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Journal articles on the topic 'Multiplex amplification'

Author: Grafiati

Published: 4 June 2021

Last updated: 19 February 2022

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1

Jeuken, Judith, Sandra Cornelissen, Sandra Boots-Sprenger, Sabine Gijsen, and Pieter Wesseling. "Multiplex Ligation-Dependent Probe Amplification." Journal of Molecular Diagnostics 8, no. 4 (September 2006): 433–43. http://dx.doi.org/10.2353/jmoldx.2006.060012.

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Broude, Natalia E., Kristina Driscoll, and Charles R. Cantor. "High-Level Multiplex DNA Amplification." Antisense and Nucleic Acid Drug Development 11, no. 5 (October 2001): 327–32. http://dx.doi.org/10.1089/108729001753231704.

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3

Römpler, Holger, Paul H. Dear, Johannes Krause, Matthias Meyer, Nadin Rohland, Torsten Schöneberg, Helen Spriggs, Mathias Stiller, and Michael Hofreiter. "Multiplex amplification of ancient DNA." Nature Protocols 1, no. 2 (July 13, 2006): 720–28. http://dx.doi.org/10.1038/nprot.2006.84.

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4

Cave, Christopher A., Kristen Hancock, and James W. Schumm. "Principles of STR multiplex amplification." Forensic Science International: Genetics Supplement Series 1, no. 1 (August 2008): 102–4. http://dx.doi.org/10.1016/j.fsigss.2007.10.016.

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5

Millholland, J., S. G. Patel, C. A. Fernandez, and A. P. Shuber. "Development of a real-time multiplex PCR assay for the detection of FGFR3 mutations in urine." Journal of Clinical Oncology 29, no. 7_suppl (March 1, 2011): 271. http://dx.doi.org/10.1200/jco.2011.29.7_suppl.271.

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271 Background: We have recently reported the development of a Multi-Analyte Diagnostic Readout (MADR) non-invasive assay using urinary matrix metalloproteinases (MMPs) and FGFR3 as triage monitors in high-risk bladder cancer populations. This concept combines the marker performance characteristics of protein and DNA biomarkers into one assay for optimal performance. Eight common FGFR3 mutations in 3 exons have been associated with bladder cancer. Analysis of mutational status for each single mutation required 8 amplification steps, which were costly and time consuming. We have now developed a real-time multiplexed FGFR3 assay, generating a cost-effective, clinically applicable assay for the detection of FGFR3 mutations in urine. Methods: Our approach involves a two-step PCR amplification process. The initial round generates exon specific PCR products, which are then used as template for real-time PCR mutation detection utilizing locked nucleic acid (LNA) oligonucleotides. The LNA suppress wild-type DNA amplification. To convert our existing FGFR3 assay to a multiplex format, primary amplifications of exons 7, 10, and 15 were combined into a single real-time PCR assay for exon specific amplification and DNA quantitation. The LNA-mediated mutation detection was then converted from 4 reactions to 2 duplex amplifications. All multiplex assays were carried out on the Roche LC 480 real-time PCR platform. Results: To validate the new multiplex format, FGFR3 multiplex analysis was performed on DNA isolated from 50 Ta stage bladder tumors. FGFR3 mutations were detected in 90% (48/50) of the tumors. To directly compare performance with single mutation analysis, 40 urine samples previously analyzed using the singleplex format were again tested using the multiplex FGFR3 assay. 100% concordance was seen between the two assay formats. Conclusions: By multiplexing the FGFR3 mutation analysis we reduced the number of amplification steps, improving assay turnaround time and throughput, without compromising assay performance. The FGFR3 multiplex analysis provides a robust, cost-effective DNA assay that in combination with MMP protein analysis delivers a clinically applicable assay with optimal performance. [Table: see text]

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Moelans, Cathy B., Hanneke N. Monsuur, Johannes H. de Pinth, Remco D. Radersma, Roel A. de Weger, and Paul J. van Diest. "ESR1 Amplification is Rare in Breast Cancer and is Associated with High Grade and High Proliferation: A Multiplex Ligation-Dependent Probe Amplification Study." Analytical Cellular Pathology 33, no. 1 (2010): 13–18. http://dx.doi.org/10.1155/2010/619180.

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Background: Expression of estrogen receptor alpha (ERα) is predictive for endocrine therapy response and an important prognostic factor in breast cancer. Overexpression of ERα can be caused by estrogen receptor 1 (ESR1) gene amplification and was originally reported to be a frequent event associated with a significantly longer survival for ER-positive women treated with adjuvant tamoxifen monotherapy, which was however questioned by subsequent studies.Methods: This study aimed to reanalyze the frequency of ESR1 amplification by multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridisation (FISH), and to assess clinicopathologic correlations. MLPA was performed in a group of 135 breast cancer patients, and gains/amplifications were subjected to FISH.Results: True ESR1 amplification by MLPA was rare (2%) and only 6% more patients showed a modest gain of ESR1. All MLPA-detected ESR1 amplifications and nearly all ESR1 gains were also FISH amplified and gained, but not all FISH amplifications/gains were MLPA amplified/gained, leading to an overall concordance of only 60% between both techniques. All 3 MLPA and FISH ESR1 amplified cases had high ERα expression, but there was no obvious correlation between ESR1 gain and ER status by IHC. ESR1 gains/amplifications were not associated with HER2 gain/amplification, but seemed to be associated with older age. Surprisingly, ESR1 gain/amplification was not associated with low grade as reported previously, but correlated with high grade and high proliferation. Furthermore, ESR1 gain/amplification by MLPA was not associated with nodal status or tumor size (pT status).Conclusion: ESR1 amplification as detected by MLPA is rare in breast cancer, and seems to be associated with high ERα expression, high age, high grade and high proliferation. This study confirms previous studies that showed differences in the ESR1 amplification frequencies detected by different techniques.

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Minarikova, Petra, Lucie Benesova, Tereza Halkova, Barbora Belsanova, Inna Tuckova, Frantisek Belina, Ladislav Dusek, Miroslav Zavoral, and Marek Minarik. "Prognostic Importance of Cell Cycle Regulators Cyclin D1 (CCND1) and Cyclin-Dependent Kinase Inhibitor 1B (CDKN1B/p27) in Sporadic Gastric Cancers." Gastroenterology Research and Practice 2016 (2016): 1–8. http://dx.doi.org/10.1155/2016/9408190.

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Background. Gastric cancer is known for a notable variety in the course of the disease. Clinical factors, such as tumor stage, grade, and localization, are key in patient survival. It is expected that molecular factors such as somatic mutations and gene amplifications are also underlying tumor biological behavior and may serve as factors for prognosis estimation.Aim. The purpose of this study was to examine gene amplifications from a panel of genes to uncover potential prognostic marker candidates.Methods. A panel of gene amplifications including 71 genes was tested by multiplex ligation-dependent probe amplification (MLPA) technique in 76 gastric cancer samples from a Caucasian population. The correlation of gene amplification status with patient survival was determined by the Kaplan-Meier method.Results. The amplification of two cell cycle regulators,CCND1andCDKN1B, was identified to have a negative prognostic role. The medial survival of patients with gastric cancer displaying amplification compared to patients without amplification was 192 versus 725 days forCCND1(P=0.0012) and 165 versus 611 days forCDKN1B(P=0.0098).Conclusion. Gene amplifications ofCCND1andCDKN1Bare potential candidates to serve as prognostic markers for the stratification of patients based on the estimate of survival in the management of gastric cancer patients.

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8

Søe, Martin Jensen, and Peter Warthoe. "RT-isoPCR: nested, high multiplex mRNA amplification." Analyst 138, no. 20 (2013): 5871. http://dx.doi.org/10.1039/c3an00803g.

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Meuzelaar, Linda Strömqvist, Owen Lancaster, J. Paul Pasche, Guido Kopal, and Anthony J. Brookes. "MegaPlex PCR: a strategy for multiplex amplification." Nature Methods 4, no. 10 (September 16, 2007): 835–37. http://dx.doi.org/10.1038/nmeth1091.

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10

Talavera Vargas-Machuca, Sergio, Ismenia Gamboa Oré, Francia Huamán Dianderas, Ricardo Fujita Alarcón, María Luisa Fajardo Loo, and María Luisa Guevara Gil. "Diagnóstico molecular de síndrome de Smith-Magenis por MLPA (Multiplex Ligation-dependent Probe Amplification)." Horizonte Médico (Lima) 17, no. 3 (June 30, 2017): 73–78. http://dx.doi.org/10.24265/horizmed.2017.v17n3.12.

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Du, Meijun, Chiang-Ching Huang, Winston Tan, Manish Kohli, and Liang Wang. "Multiplex Digital PCR to Detect Amplifications of Specific Androgen Receptor Loci in Cell-Free DNA for Prognosis of Metastatic Castration-Resistant Prostate Cancer." Cancers 12, no. 8 (August 1, 2020): 2139. http://dx.doi.org/10.3390/cancers12082139.

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Amplification of androgen receptor (AR) is a common genomic event in metastatic castration-resistant prostate cancer (mCRPC). To evaluate the prognostic value of the amplifications of specific loci in the AR gene in cell-free DNA, we developed a multiplex digital PCR (dPCR) assay that targeted AR enhancer (AR-En), AR exon 1 (AR-E1), AR exon 8 (AR-E8) and OPHN1 (downstream of AR). We selected three relatively stable genes, C2orf16, FAM111B, and GRIA3, as reference controls for copy number normalization. One hundred and eight mCRPC patients were recruited to test the association of specific AR loci amplification with clinical outcome. Using a normalized ratio ≥ 1.92 as cutoff, amplification of AR-En, AR-E1, AR-E8 and OPHN1 was observed in 28, 25, 24 and 19 of 108 mCRPC patients, respectively. Among the 41 patients with AR region amplification, 9 (21.9%) showed amplification at all four selected regions and 15 (36.6%) showed amplification at AR-En, AR-E1, and AR-E8. Six (14.6%) patients showed independent AR-En amplification, while the remaining 3 (7.3%) demonstrated AR-E8 amplification only. Kaplan–Meier analysis showed overall survival’s association with the amplification of AR-En (p = 0.02, HR = 1.68 (1.07–2.65)), AR-E8 (p = 0.02, HR = 1.78 (1.08–2.92)) and AR-En-E8 (the combination of AR-En and AR-E8 (p = 0.009, HR = 1.77 (1.15–2.73)). Multivariate models that included AR-En-E8 amplification and clinical factors significantly improved prognostic performance (p = 0.0001). With further validation, the multiplex dPCR assay may assist in prognostication of mCRPC patients.

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Wu, Zhiyuan, Yunqing Zhang, Xinju Zhang, Xiao Xu, Zhihua Kang, Shibao Li, Chen Zhang, Bing Su, and Ming Guan. "A Multiplex Snapback Primer System for the Enrichment and Detection ofJAK2V617F andMPLW515L/K Mutations in Philadelphia-Negative Myeloproliferative Neoplasms." BioMed Research International 2014 (2014): 1–11. http://dx.doi.org/10.1155/2014/458457.

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A multiplex snapback primer system was developed for the simultaneous detection ofJAK2V617F andMPLW515L/K mutations in Philadelphia chromosome- (Ph-) negative myeloproliferative neoplasms (MPNs). The multiplex system comprises two snapback versus limiting primer sets forJAK2andMPLmutation enrichment and detection, respectively. Linear-After exponential (LATE) PCR strategy was employed for the primer design to maximize the amplification efficiency of the system. Low ionic strength buffer and rapid PCR protocol allowed for selective amplification of the mutant alleles. Amplification products were analyzed by melting curve analysis for mutation identification. The multiplex system archived 0.1% mutation load sensitivity and <5% coefficient of variation inter-/intra-assay reproducibility. 120 clinical samples were tested by the multiplex snapback primer assay, and verified with amplification refractory system (ARMS), quantitative PCR (qPCR) and Sanger sequencing method. The multiplex system, with a favored versatility, provided the molecular diagnosis of Ph-negative MPNs with a suitable implement and simplified the genetic test process.

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Kornegoor, Robert, Cathy B. Moelans, Anoek H. J. Verschuur-Maes, Marieke C. H. Hogenes, Peter C. de Bruin, Joost J. Oudejans, Luigi Marchionni, and Paul J. van Diest. "Oncogene amplification in male breast cancer: analysis by multiplex ligation-dependent probe amplification." Breast Cancer Research and Treatment 135, no. 1 (April 13, 2012): 49–58. http://dx.doi.org/10.1007/s10549-012-2051-3.

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14

Moldovan, Valeriu, and Elena Moldovan. "Multiplex ligation-dependent probe amplification – a short overview." Revista Romana de Medicina de Laborator 28, no. 2 (April 1, 2020): 123–31. http://dx.doi.org/10.2478/rrlm-2020-0016.

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AbstractMultiplex Ligation-dependent Probe Amplification is a technique proposed for the detection of deletions or duplications that may lead to copy number variations in genomic DNA, mainly due to its higher resolution, and shorter overall diagnosis time, when compared with techniques traditionally used, namely karyotyping, fluorescence in situ hybridization, and array comparative genomic hybridization. Multiplex Ligation-dependent Probe Amplification is a fast (about 2 days), useful and cost-effective technique, being suitable for the diagnosis of hereditary conditions caused by complete or partial gene deletions or duplications, as these conditions are either more difficult or impossible to be diagnosed by other techniques, such as PCR, Real-Time PCR, or sequencing (Sanger or Next Generation). Due to its numerous advantages over conventional cytogenetic analysis techniques, Multiplex Ligation-dependent Probe Amplification could be used in the near future as the main technique for the molecular investigation of genetic conditions caused by copy number variations, in both rare and complex genetic disorders.

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Qiu-Ling, LIU, LÜ De-Jian, ZHU Jia-Zhen, LU Hui-Ling, LUO Yan-Min, and FANG Qun. "Fluorescent Multiplex Amplification of Three X-STR Loci." Acta Genetica Sinica 33, no. 12 (December 2006): 1053–59. http://dx.doi.org/10.1016/s0379-4172(06)60142-x.

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16

Porreca, Gregory J., Kun Zhang, Jin Billy Li, Bin Xie, Derek Austin, Sara L. Vassallo, Emily M. LeProust, et al. "Multiplex amplification of large sets of human exons." Nature Methods 4, no. 11 (October 14, 2007): 931–36. http://dx.doi.org/10.1038/nmeth1110.

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Westin, Lorelei, Xiao Xu, Carolyn Miller, Ling Wang, Carl F. Edman, and Michael Nerenberg. "Anchored multiplex amplification on a microelectronic chip array." Nature Biotechnology 18, no. 2 (February 2000): 199–204. http://dx.doi.org/10.1038/72658.

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18

Kreer, Christoph, Matthias Döring, Nathalie Lehnen, Meryem S. Ercanoglu, Lutz Gieselmann, Domnica Luca, Kanika Jain, Philipp Schommers, Nico Pfeifer, and Florian Klein. "openPrimeR for multiplex amplification of highly diverse templates." Journal of Immunological Methods 480 (May 2020): 112752. http://dx.doi.org/10.1016/j.jim.2020.112752.

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19

Barbaro, A., P. Cormaci, and A. Barbaro. "Multiplex STRs amplification from hair shaft: Validation study." International Congress Series 1288 (April 2006): 676–78. http://dx.doi.org/10.1016/j.ics.2005.12.061.

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20

Zhu, Jianjie, Lanxin Chen, Yong Mao, Huan Zhou, Rui Li, and Weipeng Wang. "Multiplex Allele-Specific Amplification from Whole Blood for Detecting Multiple Polymorphisms Simultaneously." Genetic Testing and Molecular Biomarkers 17, no. 1 (January 2013): 10–15. http://dx.doi.org/10.1089/gtmb.2012.0261.

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21

Lai, Wei, Mingshu Xiao, Haihong Yang, Li Li, Chunhai Fan, and Hao Pei. "Circularized blocker-displacement amplification for multiplex detection of rare DNA variants." Chemical Communications 56, no. 82 (2020): 12331–34. http://dx.doi.org/10.1039/d0cc05283c.

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22

Dobnik, David, Dany Morisset, and Kristina Gruden. "NASBA integrated multiplex amplification: A new method for multiplex and quantitative GMO detection." Journal of Biotechnology 136 (October 2008): S247. http://dx.doi.org/10.1016/j.jbiotec.2008.07.526.

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23

Toksoy, Güven, Birsen Karaman, Zehra Oya Uyguner, Kader Yılmaz, Recep Has, Hülya Kayserili, Peter Miny, and Seher Başaran. "APPLICATION OF MLPA (MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION) IN FETUSES WITH AN ABNORMAL SONOGRAM AND NORMAL KARYOTYPE." İstanbul Tıp Fakültesi Dergisi 82, no. 1 (March 25, 2019): 5–11. http://dx.doi.org/10.26650/iuitfd.413596.

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24

Mahony, James B. "Detection of Respiratory Viruses by Molecular Methods." Clinical Microbiology Reviews 21, no. 4 (October 2008): 716–47. http://dx.doi.org/10.1128/cmr.00037-07.

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SUMMARY Clinical laboratories historically diagnose seven or eight respiratory virus infections using a combination of techniques including enzyme immunoassay, direct fluorescent antibody staining, cell culture, and nucleic acid amplification tests. With the discovery of six new respiratory viruses since 2000, laboratories are faced with the challenge of detecting up to 19 different viruses that cause acute respiratory disease of both the upper and lower respiratory tracts. The application of nucleic acid amplification technology, particularly multiplex PCR coupled with fluidic or fixed microarrays, provides an important new approach for the detection of multiple respiratory viruses in a single test. These multiplex amplification tests provide a sensitive and comprehensive approach for the diagnosis of respiratory tract infections in individual hospitalized patients and the identification of the etiological agent in outbreaks of respiratory tract infection in the community. This review describes the molecular methods used to detect respiratory viruses and discusses the contribution that molecular testing, especially multiplex PCR, has made to our ability to detect respiratory viruses and to increase our understanding of the roles of various viral agents in acute respiratory disease.

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Luan, Chengxin, Yueshuang Xu, Fanfan Fu, Huan Wang, Qionghua Xu, Baoan Chen, and Yuanjin Zhao. "Responsive photonic barcodes for sensitive multiplex bioassay." Nanoscale 9, no. 37 (2017): 14111–17. http://dx.doi.org/10.1039/c7nr04867j.

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Søe, Martin Jensen, Mikkel Rohde, Jens Mikkelsen, and Peter Warthoe. "IsoPCR: An Analytically Sensitive, Nested, Multiplex Nucleic Acid Amplification Method." Clinical Chemistry 59, no. 2 (February 1, 2013): 436–39. http://dx.doi.org/10.1373/clinchem.2012.193664.

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BACKGROUND Nucleic acid tests that can simultaneously detect multiple targets with high sensitivity, specificity, and speed are highly desirable. To meet this need, we developed a new approach we call the isoPCR method. METHODS The isoPCR method is a 2-stage nested-like nucleic acid amplification method that combines a single multiplex preamplification PCR with subsequent distinct detection of specific targets by use of isothermal amplification. We compared isoPCR to nested quantitative PCR (qPCR), loop-mediated isothermal amplification (LAMP), and nested LAMP (PCR followed by LAMP), for detection of DNA from Candida glabrata. We evaluated the method's multiplex capability for detecting low copy numbers of pathogens commonly involved in sepsis. RESULTS IsoPCR provided detection of 1 copy of Candida glabrata, an LOD that was 5-fold lower than a nested qPCR assay (5 copies), while the amplification time was simultaneously halved. Similarly, the LOD for isoPCR was lower than that for a LAMP assay (1000 copies) and a nested LAMP assay (5 copies). IsoPCR required recognition of 6 regions for detection, thereby providing a theoretically higher specificity compared to nested qPCR (4 regions). The isoPCR multiplexing capability was demonstrated by simultaneous detection of 4 pathogens with individual LODs of 10 copies or fewer. Furthermore, the specificity of isoPCR was demonstrated by successful pathogen detection from samples with more than 1 pathogen present. CONCLUSIONS IsoPCR provides a molecular diagnostic tool for multiplex nucleic acid detection, with an LOD down to 1 copy, high theoretical specificity, and halving of the amplification time compared to a nested qPCR assay.

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Vora, Gary J., Carolyn E. Meador, David A. Stenger, and Joanne D. Andreadis. "Nucleic Acid Amplification Strategies for DNA Microarray-Based Pathogen Detection." Applied and Environmental Microbiology 70, no. 5 (May 2004): 3047–54. http://dx.doi.org/10.1128/aem.70.5.3047-3054.2004.

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ABSTRACT DNA microarray-based screening and diagnostic technologies have long promised comprehensive testing capabilities. However, the potential of these powerful tools has been limited by front-end target-specific nucleic acid amplification. Despite the sensitivity and specificity associated with PCR amplification, the inherent bias and limited throughput of this approach constrain the principal benefits of downstream microarray-based applications, especially for pathogen detection. To begin addressing alternative approaches, we investigated four front-end amplification strategies: random primed, isothermal Klenow fragment-based, φ29 DNA polymerase-based, and multiplex PCR. The utility of each amplification strategy was assessed by hybridizing amplicons to microarrays consisting of 70-mer oligonucleotide probes specific for enterohemorrhagic Escherichia coli O157:H7 and by quantitating their sensitivities for the detection of O157:H7 in laboratory and environmental samples. Although nearly identical levels of hybridization specificity were achieved for each method, multiplex PCR was at least 3 orders of magnitude more sensitive than any individual random amplification approach. However, the use of Klenow-plus-Klenow and φ29 polymerase-plus-Klenow tandem random amplification strategies provided better sensitivities than multiplex PCR. In addition, amplification biases among the five genetic loci tested were 2- to 20-fold for the random approaches, in contrast to >4 orders of magnitude for multiplex PCR. The same random amplification strategies were also able to detect all five diagnostic targets in a spiked environmental water sample that contained a 63-fold excess of contaminating DNA. The results presented here underscore the feasibility of using random amplification approaches and begin to systematically address the versatility of these approaches for unbiased pathogen detection from environmental sources.

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Silva, Arnaldo Neves Santos, Jordy Coffa, Yohei Miyagi, Varsha Menon, Daniel Bottomley, Lindsay C. Ward, Toru Aoyama, et al. "Coamplification of receptor tyrosine kinases and downstream targets in Japanese gastric cancers." Journal of Clinical Oncology 32, no. 3_suppl (January 20, 2014): 41. http://dx.doi.org/10.1200/jco.2014.32.3_suppl.41.

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41 Background: Amplifications of receptor tyrosine kinases genes (RTKs), EGFR, ERBB2, FGFR2, MET, have been associated with the pathogenesis and progression of gastric cancer (GC). Recent studies have found that coamplifications of RTKs are rare in GC. Two phase III trials using RTK targeted therapy have failed to achieve survival benefit in GC patients. Co-amplification of RTKs and downstream targets genes (DSTs), PIK3CA, KRAS, MYC, CCNE1 may be related to resistance to RTK targeted therapy. We tested the hypothesis whether RTKs and DSTs genes are coamplified in GC. Methods: DNA and RNA were extracted from 221 GC from the Kanagawa Cancer Center Hospital (Yokohama, Japan). Copy number of EGFR, ERBB2, FGFR2, PIK3CA, KRAS, MYC, CCNE1 was investigated by a newly developed multiplex ligation dependent probe amplification (MLPA) assay. RNA expression of the same genes was measured using the NanoString platform and compared to DNA copy number status. The frequency of RTK and DST co-amplifications was established and related to KRAS mutation status. Results: RTK amplification was associated with high levels of RNA expression except MYC (all p<0.05). 68% of GC had no RTK amplification. 9% of GC had RTK amplification and no DST amplification. 10% of GC had RTKs co-amplified. 23% of GC had RTK and DST co-amplified. There was no overlap between KRAS mutations and amplifications of KRAS, PIK3CA, FGFR2 or MET. Conclusions: This is the first study reporting that RTK and DST co-amplification are more frequent than RTK co-amplification in GC. These results indicate that GC patients considered for RTK targeting therapy might require DNA copy number assessment of RTKs as well as key DSTs and KRAS mutation testing in order to identify those patients who benefit most from treatment.

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Gorgannezhad, Lena, Kamalalayam Rajan Sreejith, Melody Christie, Jing Jin, Chin Hong Ooi, Mohammad Katouli, Helen Stratton, and Nam-Trung Nguyen. "Core-Shell Beads as Microreactors for Phylogrouping of E. coli Strains." Micromachines 11, no. 8 (August 7, 2020): 761. http://dx.doi.org/10.3390/mi11080761.

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Multiplex polymerase chain reaction (PCR) is an effective tool for simultaneous detection of target genes. Nevertheless, their use has been restricted due to the intrinsic interference between primer pairs. Performing several single PCRs in an array format instead of a multiplex PCR is a simple way to overcome this obstacle. However, there are still major technical challenges in designing a new generation of single PCR microreactors with a small sample volume, rapid thermal cycling, and no evaporation during amplification. We report a simple and robust core-shell bead array for a series of single amplifications. Four core-shell beads with a polymer coating and PCR mixture were synthesized using liquid marble formation and subsequent photo polymerization. Each bead can detect one target gene. We constructed a customised system for thermal cycling of these core-shell beads. Phylogrouping of the E. coli strains was carried out based on the fluorescent signal of the core-shell beads. This platform can be a promising alternative for multiplex nucleic acid analyses due to its simplicity and high throughput. The platform reported here also reduces the cycling time and avoids evaporation as well as contamination of the sample during the amplification process.

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Wen, Daxing, and Chunqing Zhang. "Universal Multiplex PCR: a novel method of simultaneous amplification of multiple DNA fragments." Plant Methods 8, no. 1 (2012): 32. http://dx.doi.org/10.1186/1746-4811-8-32.

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Berg, C., A. Hedrum, A. Holmberg, F. Pontén, M. Uhlén, and J. Lundeberg. "Direct solid-phase sequence analysis of the human p53 gene by use of multiplex polymerase chain reaction and alpha-thiotriphosphate nucleotides." Clinical Chemistry 41, no. 10 (October 1, 1995): 1461–66. http://dx.doi.org/10.1093/clinchem/41.10.1461.

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Abstract Among the candidate cancer-prognostic genes is the p53 tumor suppressor gene, which, when mutated, plays an important role in the development of many types of cancers. To facilitate robust large-scale DNA analysis of microdissected tumor biopsies, we describe a multiplex/nested PCR approach for a simultaneous outer amplification of exons 4-9 of the human p53 gene with parallel amplification of the HLA-DQB1 locus, involving a total of 14 primers. This approach reduces the required number of cells for analysis and avoids any variation in the amplifications of the individual p53 exons during the common outer amplification step. The HLA sequencing allows sample identification because the DQB1 locus is highly polymorphic and is thereby patient-specific. The p53 and HLA amplicons are analyzed by solid-phase sequencing in a semiautomated format. To improve the DNA sequence quality, we used 2'-deoxyribonucleoside 5'-O-1-thiotriphosphates in the sequencing reactions.

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GRAY, J., and L. J. COUPLAND. "The increasing application of multiplex nucleic acid detection tests to the diagnosis of syndromic infections." Epidemiology and Infection 142, no. 1 (October 7, 2013): 1–11. http://dx.doi.org/10.1017/s0950268813002367.

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SUMMARYOn 14 January 2013, the US Food and Drug Administration (FDA) announced permission for a multiplex nucleic acid test, the xTAG®Gastrointestinal Pathogen Panel (GPP) (Luminex Corporation, USA), which simultaneously detects 11 common viral, bacterial and parasitic causes of infectious gastroenteritis, to be marketed in the USA. This announcement reflects the current move towards the development and commercialization of detection technologies based on nucleic acid amplification techniques for diagnosis of syndromic infections. We discuss the limitations and advantages of nucleic acid amplification techniques and the recent advances in Conformité Européene – in-vitrodiagnostic (CE-IVD)-approved multiplex real-time PCR kits for the simultaneous detection of multiple targets within the clinical diagnostics market.

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UNO, Naoki, and Katsunori YANAGIHARA. "Ligation-Independent Mechanism of Multiplex Ligation-Dependent Probe Amplification." Analytical Sciences 30, no. 8 (2014): 805–10. http://dx.doi.org/10.2116/analsci.30.805.

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Zhang, Ye, Liben Chen, Kuangwen Hsieh, and Tza-Huei Wang. "Ratiometric Fluorescence Coding for Multiplex Nucleic Acid Amplification Testing." Analytical Chemistry 90, no. 20 (September 25, 2018): 12180–86. http://dx.doi.org/10.1021/acs.analchem.8b03266.

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Ewald, Christian, Thomas Hofmann, Susanne A. Kuhn, Thomas Deufel, Christian Beetz, and Rolf Kalff. "Methylation-specific multiplex ligation-dependent probe amplification in meningiomas." Journal of Neuro-Oncology 90, no. 3 (September 2, 2008): 267–73. http://dx.doi.org/10.1007/s11060-008-9672-8.

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Chou, Lan-Szu, Elaine Lyon, and Rong Mao. "Molecular diagnosis utility of multiplex ligation-dependent probe amplification." Expert Opinion on Medical Diagnostics 2, no. 4 (April 2008): 373–85. http://dx.doi.org/10.1517/17530059.2.4.373.

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Patel, P., Y. M. Lo, J. I. Bell, and J. S. Wainscoat. "Rapid HLA typing by multiplex amplification refractory mutation system." Journal of Clinical Pathology 46, no. 12 (December 1, 1993): 1105–8. http://dx.doi.org/10.1136/jcp.46.12.1105.

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Berry, David, Karim Ben Mahfoudh, Michael Wagner, and Alexander Loy. "Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification." Applied and Environmental Microbiology 77, no. 21 (September 2, 2011): 7846–49. http://dx.doi.org/10.1128/aem.05220-11.

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Abstract:

ABSTRACT“Barcode-tagged” PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries.

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Berry, David, Karim Ben Mahfoudh, Michael Wagner, and Alexander Loy. "Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification." Applied and Environmental Microbiology 78, no. 2 (December 30, 2011): 612. http://dx.doi.org/10.1128/aem.07448-11.

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Stambaugh, Alexandra M., Matthew A. Stott, Gopikrishnan G. Meena, Manasi Tamhankar, Ricardo Carrion, Jean L. Patterson, Aaron R. Hawkins, and Holger Schmidt. "Optofluidic Amplification-Free Multiplex Detection of Viral Hemorrhagic Fevers." IEEE Journal of Selected Topics in Quantum Electronics 27, no. 4 (July 2021): 1–6. http://dx.doi.org/10.1109/jstqe.2020.3024239.

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Willis, Alecia S., Ignatia van den Veyver, and Christine M. Eng. "Multiplex ligation-dependent probe amplification (MLPA) and prenatal diagnosis." Prenatal Diagnosis 32, no. 4 (March 30, 2012): 315–20. http://dx.doi.org/10.1002/pd.3860.

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Park, Jung Hun, Ki Soo Park, Kyungmee Lee, Hyowon Jang, and Hyun Gyu Park. "Universal probe amplification: Multiplex screening technologies for genetic variations." Biotechnology Journal 10, no. 1 (October 28, 2014): 45–55. http://dx.doi.org/10.1002/biot.201400219.

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Broude, N. E., L. Zhang, K. Woodward, D. Englert, and C. R. Cantor. "Multiplex allele-specific target amplification based on PCR suppression." Proceedings of the National Academy of Sciences 98, no. 1 (January 2, 2001): 206–11. http://dx.doi.org/10.1073/pnas.98.1.206.

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Martínez-Glez, Víctor, Carmen Franco-Hernández, Jesús Lomas, Carolina Peña-Granero, José M. de Campos, Alberto Isla, and Juan A. Rey. "Multiplex ligation-dependent probe amplification (MLPA) screening in meningioma." Cancer Genetics and Cytogenetics 173, no. 2 (March 2007): 170–72. http://dx.doi.org/10.1016/j.cancergencyto.2006.09.011.

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Fujii, K., H. Senju, K. Yoshida, K. Sekiguchi, K. Imaizumi, K. Kasai, and H. Sato. "Multiplex PCR amplification of TH01, D9S304, and D3S1744 loci." Journal of Human Genetics 45, no. 5 (September 2000): 303–4. http://dx.doi.org/10.1007/s100380070021.

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Anderson, Neil W., and Phillip I. Tarr. "Multiplex Nucleic Acid Amplification Testing to Diagnose Gut Infections." Gastroenterology Clinics of North America 47, no. 4 (December 2018): 793–812. http://dx.doi.org/10.1016/j.gtc.2018.07.006.

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Caggana, Michele, James M. Conroy, and Kenneth A. Pass. "Rapid, efficient method for multiplex amplification from filter paper." Human Mutation 11, no. 5 (1998): 404–9. http://dx.doi.org/10.1002/(sici)1098-1004(1998)11:5<404::aid-humu8>3.0.co;2-s.

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Roh, Yoon Ho, Hyun Jee Lee, Ju Yeon Kim, Hyeon Ung Kim, Sun Min Kim, and Ki Wan Bong. "Precipitation-based colorimetric multiplex immunoassay in hydrogel particles." Lab on a Chip 20, no. 16 (2020): 2841–50. http://dx.doi.org/10.1039/d0lc00325e.

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Li, D., and J. Vijg. "Multiplex Co-Amplification of 24 Retinoblastoma Gene Exons after Pre-Amplification by Long-Distance PCR." Nucleic Acids Research 24, no. 3 (February 1, 1996): 538–39. http://dx.doi.org/10.1093/nar/24.3.538.

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Tang, Yaqin, Xiao He, Rui Yuan, Xingming Liu, Yi Zhao, Tingting Wang, Hui Chen, and Xuli Feng. "Logic-signal-based multiplex detection of MiRNAs with high tension hybridization and multiple signal amplification." Analyst 145, no. 12 (2020): 4314–20. http://dx.doi.org/10.1039/d0an00550a.

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