection of hereditary thrombophilias caused by genetic defects in the coagulation system. The hereditary thrombophilias are frequently associated with higher incidences of point mutations in hemostasis (F2 20210G>A, F5 1691G>A) and folate metabolism (MTHFR 677C>Т, MTHFR 1298A>C) genes. Moreover, the combination of gene abnormalities in F2 or/and MTHFR with F5 Leiden mutation leads to increased risk of developing thrombosis. Thus, simultaneous detection of the multiple gene mutations in a sample has important clinical relevance. The microchip-based multiplex real time PCR for estimation of allele specific polymorphism in hemostatic and folate metabolism genes presented here has a high efficiency and may be used for laboratory diagnosis. The optimized protocol for estimation of 4 different types of genetic polymorphisms allowed PCR to be performed with minimal quantity of DNA template and PCR reagents including Taq polymerase and a short-term thermocycling.
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Affiliation(s)
- K V Bogdanov
- Institute of Hematology, V.A. Almazov Federal Medical Research Centre, St. Petersburg, Russia; Lumex Group, St. Petersburg, Russia
| | - M M Nikitin
- St. Petersburg State University, St. Petersburg, Russia; Lumex Group, St. Petersburg, Russia
| | - M N Slyadnev
- St. Petersburg State University, St. Petersburg, Russia; Lumex Group, St. Petersburg, Russia
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Identifying the last bloodmeal of questing sheep tick nymphs (Ixodes ricinus L.) using high resolution melting analysis. Vet Parasitol 2015; 210:194-205. [PMID: 25941127 DOI: 10.1016/j.vetpar.2015.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 11/18/2022]
Abstract
The sheep tick, Ixodes ricinus L., is an important hematophagous vector of zoonotic disease of both veterinary and public health importance in Europe. Risk models for tick-borne diseases can be improved by identifying the main hosts of this species in any given area. However, this generalist tick stays on a host for only a few days a year over its life cycle, making the study of its feeding ecology difficult. In contrast, ticks can easily be collected from vegetation when they are questing. Molecular methods have proved to be a reliable alternative to field observation, but most current methods have low sensitivity and/or low identification success (i.e. hosts are only identified to taxonomic levels higher than species). In this study we use Real-time PCR coupled with High Resolution Melting Analysis (HRMA) to identify the source of the last bloodmeal in questing tick nymphs. Twenty of the most important tick hosts were grouped taxonomically and six group-specific primer sets, targeting short mitochondrial DNA regions, were designed de novo. Firstly, we show that these primers successfully amplify target host DNA (from host tissue or engorged ticks), and that HRMA can be used to reliably identify hosts to species (or genera in the case of Sorex and Apodemus). Secondly, the new protocol was tested on field-collected questing nymphs. Bloodmeal source was identified in 65.4% of 52 individuals. In 83.3% of these, the host was identified to species or genera using HRMA alone. Moreover, the primer sets designed here can unequivocally identify mixed bloodmeals. The combination of sensitivity and identification success together with the closed-tube and single step approach that minimizes contamination, make Real-time HRMA a good alternative to current methods for bloodmeal identification.
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Gopaul KK, Sells J, Lee R, Beckstrom-Sternberg SM, Foster JT, Whatmore AM. Development and assessment of multiplex high resolution melting assay as a tool for rapid single-tube identification of five Brucella species. BMC Res Notes 2014; 7:903. [PMID: 25495428 PMCID: PMC4307374 DOI: 10.1186/1756-0500-7-903] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 11/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The zoonosis brucellosis causes economically significant reproductive problems in livestock and potentially debilitating disease of humans. Although the causative agent, organisms from the genus Brucella, can be differentiated into a number of species based on phenotypic characteristics, there are also significant differences in genotype that are concordant with individual species. This paper describes the development of a five target multiplex assay to identify five terrestrial Brucella species using real-time polymerase chain reaction (PCR) and subsequent high resolution melt curve analysis. This technology offers a robust and cost effective alternative to previously described hydrolysis-probe Single Nucleotide Polymorphism (SNP)-based species defining assays. RESULTS Through the use of Brucella whole genome sequencing five species defining SNPs were identified. Individual HRM assays were developed to these target these changes and, following optimisation of primer concentrations, it was possible to multiplex all five assays in a single tube. In a validation exercise using a panel of 135 Brucella strains of terrestrial and marine origin, it was possible to distinguish the five target species from the other species within this panel. CONCLUSION The HRM multiplex offers a number of diagnostic advantages over previously described SNP-based typing approaches. Further, and uniquely for HRM, the successful multiplexing of five assays in a single tube allowing differentiation of five Brucella species in the diagnostic laboratory in a cost-effective and timely manner is described. However there are possible limitations to using this platform on DNA extractions direct from clinical material.
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Affiliation(s)
- Krishna K Gopaul
- Department of Bacteriology, Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK.
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Sundberg SO, Wittwer CT, Howell RM, Huuskonen J, Pryor RJ, Farrar JS, Stiles HM, Palais RA, Knight IT. Microfluidic Genotyping by Rapid Serial PCR and High-Speed Melting Analysis. Clin Chem 2014; 60:1306-13. [DOI: 10.1373/clinchem.2014.223768] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Abstract
BACKGROUND
Clinical molecular testing typically batches samples to minimize costs or uses multiplex lab-on-a-chip disposables to analyze a few targets. In genetics, multiple variants need to be analyzed, and different work flows that rapidly analyze multiple loci in a few targets are attractive.
METHODS
We used a microfluidic platform tailored to rapid serial PCR and high-speed melting (HSM) to genotype 4 single nucleotide variants. A contiguous stream of master mix with sample DNA was pulsed with each primer pair for serial PCR and melting. Two study sites each analyzed 100 samples for F2 (c.*97G>A), F5 (c.1601G>A), and MTHFR (c.665C>T and c.1286A>C) after blinding for genotype and genotype proportions. Internal temperature controls improved melting curve precision. The platform's liquid-handling system automated PCR and HSM.
RESULTS
PCR and HSM were completed in a total of 12.5 min. Melting was performed at 0.5 °C/s. As expected, homozygous variants were separated by melting temperature, and heterozygotes were identified by curve shape. All samples were correctly genotyped by the instrument. Follow-up testing was required on 1.38% of the assays for a definitive genotype.
CONCLUSIONS
We demonstrate genotyping accuracy on a novel microfluidic platform with rapid serial PCR and HSM. The platform targets short turnaround times for multiple genetic variants in up to 8 samples. It is also designed to allow automatic and immediate reflexive or repeat testing depending on results from the streaming DNA. Rapid serial PCR provides a flexible genetic work flow and is nicely matched to HSM analysis.
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Affiliation(s)
- Scott O Sundberg
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
- current address: Canon U.S. Life Sciences, Newport News, VA
| | - Carl T Wittwer
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
| | | | | | - Robert J Pryor
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Jared S Farrar
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
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Venables SJ, Mehta B, Daniel R, Walsh SJ, van Oorschot RAH, McNevin D. Assessment of high resolution melting analysis as a potential SNP genotyping technique in forensic casework. Electrophoresis 2014; 35:3036-43. [PMID: 25142205 DOI: 10.1002/elps.201400089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 08/02/2014] [Accepted: 08/12/2014] [Indexed: 11/11/2022]
Abstract
High resolution melting (HRM) analysis is a simple, cost effective, closed tube SNP genotyping technique with high throughput potential. The effectiveness of HRM for forensic SNP genotyping was assessed with five commercially available HRM kits evaluated on the ViiA™ 7 Real Time PCR instrument. Four kits performed satisfactorily against forensically relevant criteria. One was further assessed to determine the sensitivity, reproducibility, and accuracy of HRM SNP genotyping. The manufacturer's protocol using 0.5 ng input DNA and 45 PCR cycles produced accurate and reproducible results for 17 of the 19 SNPs examined. Problematic SNPs had GC rich flanking regions which introduced additional melting domains into the melting curve (rs1800407) or included homozygotes that were difficult to distinguish reliably (rs16891982; a G to C SNP). A proof of concept multiplexing experiment revealed that multiplexing a small number of SNPs may be possible after further investigation. HRM enables genotyping of a number of SNPs in a large number of samples without extensive optimization. However, it requires more genomic DNA as template in comparison to SNaPshot®. Furthermore, suitably modifying pre-existing forensic intelligence SNP panels for HRM analysis may pose difficulties due to the properties of some SNPs.
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Affiliation(s)
- Samantha J Venables
- National Centre for Forensic Studies, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, Australia
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Komorowska B, Fiore N, Zamorano A, Li R. Simultaneous detection of Cherry necrotic rusty mottle virus and Cherry green ring mottle virus using real-time PCR and high resolution melting analysis. Mol Cell Probes 2014; 28:186-91. [DOI: 10.1016/j.mcp.2014.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/09/2014] [Accepted: 03/12/2014] [Indexed: 11/30/2022]
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Martinez-Serra J, Robles J, Nicolàs A, Gutierrez A, Ros T, Amat JC, Alemany R, Vögler O, Abelló A, Noguera A, Besalduch J. Fluorescence resonance energy transfer-based real-time polymerase chain reaction method without DNA extraction for the genotyping of F5, F2, F12, MTHFR, and HFE. J Blood Med 2014; 5:99-106. [PMID: 25028568 PMCID: PMC4077787 DOI: 10.2147/jbm.s64976] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Blood samples are extensively used for the molecular diagnosis of many hematological diseases. The daily practice in a clinical laboratory of molecular diagnosis in hematology involves using a variety of techniques, based on the amplification of nucleic acids. Current methods for polymerase chain reaction (PCR) use purified genomic DNA, mostly isolated from total peripheral blood cells or white blood cells (WBC). In this paper we describe a real-time fluorescence resonance energy transfer-based method for genotyping directly from blood cells. Our strategy is based on an initial isolation of the WBCs, allowing the removal of PCR inhibitors, such as the heme group, present in the erythrocytes. Once the erythrocytes have been lysed, in the LightCycler® 2.0 Instrument, we perform a real-time PCR followed by a melting curve analysis for different genes (Factors 2, 5, 12, MTHFR, and HFE). After testing 34 samples comparing the real-time crossing point (CP) values between WBC (5×106 WBC/mL) and purified DNA (20 ng/μL), the results for F5 Leiden were as follows: CP mean value for WBC was 29.26±0.566 versus purified DNA 24.79±0.56. Thus, when PCR was performed from WBC (5×106 WBC/mL) instead of DNA (20 ng/μL), we observed a delay of about 4 cycles. These small differences in CP values were similar for all genes tested and did not significantly affect the subsequent analysis by melting curves. In both cases the fluorescence values were high enough, allowing a robust genotyping of all these genes without a previous DNA purification/extraction.
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Affiliation(s)
- Jordi Martinez-Serra
- Department of Hematology, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | - Juan Robles
- Department of Clinical Analysis, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | | | - Antonio Gutierrez
- Department of Hematology, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | - Teresa Ros
- Department of Hematology, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | - Juan Carlos Amat
- Department of Hematology, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | - Regina Alemany
- Department of Cell Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Oliver Vögler
- Department of Cell Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Aina Abelló
- Department of Clinical Analysis, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | - Aina Noguera
- Department of Clinical Analysis, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | - Joan Besalduch
- Department of Hematology, Hospital Universitary Son Espases, Palma de Mallorca, Spain
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Jiang E, Li F, Jing C, Li P, Cui H, Wang B, Ding M, Pang H. High-Resolution Melting Analysis as a Developed Method for Genotyping the PD Susceptibility Loci in LRRK2 Gene. J Clin Lab Anal 2014; 29:299-304. [PMID: 24849765 DOI: 10.1002/jcla.21769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 04/02/2014] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Single-nucleotide polymorphisms (SNPs) have been reported as a highly relevant point for the mechanisms of Parkinson's disease (PD). The invention of saturating dye makes it possible to identify heteroduplex DNA without redistribution during melting, which allows using high-resolution melting (HRM) to detect SNPs. However, the HRM analysis for detection of those SNPs associated with PD was rarely applied. METHODS Two SNPs, G2385R and R1628P, located in leucine-rich repeat kinase 2 (LRRK2) gene were individually and multiplexedly genotyped using HRM analysis. The sequence variant observed in unexpected HRM curves was confirmed by DNA sequencing. RESULTS HRM analysis identified successfully all genotypes both on R1628P and G2385R loci. The unexpected HRM curves appeared in R1628P amplicon generated from combinations of R1628P and rs11176013 loci. A multiplexed HRM assay that genotyped R1628P, rs11176013, and G2385R loci was efficiently established. CONCLUSIONS The present HRM assay is a reliable and rapid method for genotyping R1628P and G2385R loci in LRRK2 gene, and multiplex HRM analysis results in high throughput and has the potential to facilitate a wide range of genotyping studies on PD susceptibility genes.
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Affiliation(s)
- Enzhu Jiang
- School of Forensic Medicine, China Medical University, Shenyang, P.R. China
| | - Fengrui Li
- School of Forensic Medicine, China Medical University, Shenyang, P.R. China
- Department of Forensic Medicine, Baotou Medical College, Baotou, P.R. China
| | - Chenchen Jing
- School of Forensic Medicine, China Medical University, Shenyang, P.R. China
| | - Pei Li
- School of Forensic Medicine, China Medical University, Shenyang, P.R. China
| | - Honggang Cui
- School of Forensic Medicine, China Medical University, Shenyang, P.R. China
| | - Baojie Wang
- School of Forensic Medicine, China Medical University, Shenyang, P.R. China
| | - Mei Ding
- School of Forensic Medicine, China Medical University, Shenyang, P.R. China
| | - Hao Pang
- School of Forensic Medicine, China Medical University, Shenyang, P.R. China
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Hasiów-Jaroszewska B, Komorowska B. A new method for detection and discrimination of Pepino mosaic virus isolates using high resolution melting analysis of the triple gene block 3. J Virol Methods 2013; 193:1-5. [DOI: 10.1016/j.jviromet.2013.04.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 04/22/2013] [Accepted: 04/29/2013] [Indexed: 11/30/2022]
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Sanford LN, Kent JO, Wittwer CT. Quantum method for fluorescence background removal in DNA melting analysis. Anal Chem 2013; 85:9907-15. [PMID: 24070125 DOI: 10.1021/ac4024928] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fluorescent high-resolution DNA melting analysis is a robust method of genotyping and mutation scanning. However, removing background fluorescence is important for accurate classification and to correctly display helicity. Linear baseline extrapolation, commonly used with absorbance, often fails at low temperatures when fluorescence is used. A new quantum method of background removal based on the inherent decrease of fluorescence with temperature is described. Absorbance and fluorescence melting curves were compared using synthetic targets including hairpins, unlabeled probes, and a 50 bp duplex. In addition, the quantum method was compared to a previously described exponential method for analysis of genotyping data produced after polymerase chain reaction (PCR), including those from small amplicons, unlabeled probes, and snapback primers. The quantum method best matched absorbance data and predicted helicity, with the exponential method displaying low-temperature bulges and domain artifacts that can lead to incorrect genotyping. When two melting domains were widely separated, quantum analysis produced a flat baseline between domains, while exponential analysis was temperature-dependent. Both methods have little effect on the melting temperature (Tm) although some differences were significant (hairpin Tm values increased 0.7 °C by the quantum method and decreased 1.5 °C by exponential method, p = 0.01). However, peak heights on derivative plots were strongly algorithm-dependent, with exponential analysis enhancing low-temperature peaks while dampening high-temperature peaks. Quantum-analyzed fluorescence curves were a better match to absorbance data in terms of shape, area, and peak height compared to other methods, indicating that DNA helicity is best approximated by the quantum method.
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Affiliation(s)
- Lindsay N Sanford
- Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States
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20
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Almeamar HA, Ramachandran V, Ismail P, Nadkarni P, Fawzi N. Analysis of partial AZFc deletions in Malaysian infertile male subjects. Syst Biol Reprod Med 2012; 59:99-107. [PMID: 23231020 DOI: 10.3109/19396368.2012.748851] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Complete deletions in the AZF (a, b, and c) sub-regions of the Y-chromosome have been shown to contribute to unexplained male infertility. However, the role of partial AZFc deletions in male infertility remains to be verified. Three types of partial AZFc deletions have been identified. They are gr/gr, b1/b3, and b2/b3 deletions. A recent meta-analysis showed that ethnic and geographical factors might contribute to the association of partial AZFc deletions with male infertility. This study analyzed the association of partial AZFc deletions in Malaysian infertile males. Fifty two oligozoospermic infertile males and 63 fertile controls were recruited to this study. Screening for partial AZFc deletions was done using the two sequence-tagged sites approach (SY1291 and SY1191) which were analyzed using both the conventional PCR gel-electrophoresis and the high resolution melt, HRM method. Gr/gr deletions were found in 11.53% of the cases and 9.52% of the controls (p = 0.725). A B2/b3 deletion was found in one of the cases (p = 0.269). No B1/b3 deletions were identified in this study. The results of HRM analysis were consistent with those obtained using the conventional PCR gel-electrophoresis method. The HRM analysis was highly repeatable (95% limit of agreement was -0.0879 to 0.0871 for SY1191 melting temperature readings). In conclusion, our study showed that partial AZFc deletions were not associated with male infertility in Malaysian subjects. HRM analysis was a reliable, repeatable, fast, cost-effective, and semi-automated method which can be used for screening of partial AZFc deletions.
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Affiliation(s)
- Hussein Ali Almeamar
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
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21
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Pereyra S, Velazquez T, Bertoni B, Sapiro R. Rapid multiplex high resolution melting method to analyze inflammatory related SNPs in preterm birth. BMC Res Notes 2012; 5:69. [PMID: 22280494 PMCID: PMC3298535 DOI: 10.1186/1756-0500-5-69] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 01/26/2012] [Indexed: 01/08/2023] Open
Abstract
Background Complex traits like cancer, diabetes, obesity or schizophrenia arise from an intricate interaction between genetic and environmental factors. Complex disorders often cluster in families without a clear-cut pattern of inheritance. Genomic wide association studies focus on the detection of tens or hundreds individual markers contributing to complex diseases. In order to test if a subset of single nucleotide polymorphisms (SNPs) from candidate genes are associated to a condition of interest in a particular individual or group of people, new techniques are needed. High-resolution melting (HRM) analysis is a new method in which polymerase chain reaction (PCR) and mutations scanning are carried out simultaneously in a closed tube, making the procedure fast, inexpensive and easy. Preterm birth (PTB) is considered a complex disease, where genetic and environmental factors interact to carry out the delivery of a newborn before 37 weeks of gestation. It is accepted that inflammation plays an important role in pregnancy and PTB. Methods Here, we used real time-PCR followed by HRM analysis to simultaneously identify several gene variations involved in inflammatory pathways on preterm labor. SNPs from TLR4, IL6, IL1 beta and IL12RB genes were analyzed in a case-control study. The results were confirmed either by sequencing or by PCR followed by restriction fragment length polymorphism. Results We were able to simultaneously recognize the variations of four genes with similar accuracy than other methods. In order to obtain non-overlapping melting temperatures, the key step in this strategy was primer design. Genotypic frequencies found for each SNP are in concordance with those previously described in similar populations. None of the studied SNPs were associated with PTB. Conclusions Several gene variations related to the same inflammatory pathway were screened through a new flexible, fast and non expensive method with the purpose of analyzing their association to PTB. It can easily be used for simultaneously analyze any set of SNPs, either as the first choice for new association studies or as a complement to large-scale genotyping analysis. Given that inflammatory pathway is in the base of several diseases, it is potentially useful to analyze a broad range of disorders.
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Affiliation(s)
- Silvana Pereyra
- Departament of Histology and Embryology, School of Medicine, University of the Republic, Gral, Flores 2125, Montevideo, Uruguay.
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22
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Songserm N, Promthet S, Sithithaworn P, Pientong C, Ekalaksananan T, Chopjitt P, Parkin DM. Risk factors for cholangiocarcinoma in high-risk area of Thailand: role of lifestyle, diet and methylenetetrahydrofolate reductase polymorphisms. Cancer Epidemiol 2011; 36:e89-94. [PMID: 22189445 DOI: 10.1016/j.canep.2011.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 11/24/2011] [Accepted: 11/26/2011] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIM Cholangiocarcinoma (CCA) is the most common cancer in Northeast Thailand. Endemicity of Opisthorchis viverrini (OV) - a known carcinogen - is responsible, but although infection is very common, the lifetime risk of CCA is only 5%. Other co-factors must exist, including aspects of lifestyle or diet along with variations in genetic susceptibility to them. Change in methylenetetrahydrofolate reductase (MTHFR) activity may influence both DNA methylation and synthesis. This study investigates risk factors for CCA with a focus on lifestyle, diet and MTHFR polymorphisms. METHODS Nested case-control study within cohort study was conducted. 219 subjects with primary CCA were each matched with two non-cancer controls from the same cohort on sex, age at recruitment and presence/absence of OV eggs in stool. Lifestyle and dietary data were obtained at recruitment. MTHFR polymorphisms were analyzed using PCR with high resolution melting analysis. The associations were assessed using conditional logistic regression. RESULTS Consumption of alcohol, raw freshwater fish and beef sausage increased the risk of CCA, while fruit and/or vegetables consumption reduced risk. There were interactions between MTHFR and preserved freshwater fish and beef. These dietary items are either a source of OV or of pre-formed nitrosamine, folate and antioxidants that are of possible relevance in OV carcinogenesis. CONCLUSIONS Primary prevention of CCA in high-risk population is based upon efforts to reduce OV infection. Reduced consumption of alcohol and preserved meats, and increased consumption of dietary folate, actions with a wider preventive potential, may also help in the reduction of CCA burden.
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Affiliation(s)
- Nopparat Songserm
- Department of Epidemiology, Faculty of Public Health, Khon Kaen University, Thailand.
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Milbury CA, Chen CC, Mamon H, Liu P, Santagata S, Makrigiorgos GM. Multiplex amplification coupled with COLD-PCR and high resolution melting enables identification of low-abundance mutations in cancer samples with low DNA content. J Mol Diagn 2011; 13:220-32. [PMID: 21354058 DOI: 10.1016/j.jmoldx.2010.10.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 09/09/2010] [Accepted: 10/18/2010] [Indexed: 01/18/2023] Open
Abstract
Thorough screening of cancer-specific biomarkers, such as DNA mutations, can require large amounts of genomic material; however, the amount of genomic material obtained from some specimens (such as biopsies, fine-needle aspirations, circulating-DNA or tumor cells, and histological slides) may limit the analyses that can be performed. Furthermore, mutant alleles may be at low-abundance relative to wild-type DNA, reducing detection ability. We present a multiplex-PCR approach tailored to amplify targets of interest from small amounts of precious specimens, for extensive downstream detection of low-abundance alleles. Using 3 ng of DNA (1000 genome-equivalents), we amplified the 1 coding exons (2-11) of TP53 via multiplex-PCR. Following multiplex-PCR, we performed COLD-PCR (co-amplification of major and minor alleles at lower denaturation temperature) to enrich low-abundance variants and high resolution melting (HRM) to screen for aberrant melting profiles. Mutation-positive samples were sequenced. Evaluation of mutation-containing dilutions revealed improved sensitivities after COLD-PCR over conventional-PCR. COLD-PCR improved HRM sensitivity by approximately threefold to sixfold. Similarly, COLD-PCR improved mutation identification in sequence-chromatograms over conventional PCR. In clinical specimens, eight mutations were detected via conventional-PCR-HRM, whereas 12 were detected by COLD-PCR-HRM, yielding a 33% improvement in mutation detection. In summary, we demonstrate an efficient approach to increase screening capabilities from limited DNA material via multiplex-PCR and improve mutation detection sensitivity via COLD-PCR amplification.
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Affiliation(s)
- Coren A Milbury
- Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, Massachusetts 02115, USA
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25
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Seipp MT, Wittwer CT. Detecting Rare Thrombophilia Variants by High-Resolution Melting. Clin Chem 2011; 57:639-41. [DOI: 10.1373/clinchem.2010.159160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Carl T Wittwer
- ARUP Institute for Clinical and Experimental Pathology, and
- ARUP Laboratories Salt Lake City, UT
- Department of Pathology University of Utah Medical School Salt Lake City, UT
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Cheng HL, Chiou SS, Liao YM, Chen YL, Wu SM. Genotyping of two single nucleotide polymorphisms in 5,10-methylenetetrahydrofolate reductase by multiplex polymerase chain reaction and capillary electrophoresis. J Chromatogr A 2011; 1218:2114-20. [DOI: 10.1016/j.chroma.2010.08.080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 08/25/2010] [Accepted: 08/30/2010] [Indexed: 11/25/2022]
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He X, Sheng M, Xu M, Xiong C, Ren Z. Rapid Identification of Common β-Thalassemia Mutations in the Chinese Population Using Duplex or Triplex Amplicon Genotyping by High-Resolution Melting Analysis. Genet Test Mol Biomarkers 2010; 14:851-6. [PMID: 21034280 DOI: 10.1089/gtmb.2010.0048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xiang He
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Lab of Embryo Molecular Biology, Ministry of Health, China, and Shanghai Lab of Embryo and Reproduction Engineering, Shanghai, China
| | - Min Sheng
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Miao Xu
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Can Xiong
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaorui Ren
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Lab of Embryo Molecular Biology, Ministry of Health, China, and Shanghai Lab of Embryo and Reproduction Engineering, Shanghai, China
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Senapin S, Molthathong S, Phiwsaiya K, Jaengsanong C, Chuchird N. Application of high resolution melt (HRM) analysis for duplex detection of Macrobrachium rosenbergii nodavirus (MrNV) and extra small virus (XSV) in shrimp. Mol Cell Probes 2010; 24:291-7. [DOI: 10.1016/j.mcp.2010.06.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 06/08/2010] [Accepted: 06/09/2010] [Indexed: 11/30/2022]
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Montgomery JL, Sanford LN, Wittwer CT. High-resolution DNA melting analysis in clinical research and diagnostics. Expert Rev Mol Diagn 2010; 10:219-40. [PMID: 20214540 DOI: 10.1586/erm.09.84] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Among nucleic acid analytical methods, high-resolution melting analysis is gaining more and more attention. High-resolution melting provides simple, homogeneous solutions for variant scanning and genotyping, addressing the needs of today's overburdened laboratories with rapid turnaround times and minimal cost. The flexibility of the technique has allowed it to be adopted by a wide range of disciplines for a variety of applications. In this review we examine the broad use of high-resolution melting analysis, including gene scanning, genotyping (including small amplicon, unlabeled probe and snapback primers), sequence matching and methylation analysis. Four major application arenas are examined to demonstrate the methods and approaches commonly used in particular fields. The appropriate usage of high-resolution melting analysis is discussed in the context of known constraints, such as sample quality and quantity, with a particular focus placed on proper experimental design in order to produce successful results.
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Affiliation(s)
- Jesse L Montgomery
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA
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Erali M, Wittwer CT. High resolution melting analysis for gene scanning. Methods 2010; 50:250-61. [PMID: 20085814 PMCID: PMC2836412 DOI: 10.1016/j.ymeth.2010.01.013] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 01/03/2010] [Accepted: 01/14/2010] [Indexed: 01/07/2023] Open
Abstract
High resolution melting is a new method of genotyping and variant scanning that can be seamlessly appended to PCR amplification. Limitations of genotyping by amplicon melting can be addressed by unlabeled probe or snapback primer analysis, all performed without labeled probes. High resolution melting can also be used to scan for rare sequence variants in large genes with multiple exons and is the focus of this article. With the simple addition of a heteroduplex-detecting dye before PCR, high resolution melting is performed without any additions, processing or separation steps. Heterozygous variants are identified by atypical melting curves of a different shape compared to wild-type homozygotes. Homozygous or hemizygous variants are detected by prior mixing with wild-type DNA. Design, optimization, and performance considerations for high resolution scanning assays are presented for rapid turnaround of gene scanning. Design concerns include primer selection and predicting melting profiles in silico. Optimization includes temperature gradient selection of the annealing temperature, random population screening for common variants, and batch preparation of primer plates with robotically deposited and dried primer pairs. Performance includes rapid DNA preparation, PCR, and scanning by high resolution melting that require, in total, only 3h when no variants are present. When variants are detected, they can be identified in an additional 3h by rapid cycle sequencing and capillary electrophoresis. For each step in the protocol, a general overview of principles is provided, followed by an in depth analysis of one example, scanning of CYBB, the gene that is mutated in X-linked chronic granulomatous disease.
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Affiliation(s)
- Maria Erali
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, 84108
| | - Carl T. Wittwer
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, 84108
- Department of Pathology, University of Utah Medical School, Salt Lake City, UT, 84132
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Ugo V, Tondeur S, Menot ML, Bonnin N, Le Gac G, Tonetti C, Mas VMD, Lecucq L, Kiladjian JJ, Chomienne C, Dosquet C, Parquet N, Darnige L, Porneuf M, Escoffre-Barbe M, Giraudier S, Delabesse E, Cassinat B. Interlaboratory development and validation of a HRM method applied to the detection of JAK2 exon 12 mutations in polycythemia vera patients. PLoS One 2010; 5:e8893. [PMID: 20126644 PMCID: PMC2811183 DOI: 10.1371/journal.pone.0008893] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 12/28/2009] [Indexed: 11/29/2022] Open
Abstract
Background Myeloproliferative disorders are characterized by clonal expansion of normal mature blood cells. Acquired mutations giving rise to constitutive activation of the JAK2 tyrosine kinase has been shown to be present in the majority of patients. Since the demonstration that the V617F mutation in the exon 14 of the JAK2 gene is present in about 90% of patients with Polycythemia Vera (PV), the detection of this mutation has become a key tool for the diagnosis of these patients. More recently, additional mutations in the exon 12 of the JAK2 gene have been described in 5 to 10% of the patients with erythrocytosis. According to the updated WHO criteria the presence of these mutations should be looked for in PV patients with no JAK2 V617F mutation. Reliable and accurate methods dedicated to the detection of these highly variable mutations are therefore necessary. Methods/Findings For these reasons we have defined the conditions of a High Resolution DNA Melting curve analysis (HRM) method able to detect JAK2 exon 12 mutations. After having validated that the method was able to detect mutated patients, we have verified that it gave reproducible results in repeated experiments, on DNA extracted from either total blood or purified granulocytes. This HRM assay was further validated using 8 samples bearing different mutant sequences in 4 different laboratories, on 3 different instruments. Conclusion The assay we have developed is thus a valid method, adapted to routine detection of JAK2 exon 12 mutations with highly reproducible results.
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Affiliation(s)
- Valerie Ugo
- CHU BREST, Laboratoire d'Hematologie, Brest, France
- INSERM U613, Brest, France
| | - Sylvie Tondeur
- CHU Montpellier, Laboratoire d'Hématologie, Hôpital Saint-Eloi, Montpellier, France
| | | | - Nadine Bonnin
- AP-HP, Unite de Biologie Cellulaire, Hopital Saint-Louis, Paris, France
| | | | - Carole Tonetti
- AP-HP, Laboratoire d'Hematologie, Hopital Henri Mondor, Creteil, France
| | | | - Lydie Lecucq
- CHU BREST, Laboratoire d'Hematologie, Brest, France
| | - Jean-Jacques Kiladjian
- AP-HP, Hematology Department, Hopital Avicenne, Bobigny, France
- PV-Nord Group, Hopital Saint-Louis, Paris, France
| | - Christine Chomienne
- AP-HP, Unite de Biologie Cellulaire, Hopital Saint-Louis, Paris, France
- PV-Nord Group, Hopital Saint-Louis, Paris, France
| | - Christine Dosquet
- AP-HP, Unite de Thérapie Cellulaire, Hopital Saint-Louis, Paris, France
| | - Nathalie Parquet
- AP-HP, Unite de Thérapie Cellulaire, Hopital Saint-Louis, Paris, France
- PV-Nord Group, Hopital Saint-Louis, Paris, France
| | - Luc Darnige
- AP-HP, Laboratoire d'Hematologie, Hopital Europeen G. Pompidou, Paris, France
| | - Marc Porneuf
- CH Le Foll, Service d'Hématologie, Saint Brieuc, France
| | | | | | - Eric Delabesse
- CHU Toulouse, Laboratoire d'Hematologie, Hôpital Purpan, Toulouse, France
| | - Bruno Cassinat
- AP-HP, Unite de Biologie Cellulaire, Hopital Saint-Louis, Paris, France
- PV-Nord Group, Hopital Saint-Louis, Paris, France
- * E-mail:
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Niederstätter H, Parson W. Fluorescent duplex allele-specific PCR and amplicon melting for rapid homogeneous mtDNA haplogroup H screening and sensitive mixture detection. PLoS One 2009; 4:e8374. [PMID: 20020064 PMCID: PMC2793010 DOI: 10.1371/journal.pone.0008374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 11/23/2009] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND For large scale studies aiming at a better understanding of mitochondrial DNA (mtDNA), sequence variation in particular mt haplogroups (hgs) and population structure, reliable low-cost high-throughput genotyping assays are needed. Furthermore, methods facilitating sensitive mixture detection and relative quantification of allele proportions are indispensable for the study of heteroplasmy, mitochondrial sequence evolution, and mitochondrial disorders. Here the properties of a homogeneous competitive duplex allele specific PCR (ARMS) assay were scrutinized in the light of these requirements. METHODOLOGY/PRINCIPAL FINDINGS A duplex ARMS assay amplifying either the ancestral mtDNA 2706G allele (non-hg H samples) or the derived 7028C allele (hg H samples) in the presence of SYBR Green fluorescent reporter dye was developed and characterized. Product detection, allele calling, and hg inference were based on the amplicon-characteristic melting-point temperatures obtained with on-line post-PCR fluorescent dissociation curve analysis (DCA). The analytical window of the assay covered at least 5 orders of magnitude of template DNA input with a detection limit in the low picogram range of genomic DNA. A set of forensically relevant test specimens was analyzed successfully. The presence of mtDNA mixtures was detected over a broad range of input DNA amounts and mixture ratios, and the estimation of allele proportions in samples with known total mtDNA content was feasible with limitations. A qualified DNA analyst successfully analyzed approximately 2,200 DNA extracts within three regular working days, without using robotic lab-equipment. By performing the amplification on-line, the assay also facilitated absolute mtDNA quantification. CONCLUSIONS Although this assay was developed just for a particular purpose, the approach is general in that it is potentially suitable in a broad variety of assay-layouts for many other applications, including the analysis of mixtures. Homogeneous ARMS-DCA is a valuable tool for large-volume studies targeting small numbers of single nucleotide polymorphisms (SNPs).
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van Eijk R, van Puijenbroek M, Chhatta AR, Gupta N, Vossen RHAM, Lips EH, Cleton-Jansen AM, Morreau H, van Wezel T. Sensitive and specific KRAS somatic mutation analysis on whole-genome amplified DNA from archival tissues. J Mol Diagn 2009; 12:27-34. [PMID: 19959798 DOI: 10.2353/jmoldx.2010.090028] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Kirsten RAS (KRAS) is a small GTPase that plays a key role in Ras/mitogen-activated protein kinase signaling; somatic mutations in KRAS are frequently found in many cancers. The most common KRAS mutations result in a constitutively active protein. Accurate detection of KRAS mutations is pivotal to the molecular diagnosis of cancer and may guide proper treatment selection. Here, we describe a two-step KRAS mutation screening protocol that combines whole-genome amplification (WGA), high-resolution melting analysis (HRM) as a prescreen method for mutation carrying samples, and direct Sanger sequencing of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue, from which limited amounts of DNA are available. We developed target-specific primers, thereby avoiding amplification of homologous KRAS sequences. The addition of herring sperm DNA facilitated WGA in DNA samples isolated from as few as 100 cells. KRAS mutation screening using high-resolution melting analysis on wgaDNA from formalin-fixed, paraffin-embedded tissue is highly sensitive and specific; additionally, this method is feasible for screening of clinical specimens, as illustrated by our analysis of pancreatic cancers. Furthermore, PCR on wgaDNA does not introduce genotypic changes, as opposed to unamplified genomic DNA. This method can, after validation, be applied to virtually any potentially mutated region in the genome.
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Affiliation(s)
- Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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Milbury CA, Li J, Makrigiorgos GM. COLD-PCR-enhanced high-resolution melting enables rapid and selective identification of low-level unknown mutations. Clin Chem 2009; 55:2130-43. [PMID: 19815609 DOI: 10.1373/clinchem.2009.131029] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Analysis of clinical samples often necessitates identification of low-level somatic mutations within wild-type DNA; however, the selectivity and sensitivity of the methods are often limiting. COLD-PCR (coamplification at lower denaturation temperature-PCR) is a new form of PCR that enriches mutation-containing amplicons to concentrations sufficient for direct sequencing; nevertheless, sequencing itself remains an expensive mutation-screening approach. Conversely, high-resolution melting (HRM) is a rapid, inexpensive scanning method, but it cannot specifically identify the detected mutation. To enable enrichment, quick scanning, and identification of low-level unknown mutations, we combined COLD-PCR with HRM mutation scanning, followed by sequencing of positive samples. METHODS Mutation-containing cell-line DNA serially diluted into wild-type DNA and DNA samples from human lung adenocarcinomas containing low-level mutations were amplified via COLD-PCR and via conventional PCR for TP53 (tumor protein p53) exons 6-8, and the 2 approaches were compared. HRM analysis was used to screen amplicons for mutations; mutation-positive amplicons were sequenced. RESULTS Dilution experiments indicated an approximate 6- to 20-fold improvement in selectivity with COLD-PCR/HRM. Conventional PCR/HRM exhibited mutation-detection limits of approximately 2% to 10%, whereas COLD-PCR/HRM exhibited limits from approximately 0.1% to 1% mutant-to-wild-type ratio. After HRM analysis of lung adenocarcinoma samples, we detected 7 mutations by both PCR methods in exon 7; however, in exon 8 we detected 9 mutations in COLD-PCR amplicons, compared with only 6 mutations in conventional-PCR amplicons. Furthermore, 94% of the HRM-detected mutations were successfully sequenced with COLD-PCR amplicons, compared with 50% with conventional-PCR amplicons. CONCLUSIONS COLD-PCR/HRM improves the mutation-scanning capabilities of HRM and combines high selectivity, convenience, and low cost with the ability to sequence unknown low-level mutations in clinical samples.
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Affiliation(s)
- Coren A Milbury
- Department of Radiation Oncology, Division of Medical Physics and Biophysics, and Division of Genome Stability and DNA Repair, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
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Tindall EA, Petersen DC, Woodbridge P, Schipany K, Hayes VM. Assessing high-resolution melt curve analysis for accurate detection of gene variants in complex DNA fragments. Hum Mutat 2009; 30:876-83. [PMID: 19280649 DOI: 10.1002/humu.20919] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mutation detection has, until recently, relied heavily on the use of gel-based methods that can be both time consuming and difficult to design. Nongel-based systems are therefore important to increase simplicity and improve turn around time without compromising assay sensitivity and accuracy, especially in the diagnostic/clinical setting. In this study, we assessed the latest of the nongel-based methods, namely high-resolution melt (HRM) curve analysis. HRM is a closed-tube method that incorporates a saturating dye during DNA amplification followed by a monitoring of the change in fluorescence as the DNA duplex is denatured by an increasing temperature. We assessed 10 amplicons derived from eight genes, namely SERPINA1, CXCR7, MBL, VDR, NKX3A, NPY, TP53, and HRAS using two platforms, the LightScanner System using LC Green PLUS DNA binding dye (Idaho Technology, Salt Lake City, UT, USA) and the LightCycler 480 using the HRM Master dye (Roche Diagnostics, Indianapolis, IN, USA). DNA variants (mutations or polymorphims) were previously identified using denaturing gradient gel electrophoresis (DGGE) a method, similarly to HRM, based upon the different melting properties of double-stranded DNA. Fragments were selected based on variant and fragment complexity. This included the presence of multiple sequence variants, variants in alternate orientations, and single or multiple variants (constitutional or somatic) in GC-rich fragments. We demonstrate current limitations of the HRM method for the analysis of complex DNA regions and call for caution when using HRM as the sole method to make a clinical diagnosis based on genetic analysis.
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Affiliation(s)
- Elizabeth A Tindall
- Cancer Genetics Group, Children's Cancer Institute Australia for Medical Research, Sydney Children's Hospital, Randwick, Sydney, NSW, Australia
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Vossen RHAM, Aten E, Roos A, den Dunnen JT. High-Resolution Melting Analysis (HRMA)-More than just sequence variant screening. Hum Mutat 2009; 30:860-6. [PMID: 19418555 DOI: 10.1002/humu.21019] [Citation(s) in RCA: 357] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rolf H A M Vossen
- Leiden Genome Technology Center (LGTC), Human and Clincal Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Audrezet MP, Dabricot A, Le Marechal C, Ferec C. Validation of high-resolution DNA melting analysis for mutation scanning of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. J Mol Diagn 2008; 10:424-34. [PMID: 18687795 PMCID: PMC2518737 DOI: 10.2353/jmoldx.2008.080056] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2008] [Indexed: 01/08/2023] Open
Abstract
High-resolution melting analysis of polymerase chain reaction products for mutation scanning, which began in the early 2000s, is based on monitoring of the fluorescence released during the melting of double-stranded DNA labeled with specifically developed saturation dye, such as LC-Green. We report here the validation of this method to scan 98% of the coding sequence of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. We designed 32 pairs of primers to amplify and analyze the 27 exons of the gene. Thanks to the addition of a small GC-clamp at the 5' ends of the primers, one single melting domain and one identical annealing temperature were obtained to co-amplify all of the fragments. A total of 307 DNA samples, extracted by the salt precipitation method, carrying 221 mutations and 21 polymorphisms, plus 20 control samples free from variations (confirmed by denaturing high-performance liquid chromatography analysis), was used. With the conditions described in this study, 100% of samples that carry heterozygous mutations and 60% of those with homozygous mutations were identified. The study of a cohort of 136 idiopathic chronic pancreatitis patients enabled us to prospectively evaluate this technique. Thus, high-resolution melting analysis is a robust and sensitive single-tube technique for screening mutations in a gene and promises to become the gold standard over denaturing high-performance liquid chromatography, particularly for highly mutated genes such as CFTR, and appears suitable for use in reference diagnostic laboratories.
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Zhou L, Errigo RJ, Lu H, Poritz MA, Seipp MT, Wittwer CT. Snapback primer genotyping with saturating DNA dye and melting analysis. Clin Chem 2008; 54:1648-56. [PMID: 18676584 DOI: 10.1373/clinchem.2008.107615] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND DNA hairpins have been used in molecular analysis of PCR products as self-probing amplicons. Either physical separation or fluorescent oligonucleotides with covalent modifications were previously necessary. METHODS We performed asymmetric PCR for 40-45 cycles in the presence of the saturating DNA dye, LCGreen Plus, with 1 primer including a 5' tail complementary to its extension product, but without any special covalent modifications. Samples were amplified either on a carousel LightCycler for speed or on a 96/384 block cycler for throughput. In addition to full-length amplicon duplexes, single-stranded hairpins were formed by the primer tail "snapping back" and hybridizing to its extension product. High-resolution melting was performed on a HR-1 (for capillaries) or a LightScanner (for plates). RESULTS PCR products amplified with a snapback primer showed both hairpin melting at lower temperature and full-length amplicon melting at higher temperature. The hairpin melting temperature was linearly related to the stem length (6-28 bp) and inversely related to the log of the loop size (17-135 bases). We easily genotyped heterozygous and homozygous variants within the stem, and 100 blinded clinical samples previously typed for F5 1691G>A (Leiden) were completely concordant by snapback genotyping. We distinguished 7 genotypes in 2 regions of CFTR exon 10 with symmetric PCR using 2 snapback primers followed by product dilution to favor intramolecular hybridization. CONCLUSIONS Snapback primer genotyping with saturating dyes provides the specificity of a probe with only 2 primers that are free of special covalent labels in a closed-tube system.
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Affiliation(s)
- Luming Zhou
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84132, USA
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Erali M, Voelkerding KV, Wittwer CT. High resolution melting applications for clinical laboratory medicine. Exp Mol Pathol 2008; 85:50-8. [PMID: 18502416 DOI: 10.1016/j.yexmp.2008.03.012] [Citation(s) in RCA: 197] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 03/11/2008] [Indexed: 01/03/2023]
Abstract
Separation of the two strands of DNA with heat (melting) is a fundamental property of DNA that is conveniently monitored with fluorescence. Conventional melting is performed after PCR on any real-time instrument to monitor product purity (dsDNA dyes) and sequence (hybridization probes). Recent advances include high resolution instruments and saturating DNA dyes that distinguish many different species. For example, mutation scanning (identifying heterozygotes) by melting is closed-tube and has similar or superior sensitivity and specificity compared to methods that require physical separation. With high resolution melting, SNPs can be genotyped without probes and more complex regions can be typed with unlabeled hybridization probes. Highly polymorphic HLA loci can be melted to establish sequence identity for transplantation matching. Simultaneous genotyping with one or more unlabeled probes and mutation scanning of the entire amplicon can be performed at the same time in the same tube, vastly decreasing or eliminating the need for re-sequencing in genetic analysis. High resolution PCR product melting is homogeneous, closed-tube, rapid (1-5 min), non-destructive and does not require covalently-labeled fluorescent probes. In the clinical laboratory, it is an ideal format for in-house testing, with minimal cost and time requirements for new assay development.
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Affiliation(s)
- Maria Erali
- ARUP Institute for Clinical and Experimental Pathology, University of Utah, Salt Lake City, UT 84108, USA.
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