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Kullberg J, Colton J, Gregory CT, Bay A, Munro T. Demonstration of Neural Networks to Reconstruct Temperatures from Simulated Fluorescent Data Toward Use in Bio-microfluidics. INTERNATIONAL JOURNAL OF THERMOPHYSICS 2022; 43:172. [PMID: 36349060 PMCID: PMC9639173 DOI: 10.1007/s10765-022-03102-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Biological systems often have a narrow temperature range of operation, which require highly accurate spatially resolved temperature measurements, often near ±0.1 K. However, many temperature sensors cannot meet both accuracy and spatial distribution requirements, often because their accuracy is limited by data fitting and temperature reconstruction models. Machine learning algorithms have the potential to meet this need, but their usage in generating spatial distributions of temperature is severely lacking in the literature. This work presents the first instance of using neural networks to process fluorescent images to map the spatial distribution of temperature. Three standard network architectures were investigated using non-spatially resolved fluorescent thermometry (simply-connected feed-forward network) or during image or pixel identification (U-net and convolutional neural network, CNN). Simulated fluorescent images based on experimental data were generated based on known temperature distributions where Gaussian white noise with a standard deviation of ±0.1 K was added. The poor results from these standard networks motivated the creation of what is termed a moving CNN, with an RMSE error of ±0.23 K, where the elements of the matrix represent the neighboring pixels. Finally, the performance of this MCNN is investigated when trained and applied to three distinctive temperature distributions characteristic within microfluidic devices, where the fluorescent image is simulated at either three or five different wavelengths. The results demonstrate that having a minimum of 10 3.5 data points per temperature and the broadest range of temperatures during training provides temperature predictions nearest to the true temperatures of the images, with a minimum RMSE of ±0.15 K. When compared to traditional curve fitting techniques, this work demonstrates that greater accuracy when spatially mapping temperature from fluorescent images can be achieved when using convolutional neural networks.
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Affiliation(s)
- Jacob Kullberg
- Computer Science Department, Brigham Young University, 3361 TMCB, Provo, 84602, UT, USA
| | - Jacob Colton
- Mechanical Engineering department, Brigham Young University, 3361 TMCB, Provo, 84602, UT, USA
| | - C. Tolex Gregory
- Computer Science Department, Brigham Young University, 3361 TMCB, Provo, 84602, UT, USA
| | - Austin Bay
- Neuroscience Department, Brigham Young University, S-192 ESC, Provo, 84602, UT, USA
| | - Troy Munro
- Mechanical Engineering department, Brigham Young University, 3361 TMCB, Provo, 84602, UT, USA
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2
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Wang R, Li Y, Pang Y, Zhang F, Li F, Luo S, Qian C. VIR-CRISPR: Visual in-one-tube ultrafast RT-PCR and CRISPR method for instant SARS-CoV-2 detection. Anal Chim Acta 2022; 1212:339937. [PMID: 35623788 PMCID: PMC9100291 DOI: 10.1016/j.aca.2022.339937] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 02/07/2023]
Abstract
Until now, corona virus disease 2019 (COVID-19) remained to be an enormous threat for global health. As one viral illness induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), versatile, rapid and sensitive method for SARS-CoV-2 detection in early stage is urgently needed. Here, we reported an ultrasensitive and visual in-one-tube detection method which could be accomplished within half an hour from sampling-to-result. By integrating all reactions in one tube, liquid handling steps were omitted and amplicon contamination could be totally avoided. Magnetic beads were employed to achieve the fast extraction of viral nucleic acid and increase the sensitivity. Using portable thermocycler and blue light, the fluorescent results could be directly observed by naked eyes. The proposed method is of higher specificity and sensitivity, nearly at single molecule level. More important, results demonstrated 100% positive detection rate for 40 clinical samples, which was consistent with standard RT-PCR. Thus, our method is considerably simple, rapid, sensitive and accurate, holding great promise for the instant detecting of viruses including SARS-CoV-2 and the next generation of molecular diagnosis.
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Affiliation(s)
- Rui Wang
- Department of Chemistry & State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China,Human Phenome Institute, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200438, China
| | - Yongfang Li
- Department of Chemistry & State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China,Corresponding author
| | - Yanan Pang
- Changhai Hospital, Second Military Medical University, Shanghai, 200433, China,Corresponding author
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Fuyou Li
- Department of Chemistry & State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China
| | - Shihua Luo
- Department of Traumatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China,Corresponding author
| | - Chunyan Qian
- Clinical Laboratory, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 311100, China,School of Life Sciences, Fudan University, Shanghai, 200438, China,Corresponding author. Clinical Laboratory, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 311100, China
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3
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Lownik JC, Way G, Farrar JS, Martin RK. Extraction-Free Rapid Cycle Quantitative RT-PCR and Extreme RT-PCR for SARS-CoV-2 Virus Detection. J Mol Diagn 2021; 23:1671-1679. [PMID: 34454108 PMCID: PMC8386134 DOI: 10.1016/j.jmoldx.2021.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/19/2021] [Accepted: 08/18/2021] [Indexed: 12/26/2022] Open
Abstract
Since the start of the coronavirus disease 2019 (COVID-19) pandemic, molecular diagnostic testing for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has faced substantial supply chain shortages and noteworthy delays in result reporting after sample collection. Supply chain shortages have been most evident in reagents for RNA extraction and rapid diagnostic testing. This study explored the kinetic limitations of extraction-free rapid cycle quantitative real-time RT-PCR for SARS-CoV-2 virus detection using the commercially available capillary-based LightCycler. After optimizing for time and reaction conditions, a protocol for sensitive and specific quantitative RT-PCR of SARS-CoV-2 RNA from nasopharyngeal swabs in <20 minutes was developed, with minimal hands-on time requirements. This protocol improves detection speed while maintaining the sensitivity and specificity of hydrolysis probe-based detection. Percentage agreement between the developed assay and previously tested positive patient samples was 97.6% (n = 40/41), and negative patient samples was 100% (40/40). The study further demonstrates that using purified RNA, SARS-CoV-2 testing using extreme RT-PCR, and product verification by melting can be completed in <3 minutes. Overall, these studies provide a framework for increasing the speed of SARS-CoV-2 and other infectious disease testing.
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Affiliation(s)
- Joseph C Lownik
- Center for Clinical and Translational Research, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Grayson Way
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Jared S Farrar
- Center for Clinical and Translational Research, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Rebecca K Martin
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia.
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4
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Progress in molecular detection with high-speed nucleic acids thermocyclers. J Pharm Biomed Anal 2020; 190:113489. [DOI: 10.1016/j.jpba.2020.113489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/26/2022]
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5
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Langaee T, El Rouby N, Stauffer L, Galloway C, Cavallari LH. Development and Cross-Validation of High-Resolution Melting Analysis-Based Cardiovascular Pharmacogenetics Genotyping Panel. Genet Test Mol Biomarkers 2019; 23:209-214. [DOI: 10.1089/gtmb.2018.0298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Taimour Langaee
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida
| | - Nihal El Rouby
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida
| | - Lynda Stauffer
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida
| | - Cheryl Galloway
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida
| | - Larisa H. Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida
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Sinha M, Mack H, Coleman TP, Fraley SI. A High-Resolution Digital DNA Melting Platform for Robust Sequence Profiling and Enhanced Genotype Discrimination. SLAS Technol 2018; 23:580-591. [DOI: 10.1177/2472630318769846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA melting analysis provides a rapid method for genotyping a target amplicon directly after PCR amplification. To transform melt genotyping into a broad-based profiling approach for heterogeneous samples, we previously proposed the integration of universal PCR and melt analysis with digital PCR. Here, we advanced this concept by developing a high-resolution digital melt platform with precise thermal control to accomplish reliable, high-throughput heat ramping of microfluidic chip digital PCR reactions. Using synthetic DNA oligos with defined melting temperatures, we characterized sources of melting variability and minimized run-to-run variations. Within-run comparisons throughout a 20,000-reaction chip revealed that high-melting-temperature sequences were significantly less prone to melt variation. Further optimization using bacterial 16S amplicons revealed a strong dependence of the number of melting transitions on the heating rate during curve generation. These studies show that reliable high-resolution melt curve genotyping can be achieved in digital, picoliter-scale reactions and demonstrate that rate-dependent melt signatures may be useful for enhancing automated melt genotyping.
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Affiliation(s)
- Mridu Sinha
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Clinical Translational Research Institute, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Hannah Mack
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Clinical Translational Research Institute, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Todd P. Coleman
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Stephanie I. Fraley
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Clinical Translational Research Institute, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
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7
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Wang R, Zhang F, Qian C, Wu C, Ye Z, Wang L, Qian W, Ping J, Wu J, Ying Y. Counting DNA molecules with visual segment-based readouts in minutes. Chem Commun (Camb) 2018; 54:1105-1108. [PMID: 29333552 DOI: 10.1039/c7cc09515e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
An ultrafast and extremely simple approach was proposed to count the number of DNA molecules without any microfluidic-based device. By directly counting the number of amplicon clusters in a capillary, the absolute amount of DNA molecules could be easily determined.
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Affiliation(s)
- Rui Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China.
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Pryor RJ, Myrick JT, Palais RA, Sundberg SO, Paek JY, Wittwer CT, Knight IT. High-Speed Melting Analysis: The Effect of Melting Rate on Small Amplicon Microfluidic Genotyping. Clin Chem 2017; 63:1624-1632. [PMID: 28818830 DOI: 10.1373/clinchem.2017.276147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 07/06/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND High-resolution DNA melting analysis of small amplicons is a simple and inexpensive technique for genotyping. Microfluidics allows precise and rapid control of temperature during melting. METHODS Using a microfluidic platform for serial PCR and melting analysis, 4 targets containing single nucleotide variants were amplified and then melted at different rates over a 250-fold range from 0.13 to 32 °C/s. Genotypes (n = 1728) were determined manually by visual inspection after background removal, normalization, and conversion to negative derivative plots. Differences between genotypes were quantified by a genotype discrimination ratio on the basis of inter- and intragenotype differences using the absolute value of the maximum vertical difference between curves as a metric. RESULTS Different homozygous curves were genotyped by melting temperature and heterozygous curves were identified by shape. Technical artifacts preventing analysis (0.3%), incorrect (0.06%), and indeterminate (0.4%) results were minimal, occurring mostly at slow melting rates (0.13-0.5 °C/s). Genotype discrimination was maximal at around 8 °C/s (2-8 °C/s for homozygotes and 8-16 °C/s for heterozygotes), and no genotyping errors were made at rates >0.5 °C/s. PCR was completed in 10-12.2 min, followed by melting curve acquisition in 4 min down to <1 s. CONCLUSIONS Microfluidics enables genotyping by melting analysis at rates up to 32 °C/s, requiring <1 s to acquire an entire melting curve. High-speed melting reduces the time for melting analysis, decreases errors, and improves genotype discrimination of small amplicons. Combined with extreme PCR, high-speed melting promises nucleic acid amplification and genotyping in < 1 min.
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Affiliation(s)
- Robert J Pryor
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
| | | | - Robert A Palais
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT.,Department of Mathematics, Utah Valley University, Orem, UT
| | - Scott O Sundberg
- Canon Virginia, Inc., Newport News, VA.,Canon U.S. Life Sciences, Inc., Rockville, MD
| | | | - Carl T Wittwer
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT;
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Langaee T, Stauffer L, Galloway C, Solayman MH, Cavallari L. Cross-Validation of High-Resolution Melting Analysis-Based Genotyping Platform. Genet Test Mol Biomarkers 2017; 21:259-264. [DOI: 10.1089/gtmb.2016.0317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Taimour Langaee
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, Florida
| | - Lynda Stauffer
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, Florida
| | - Cheryl Galloway
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, Florida
| | - Mohamed H. Solayman
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, Florida
| | - Larisa Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, Florida
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PCR-Based Detection Methods for Single-Nucleotide Polymorphism or Mutation: Real-Time PCR and Its Substantial Contribution Toward Technological Refinement. Adv Clin Chem 2017; 80:45-72. [PMID: 28431642 DOI: 10.1016/bs.acc.2016.11.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) and single-nucleotide mutations result from the substitution of only a single base. The SNP or mutation can be relevant to disease susceptibility, pathogenesis of disease, and efficacy of specific drugs. It is important to detect SNPs or mutations clinically. Methods to distinguish/detect SNPs or mutations should be highly specific and sensitive. In this regard, polymerase chain reaction (PCR) has provided the necessary analytical performance for many molecular analyses. PCR-based methods for SNP/mutation detection are broadly categorized into two types-(1) polymorphic or mutant allele-directed specific analysis using primers matched with substituted nucleotide or using oligonucleotides to block or clamp the nontargeted template, and (2) melting curve analysis, which is combined with the real-time PCR techniques using hydrolysis probes, hybridization probes, or double-stranded DNA-binding fluorescent dyes. Innovative and novel approaches as well as technical improvements have made SNP- or mutation-detection methods increasingly more sophisticated. These advances include DNA/RNA preparation and subsequent amplification steps, and miniaturization of PCR instruments such that testing may be performed with relative ease in clinical laboratories or as a point-of-care test in clinical settings.
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Ahrberg CD, Manz A, Chung BG. Polymerase chain reaction in microfluidic devices. LAB ON A CHIP 2016; 16:3866-3884. [PMID: 27713993 DOI: 10.1039/c6lc00984k] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The invention of the polymerase chain reaction (PCR) has caused a revolution in molecular biology, giving access to a method of amplifying deoxyribonucleic acid (DNA) molecules across several orders of magnitude. Since the first application of PCR in a microfluidic device was developed in 1998, an increasing number of researchers have continued the development of microfluidic PCR systems. In this review, we introduce recent developments in microfluidic-based space and time domain devices as well as discuss various designs integrated with multiple functions for sample preparation and detection. The development of isothermal nucleic acid amplification and digital PCR microfluidic devices within the last five years is also highlighted. Furthermore, we introduce various commercial microfluidic PCR devices.
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Affiliation(s)
| | - Andreas Manz
- Microfluidics group, KIST-Europe, Saarbrücken, Germany and Mechanotronics Department, Universität des Saarlandes, Saarbrücken, Germany
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
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Cao W, Bean B, Corey S, Coursey JS, Hasson KC, Inoue H, Isano T, Kanderian S, Lane B, Liang H, Murphy B, Owen G, Shinoda N, Zeng S, Knight IT. Automated Microfluidic Platform for Serial Polymerase Chain Reaction and High-Resolution Melting Analysis. ACTA ACUST UNITED AC 2016; 21:402-11. [DOI: 10.1177/2211068215579015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Indexed: 11/16/2022]
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13
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Sueki A, Matsuda K, Yamaguchi A, Uehara M, Sugano M, Uehara T, Honda T. Evaluation of saliva as diagnostic materials for influenza virus infection by PCR-based assays. Clin Chim Acta 2016; 453:71-4. [DOI: 10.1016/j.cca.2015.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/03/2015] [Accepted: 12/04/2015] [Indexed: 11/15/2022]
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15
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Kanderian S, Jiang L, Knight I. Automated Classification and Cluster Visualization of Genotypes Derived from High Resolution Melt Curves. PLoS One 2015; 10:e0143295. [PMID: 26605797 PMCID: PMC4659556 DOI: 10.1371/journal.pone.0143295] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/03/2015] [Indexed: 11/19/2022] Open
Abstract
Introduction High Resolution Melting (HRM) following PCR has been used to identify DNA genotypes. Fluorescent dyes bounded to double strand DNA lose their fluorescence with increasing temperature, yielding different signatures for different genotypes. Recent software tools have been made available to aid in the distinction of different genotypes, but they are not fully automated, used only for research purposes, or require some level of interaction or confirmation from an analyst. Materials and Methods We describe a fully automated machine learning software algorithm that classifies unknown genotypes. Dynamic melt curves are transformed to multidimensional clusters of points whereby a training set is used to establish the distribution of genotype clusters. Subsequently, probabilistic and statistical methods were used to classify the genotypes of unknown DNA samples on 4 different assays (40 VKORC1, CYP2C9*2, CYP2C9*3 samples in triplicate, and 49 MTHFR c.665C>T samples in triplicate) run on the Roche LC480. Melt curves of each of the triplicates were genotyped separately. Results Automated genotyping called 100% of VKORC1, CYP2C9*3 and MTHFR c.665C>T samples correctly. 97.5% of CYP2C9*2 melt curves were genotyped correctly with the remaining 2.5% given a no call due to the inability to decipher 3 melt curves in close proximity as either homozygous mutant or wild-type with greater than 99.5% posterior probability. Conclusions We demonstrate the ability to fully automate DNA genotyping from HRM curves systematically and accurately without requiring any user interpretation or interaction with the data. Visualization of genotype clusters and quantification of the expected misclassification rate is also available to provide feedback to assay scientists and engineers as changes are made to the assay or instrument.
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Affiliation(s)
- Sami Kanderian
- Canon U.S. Life Sciences, Rockville, MD, United States of America
- * E-mail:
| | - Lingxia Jiang
- Canon U.S. Life Sciences, Rockville, MD, United States of America
| | - Ivor Knight
- Canon U.S. Life Sciences, Rockville, MD, United States of America
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Shu B, Zhang C, Xing D. A handheld flow genetic analysis system (FGAS): towards rapid, sensitive, quantitative and multiplex molecular diagnosis at the point-of-care level. LAB ON A CHIP 2015; 15:2597-605. [PMID: 25953325 DOI: 10.1039/c5lc00139k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A handheld flow genetic analysis system (FGAS) is proposed for rapid, sensitive, multiplex and real-time quantification of nucleic acids at the point-of-care (POC) level. The FGAS includes a helical thermal-gradient microreactor and a microflow actuator, as well as control circuitry for temperature, fluid and power management, and smartphone fluorescence imaging. All of these features are integrated into a field-portable and easy-to-use molecular diagnostic platform powered by lithium batteries. Due to the unique design of the microreactor, not only steady temperatures for denaturation and annealing/extension but also a linear thermal gradient for spatial high-resolution melting can be achieved through simply maintaining a single heater at constant temperature. The smartphone fluorescence imaging system has a wide field of view that captures all PCR channels of the microreactor in a single snapshot without the need for any mechanical scanning. By these designs, the FGAS enables real-time monitoring of the temporal and spatial fluorescence signatures of amplicons during continuous-flow amplification. On the current FGAS, visual detection of as little as 10 copies per μL of genomic DNA of Salmonella enterica was achieved in 15 min, with real-time quantitative detection of the DNA over 6 orders of magnitude concentration from 10(6) to 10(1) copies per μL also completed in 7.5-15 min. In addition, multiple pathogenic DNA targets could be simultaneously discriminated with direct bar-chart readout or multiplex spatial melting in serial flow. We anticipate that the FGAS has great potential to become a next-generation gene analyzer for POC molecular diagnostics.
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Affiliation(s)
- Bowen Shu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
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