Please wait a minute...
Shopping Cart Email List Chinese
Advanced Search Fig/Tab
Quantitative Biology

ISSN 2095-4689

ISSN 2095-4697(Online)

CN 10-1028/TM

Postal Subscription Code 80-971

Featured Articles  |  Most Downloaded  |  Most Reading
Online Submission Subscribe to Our RSS Content Feed
Quant. Biol.    2020, Vol. 8 Issue (4) : 279-294    https://doi.org/10.1007/s40484-020-0217-2
REVIEW
Recent advances and application in whole-genome multiple displacement amplification
Naiyun Long, Yi Qiao, Zheyun Xu, Jing Tu(), Zuhong Lu()
State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
 Download: PDF(1083 KB)   HTML
 Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks
Abstract

Background: The extremely small amount of DNA in a cell makes it difficult to study the whole genome of single cells, so whole-genome amplification (WGA) is necessary to increase the DNA amount and enable downstream analyses. Multiple displacement amplification (MDA) is the most widely used WGA technique.

Results: Compared with amplification methods based on PCR and other methods, MDA renders high-quality DNA products and better genome coverage by using phi29 DNA polymerase. Moreover, recently developed advanced MDA technologies such as microreactor MDA, emulsion MDA, and micro-channel MDA have improved amplification uniformity. Additionally, the development of other novel methods such as TruePrime WGA allows for amplification without primers.

Conclusion: Here, we reviewed a selection of recently developed MDA methods, their advantages over other WGA methods, and improved MDA-based technologies, followed by a discussion of future perspectives. With the continuous development of MDA and the successive update of detection technologies, MDA will be applied in increasingly more fields and provide a solid foundation for scientific research.
Keywords whole genome amplification      multiple displacement amplification      improved MDA-based approaches     
Corresponding Author(s): Jing Tu,Zuhong Lu   
Just Accepted Date: 20 October 2020   Online First Date: 07 December 2020    Issue Date: 24 December 2020
 Cite this article:   
Naiyun Long,Yi Qiao,Zheyun Xu, et al. Recent advances and application in whole-genome multiple displacement amplification[J]. Quant. Biol., 2020, 8(4): 279-294.
 URL:  
https://academic.hep.com.cn/qb/EN/10.1007/s40484-020-0217-2
https://academic.hep.com.cn/qb/EN/Y2020/V8/I4/279
Fig.1  Multiple displacement amplification (MDA) process diagram.
WGA methods Enzyme Product length Coverage Advantage Disadvantage Refs.
PEP DNA polymerase <2 kb ~50% Low template quality requirements, simple operation, and easy improvement Low yield and fidelity; easy to cause amplification bias and fragment loss [5,42]
DOP-PCR DNA polymerase <2 kb ~40% Simple operation, the minimum template amount can reach 50 pg, and the product fragment is 0.5~10 kb Large amplification bias at low template amounts [6,43]
MDA Phi29 DNA polymerase <100 kb ~70% High product, low DNA template amount, great fidelity Non-uniformity, may have non-specific products [8,37]
MALBAC Bst enzyme and Taq DNA polymerase <2 kb ~90% Simple operation, high yield, minimum template amount is several pg, uniform amplification Amplification is difficult when the amount of initial template is low, and non-specific amplification may occur [9,44]
LIANTI Transcriptase and T7 RNA polymerase ~400 bp ~97% Linear amplification enhances amplification stability and high coverage Multiple amplification steps and few applications [10]
Tab.1  Comparison of mainstream WGA methods
Fig.2  Schematic diagram of the TruePrime reaction process.
Fig.3  Schematic diagram of PTA.
Methods Characteristics Advantages Refs.
TruePrime TthPrimPol enzyme Primer-free, evenness of genome coverage, preeminent SNP detection with low ADO, better CNV calling. TruePrime single-cell WGA kit (Sygnis GmbH, Germany) is currently in the market [48]
WGA-X A thermostable mutant of phi29 polymerase Better genome recovery from individual microbial cells and viral particles, the higher reaction temperature (45°C), may address the potential bias of high GC templates [50]
PTA Extension terminator A quasi-linear amplification process, excellent genome uniformity performance, SNV sensitivity, SNV specificity, and greater cell-to-cell reproducibility [51]
Tab.2  Characteristics and advantages of representative improved approaches
Fig.4  Reaction mode of MDA in different systems.
Fig.5  Some innovative droplet generation methods.
Fig.6  Schematic diagram of µcMDA.
Evaluation parameter MDA Microreactor MDA Emulsion MDA Micro-channel MDA
Uniformity Low Intermediate High High
Efficiency High Intermediate High High
Equipment requirements Low High High or intermediate Low
Experimental difficulty Low High High or intermediate Intermediate
Tab.3  Comparison between microfluidics-based improved approaches
Fig.7  MDA single-cell genome sequencing process.
1 O. Feinerman, , J. Veiga, , J. R. Dorfman, , R. N. Germain, and G. Altan-Bonnet, (2008) Variability and robustness in T cell activation from regulated heterogeneity in protein levels. Science, 321, 1081–1084
https://doi.org/10.1126/science.1158013 pmid: 18719282
2 T. Hoey, (2010) Drug resistance, epigenetics, and tumor cell heterogeneity. Sci. Transl. Med., 2, 28ps19
https://doi.org/10.1126/scitranslmed.3001056 pmid: 20410528
3 L. Yan, , L. Huang, , L. Xu, , J. Huang, , F. Ma, , X. Zhu, , Y. Tang, , M. Liu, , Y. Lian, , P. Liu, , et al. (2015) Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses. Proc. Natl. Acad. Sci. U.S.A., 112, 15964–15969
https://doi.org/10.1073/pnas.1523297113 pmid: 26712022
4 X. Ni, , M. Zhuo, , Z. Su, , J. Duan, , Y. Gao, , Z. Wang, , C. Zong, , H. Bai, , A. R. Chapman, , J. Zhao, , et al. (2013) Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients. Proc. Natl. Acad. Sci. USA, 110, 21083–21088
https://doi.org/10.1073/pnas.1320659110 pmid: 24324171
5 L. Zhang, , X. Cui, , K. Schmitt, , R. Hubert, , W. Navidi, , and N. Arnheim, (1992) Whole genome amplification from a single cell: implications for genetic analysis. Proc. Natl. Acad. Sci. USA, 89, 5847–5851
6 H. Telenius, , N. P. Carter, , C. E. Bebb, , M. Nordenskjöld, , B. A. J. Ponder, and A. Tunnacliffe, (1992) Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics, 13, 718–725
https://doi.org/10.1016/0888-7543(92)90147-K pmid: 1639399
7 P. M. Lizardi, , X. Huang, , Z. Zhu, , P. Bray-Ward, , D. C. Thomas, and D. C. Ward, (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat. Genet., 19, 225–232
https://doi.org/10.1038/898 pmid: 9662393
8 F. B. Dean, , S. Hosono, , L. Fang, , X. Wu, , A. F. Faruqi, , P. Bray-Ward, , Z. Sun, , Q. Zong, , Y. Du, , J. Du, , et al. (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. USA, 99, 5261–5266
https://doi.org/10.1073/pnas.082089499 pmid: 11959976
9 C. Zong, , S. Lu, , A. R. Chapman, and X. S. Xie, (2012) Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science, 338, 1622–1626
https://doi.org/10.1126/science.1229164 pmid: 23258894
10 C. Chen, , D. Xing, , L. Tan, , H. Li, , G. Zhou, , L. Huang, and X. S. Xie, (2017) Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI). Science, 356, 189–194
https://doi.org/10.1126/science.aak9787 pmid: 28408603
11 L. Huang, , F. Ma, , A. Chapman, , S. Lu, and X. S. Xie, (2015) Single-cell whole-genome amplification and sequencing: methodology and applications. Annu. Rev. Genomics Hum. Genet., 16, 79–102
https://doi.org/10.1146/annurev-genom-090413-025352 pmid: 26077818
12 C. Gawad, , W. Koh, and S. R. Quake, (2016) Single-cell genome sequencing: current state of the science. Nat. Rev. Genet., 17, 175–188
https://doi.org/10.1038/nrg.2015.16 pmid: 26806412
13 J. C. Detter, , J. M. Jett, , S. M. Lucas, , E. Dalin, , A. R. Arellano, , M. Wang, , J. R. Nelson, , J. Chapman, , Y. Lou, , D. Rokhsar, , et al. (2002) Isothermal strand-displacement amplification applications for high-throughput genomics. Genomics, 80, 691–698
https://doi.org/10.1006/geno.2002.7020 pmid: 12523365
14 Y. Fu, , C. Li, , S. Lu, , W. Zhou, , F. Tang, , X. S. Xie, and Y. Huang, (2015) Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification. Proc. Natl. Acad. Sci. USA, 112, 11923–11928
https://doi.org/10.1073/pnas.1513988112 pmid: 26340991
15 K. N. Ballantyne, , R. A. H. van Oorschot, , R. John Mitchell, and I. Koukoulas, (2006) Molecular crowding increases the amplification success of multiple displacement amplification and short tandem repeat genotyping. Anal. Biochem., 355, 298–303
https://doi.org/10.1016/j.ab.2006.04.039 pmid: 16737679
16 G. de Cesare, , A. Nascetti, and D. Caputo, (2015) Amorphous silicon p-i-n structure acting as light and temperature sensor. Sensors (Basel), 15, 12260–12272
https://doi.org/10.3390/s150612260 pmid: 26016913
17 B. B. Bruijns, , F. Costantini, , N. Lovecchio, , R. M. Tiggelaar, , G. Di Timoteo, , A. Nascetti, , G. de Cesare, , J. G. E. Gardeniers, and D. Caputo, (2019) On-chip real-time monitoring of multiple displacement amplification of DNA. Sens. Actuators B Chem., 293, 16–22
https://doi.org/10.1016/j.snb.2019.04.144
18 X. Y. Li, , Y. C. Du, , Y. P. Zhang, and D. M. Kong, (2017) Dual functional Phi29 DNA polymerase-triggered exponential rolling circle amplification for sequence-specific detection of target DNA embedded in long-stranded genomic DNA. Sci. Rep., 7, 6263
https://doi.org/10.1038/s41598-017-06594-1 pmid: 28740223
19 B. J. Toley, , I. Covelli, , Y. Belousov, , S. Ramachandran, , E. Kline, , N. Scarr, , N. Vermeulen, , W. Mahoney, , B. R. Lutz, and P. Yager, (2015) Isothermal strand displacement amplification (iSDA): a rapid and sensitive method of nucleic acid amplification for point-of-care diagnosis. Analyst (Lond.), 140, 7540–7549
https://doi.org/10.1039/C5AN01632K pmid: 26393240
20 L. Blanco, , A. Bernad, , J. M. Lázaro, , G. Martín, , C. Garmendia, and M. Salas, (1989) Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J. Biol. Chem., 264, 8935–8940
pmid: 2498321
21 A. H. Handyside, , M. D. Robinson, , R. J. Simpson, , M. B. Omar, , M. A. Shaw, , J. G. Grudzinskas, and A. Rutherford, (2004) Isothermal whole genome amplification from single and small numbers of cells: a new era for preimplantation genetic diagnosis of inherited disease. Mol. Hum. Reprod., 10, 767–772
https://doi.org/10.1093/molehr/gah101 pmid: 15322224
22 J. Banér, , M. Nilsson, , M. Mendel-Hartvig, and U. Landegren, (1998) Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res., 26, 5073–5078
https://doi.org/10.1093/nar/26.22.5073 pmid: 9801302
23 T. Krzywkowski, , M. Kühnemund, , D. Wu, and M. Nilsson, (2018) Limited reverse transcriptase activity of phi29 DNA polymerase. Nucleic Acids Res., 46, 3625–3632
https://doi.org/10.1093/nar/gky190 pmid: 29554297
24 S. Coskun, and O. Alsmadi, (2007) Whole genome amplification from a single cell: a new era for preimplantation genetic diagnosis. Prenat. Diagn., 27, 297–302
https://doi.org/10.1002/pd.1667 pmid: 17278176
25 C. Spits, , C. Le Caignec, , M. De Rycke, , L. Van Haute, , A. Van Steirteghem, , I. Liebaers, and K. Sermon, (2006) Optimization and evaluation of single-cell whole-genome multiple displacement amplification. Hum. Mutat., 27, 496–503
https://doi.org/10.1002/humu.20324 pmid: 16619243
26 A. del Prado, , I. Rodríguez, , J. M. Lázaro, , M. Moreno-Morcillo, , M. de Vega, and M. Salas, (2019) New insights into the coordination between the polymerization and 3′-5′ exonuclease activities in f29 DNA polymerase. Sci. Rep., 9, 923
https://doi.org/10.1038/s41598-018-37513-7. pmid: 30696917
27 M. Xu, (2015) Patent CN 104560950A
28 W. Huang, , H. Cai, , S. Wei, , X. Bo, and F. Li, (2016) MDAGenera: an efficient and accurate simulator for multiple displacement amplification. In: Intelligent Computing Theories and Application, Huang, D.S., Bevilacqua, V., Premaratne, P. (eds.),pp. 258–267. Springer, Cham
29 E. Tenaglia, , Y. Imaizumi, , Y. Miyahara, and C. Guiducci, (2018) Isothermal multiple displacement amplification of DNA templates in minimally buffered conditions using phi29 polymerase. Chem. Commun. (Camb.), 54, 2158–2161
https://doi.org/10.1039/C7CC09609G pmid: 29431761
30 G. Wang, , C. Brennan, , M. Rook, , J. L. Wolfe, , C. Leo, , L. Chin, , H. Pan, , W. H. Liu, , B. Price, and G. M. Makrigiorgos, (2004) Balanced-PCR amplification allows unbiased identification of genomic copy changes in minute cell and tissue samples. Nucleic Acids Res., 32, e76
https://doi.org/10.1093/nar/gnh070 pmid: 15155823
31 A. W. Bergen, , K. A. Haque, , Y. Qi, , M. B. Beerman, , M. Garcia-Closas, , N. Rothman, and S. J. Chanock, (2005) Comparison of yield and genotyping performance of multiple displacement amplification and OmniPlex whole genome amplified DNA generated from multiple DNA sources. Hum. Mutat., 26, 262–270
https://doi.org/10.1002/humu.20213 pmid: 16086324
32 L. Lovmar, , M. Fredriksson, , U. Liljedahl, , S. Sigurdsson, and A. C. Syvänen, (2003) Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA. Nucleic Acids Res., 31, e129
https://doi.org/10.1093/nar/gng129 pmid: 14576329
33 T. L. Hawkins, , J. C. Detter, and P. M. Richardson, (2002) Whole genome amplification–applications and advances. Curr. Opin. Biotechnol., 13, 65–67
https://doi.org/10.1016/S0958-1669(02)00286-0 pmid: 11849960
34 R. S. Lasken, , M. Egholm, and O. A. Alsmadi, (2004) Patent US 9487823B2
35 G. M. G. Theunissen, , B. Rolf, , A. Gibb, and R. Jäger, (2017) DNA profiling of sperm cells by using micromanipulation and whole genome amplification. Forensic Sci. International. Genet. Suppl. Ser., 6, e497–e499.
https://doi.org/10.1016/j.fsigss.2017.09.183
36 R. S. Lasken, (2013) Single-cell sequencing in its prime. Nat. Biotechnol., 31, 211–212
https://doi.org/10.1038/nbt.2523 pmid: 23471069
37 C. F. de Bourcy, , I. De Vlaminck, , J. N. Kanbar, , J. Wang, , C. Gawad, and S. R. Quake, (2014) A quantitative comparison of single-cell whole genome amplification methods. PLoS One, 9, e105585
https://doi.org/10.1371/journal.pone.0105585 pmid: 25136831
38 W. Liu, , H. Zhang, , D. Hu, , S. Lu, and X. Sun, (2018) The performance of MALBAC and MDA methods in the identification of concurrent mutations and aneuploidy screening to diagnose beta-thalassaemia disorders at the single- and multiple-cell levels. J. Clin. Lab. Anal., 32, e22267
https://doi.org/10.1002/jcla.22267 pmid: 28548214
39 J. del Rey, , F. Vidal, , L. Ramírez, , N. Borràs, , I. Corrales, , I. Garcia, , O. Martinez-Pasarell, , S. F. Fernandez, , R. Garcia-Cruz, , A. Pujol, , et al. (2018) Novel Double Factor PGT strategy analyzing blastocyst stage embryos in a single NGS procedure. PLoS One, 13, e0205692
https://doi.org/10.1371/journal.pone.0205692 pmid: 30332465
40 F. He, , W. Zhou, , R. Cai, , T. Yan, and X. Xu, (2018) Systematic assessment of the performance of whole-genome amplification for SNP/CNV detection and β-thalassemia genotyping. J. Hum. Genet., 63, 407–416
https://doi.org/10.1038/s10038-018-0411-5 pmid: 29440707
41 C. Li, , Z. Yu, , Y. Fu, , Y. Pang, and Y. Huang, (2017) Single-cell-based platform for copy number variation profiling through digital counting of amplified genomic DNA fragments. ACS Appl. Mater. Interfaces, 9, 13958–13964
https://doi.org/10.1021/acsami.7b03146 pmid: 28337907
42 X. Pan, and X. Liang, (2014) Principle of whole genome amplification technology and its progress. Biotechnology Bulletin, 12, 47–54, in Chinese
43 Y. Hou, , W. Fan, , L. Yan, , R. Li, , Y. Lian, , J. Huang, , J. Li, , L. Xu, , F. Tang, , X. S. Xie, , et al. (2013) Genome analyses of single human oocytes. Cell, 155, 1492–1506
https://doi.org/10.1016/j.cell.2013.11.040 pmid: 24360273
44 W. K. Chu, , P. Edge, , H. S. Lee, , V. Bansal, , V. Bafna, , X. Huang, and K. Zhang, (2017) Ultraaccurate genome sequencing and haplotyping of single human cells. Proc. Natl. Acad. Sci. U.S.A., 114, 12512–12517
https://doi.org/10.1073/pnas.1707609114 pmid: 29078313
45 P. C. Blainey, and S. R. Quake, (2011) Digital MDA for enumeration of total nucleic acid contamination. Nucleic Acids Res., 39, e19
https://doi.org/10.1093/nar/gkq1074 pmid: 21071419
46 W. Wang, , Y. Ren, , Y. Lu, , Y. Xu, , S. D. Crosby, , A. M. Di Bisceglie, and X. Fan, (2017) Template-dependent multiple displacement amplification for profiling human circulating RNA. Biotechniques, 63, 21–27
https://doi.org/10.2144/000114566 pmid: 28701144
47 A. Guria, , K. Velayudha Vimala Kumar, , N. Srikakulam, , A. Krishnamma, , S. Chanda, , S. Sharma, , X. Fan, and G. Pandi, (2019) Circular RNA profiling by Illumina sequencing via template-dependent multiple displacement amplification. BioMed Res. Int., 2019, 2756516
https://doi.org/10.1155/2019/2756516 pmid: 30834258
48 Á. J. Picher, , B. Budeus, , O. Wafzig, , C. Krüger, , S. García-Gémez, , M. I. Martínez-Jimónez, , A. Díaz-Talavera, , D. Weber, , L. Blanco, and A. Schneider, (2016) TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol. Nat. Commun., 7, 13296
https://doi.org/10.1038/ncomms13296 pmid: 27897270
49 C. Rinke, , P. Schwientek, , A. Sczyrba, , N. N. Ivanova, , I. J. Anderson, , J. F. Cheng, , A. Darling, , S. Malfatti, , B. K. Swan, , E. A. Gies, , et al. (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499, 431–437
https://doi.org/10.1038/nature12352 pmid: 23851394
50 R. Stepanauskas, , E. A. Fergusson, , J. Brown, , N. J. Poulton, , B. Tupper, , J. M. Labonté, , E. D. Becraft, , J. M. Brown, , M. G. Pachiadaki, , T. Povilaitis, , et al. (2017) Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles. Nat. Commun., 8, 84
https://doi.org/10.1038/s41467-017-00128-z pmid: 28729688
51 C. Gawad. , , J. Easton, and V. Gonzalez-pena, (2019) Patent WO 2019/148119 A1
52 Y. Marcy, , T. Ishoey, , R. S. Lasken, , T. B. Stockwell, , B. P. Walenz, , A. L. Halpern, , K. Y. Beeson, , S. M. D. Goldberg, and S. R. Quake, (2007) Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet., 3, 1702–1708
https://doi.org/10.1371/journal.pgen.0030155 pmid: 17892324
53 J. Gole, , A. Gore, , A. Richards, , Y. J. Chiu, , H. L. Fung, , D. Bushman, , H. I. Chiang, , J. Chun, , Y. H. Lo, and K. Zhang, (2013) Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat. Biotechnol., 31, 1126–1132
https://doi.org/10.1038/nbt.2720 pmid: 24213699
54 M. Hosokawa, , Y. Nishikawa, , M. Kogawa, and H. Takeyama, (2017) Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics. Sci. Rep., 7, 5111–5199
https://doi.org/10.1038/s41598-017-05436-4 pmid: 28701744
55 A. M. Sidore, , F. Lan, , S. W. Lim, and A. R. Abate, (2016) Enhanced sequencing coverage with digital droplet multiple displacement amplification. Nucleic Acids Res., 44, e66
https://doi.org/10.1093/nar/gkv1493 pmid: 26704978
56 M. Rhee, , Y. K. Light, , R. J. Meagher, and A. K. Singh, (2016) Digital Droplet Multiple Displacement Amplification (ddMDA) for whole genome sequencing of limited DNA samples. PLoS One, 11, e0153699
https://doi.org/10.1371/journal.pone.0153699 pmid: 27144304
57 Z. Chen, , Y. Fu, , F. Zhang, , L. Liu,, , N. Zhang, , D. Zhou, , J. Yang, , Y. Pang, and Y. Huang, (2016) Spinning micropipette liquid emulsion generator for single cell whole genome amplification. Lab Chip, 16, 4512–4516
https://doi.org/10.1039/C6LC01084A pmid: 27775138
58 Y. Fu, , F. Zhang, , X. Zhang, , J. Yin, , M. Du, , M. Jiang, , L. Liu, , J. Li, , Y. Huang, and J. Wang, (2019) High-throughput single-cell whole-genome amplification through centrifugal emulsification and eMDA. Commun. Biol., 2, 147
https://doi.org/10.1038/s42003-019-0401-y pmid: 31044172
59 S. C. Kim, , G. Premasekharan, , I. C. Clark, , H. B. Gemeda, , P. L. Paris, and A. R. Abate, (2017) Measurement of copy number variation in single cancer cells using rapid-emulsification digital droplet MDA. Microsyst. Nanoeng., 3, 17018
https://doi.org/10.1038/micronano.2017.18 pmid: 30147985
60 Z. Chen, , P. Liao, , F. Zhang, , M. Jiang, , Y. Zhu, and Y. Huang, (2017) Centrifugal micro-channel array droplet generation for highly parallel digital PCR. Lab Chip, 17, 235–240
https://doi.org/10.1039/C6LC01305H pmid: 28009866
61 J. Li, , N. Lu, , X. Shi, , Y. Qiao, , L. Chen, , M. Duan, , Y. Hou, , Q. Ge, , Y. Tao, , J. Tu, , et al. (2017) 1D-reactor decentralized MDA for uniform and accurate whole genome amplification. Anal. Chem., 89, 10147–10152
https://doi.org/10.1021/acs.analchem.7b02183 pmid: 28853542
62 J. Li, , N. Lu, , Y. Tao, , M. Duan,, , Y. Qiao, , Y. Xu, , Q. Ge, , C. Bi, , J. Fu, , J. Tu, , et al. (2018) Accurate and sensitive single-cell-level detection of copy number variations by micro-channel multiple displacement amplification (mcMDA). Nanoscale, 10, 17933–17941
https://doi.org/10.1039/C8NR04917C pmid: 30226245
63 D. Zhu, , Y. Yan, , P. Lei, , B. Shen, , W. Cheng, , H. Ju, and S. Ding, (2014) A novel electrochemical sensing strategy for rapid and ultrasensitive detection of Salmonella by rolling circle amplification and DNA-AuNPs probe. Anal. Chim. Acta, 846, 44–50
https://doi.org/10.1016/j.aca.2014.07.024 pmid: 25220140
64 R. M. Bowers, , N. C. Kyrpides, , R. Stepanauskas, , M. Harmon-Smith, , D. Doud, , T. B. K. Reddy, , F. Schulz, , J. Jarett, , A. R. Rivers, , E. A. Eloe-Fadrosh, , et al. (2017) Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol., 35, 725–731
https://doi.org/10.1038/nbt.3893 pmid: 28787424
65 Y. Liu, , J. Yao, and M. Walther-Antonio, (2019) Whole genome amplification of single epithelial cells dissociated from snap-frozen tissue samples in microfluidic platform. Biomicrofluidics, 13, 034109
https://doi.org/10.1063/1.5090235 pmid: 31149320
66 M. Chen, , J. Zhang, , J. Zhao, , T. Chen, , Z. Liu, , F. Cheng, , Q. Fan, and J. Yan, (2020) Comparison of CE- and MPS-based analyses of forensic markers in a single cell after whole genome amplification. Forensic Sci. Int. Genet., 45, 102211
https://doi.org/10.1016/j.fsigen.2019.102211 pmid: 31812097
67 B. Bruijns, , A. Veciana, , R. Tiggelaar, and H. Gardeniers, (2019) Cyclic olefin copolymer microfluidic devices for forensic applications. Biosensors (Basel), 9, 85
https://doi.org/10.3390/bios9030085 pmid: 31277382
68 K. A. Lipinski, , L. J. Barber, , M. N. Davies, , M. Ashenden, , A. Sottoriva, and M. Gerlinger, (2016) Cancer evolution and the limits of predictability in precision cancer medicine. Trends Cancer, 2, 49–63
https://doi.org/10.1016/j.trecan.2015.11.003 pmid: 26949746
69 X. Xu, , Y. Hou, , X. Yin, , L. Bao, , A. Tang, , L. Song, , F. Li, , S. Tsang, , K. Wu,, , H. Wu, , et al. (2012) Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell, 148, 886–895
https://doi.org/10.1016/j.cell.2012.02.025 pmid: 22385958
70 Y. Hou, , L. Song, , P. Zhu, , B. Zhang, , Y. Tao, , X. Xu, , F. Li, , K. Wu, , J. Liang, , D. Shao, , et al. (2012) Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell, 148, 873–885
https://doi.org/10.1016/j.cell.2012.02.028 pmid: 22385957
71 Y. Wang, , J. Waters, , M. L. Leung, , A. Unruh, , W. Roh, , X. Shi, , K. Chen, , P. Scheet, , S. Vattathil, , H. Liang, , et al. (2014) Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature, 512, 155–160
https://doi.org/10.1038/nature13600 pmid: 25079324
72 H. E. Liu, , M. Triboulet, , A. Zia, , M. Vuppalapaty, , E. Kidess-Sigal, , J. Coller, , V. S. Natu, , V. Shokoohi, , J. Che, , C. Renier, , et al. (2017) Workflow optimization of whole genome amplification and targeted panel sequencing for CTC mutation detection. NPJ Genom. Med., 2, 34
https://doi.org/10.1038/s41525-017-0034-3 pmid: 29263843
73 A. Edwards, , A. Civitello, , H. A. Hammond, and C. T. Caskey, (1991) DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am. J. Hum. Genet., 49, 746–756
pmid: 1897522
74 L. Deleye, , A. S. Vander Plaetsen, , J. Weymaere, , D. Deforce, and F. Van Nieuwerburgh, (2018) Short tandem repeat analysis after whole genome amplification of single B-lymphoblastoid cells. Sci. Rep., 8, 1255
https://doi.org/10.1038/s41598-018-19509-5 pmid: 29352241
75 Y. Michikawa, , K. Sugahara, , T. Suga, , Y. Ohtsuka, , K. Ishikawa, , A. Ishikawa, , N. Shiomi, , T. Shiomi, , M. Iwakawa, and T. Imai, (2008) In-gel multiple displacement amplification of long DNA fragments diluted to the single molecule level. Anal. Biochem., 383, 151–158
https://doi.org/10.1016/j.ab.2008.08.011 pmid: 18768135
76 L. Deleye, , Y. Gansemans, , D. De Coninck, , F. Van Nieuwerburgh, , andD Deforce, (2018) Massively parallel sequencing of micro-manipulated cells targeting a comprehensive panel of disease-causing genes: A comparative evaluation of upstream whole-genome amplification methods. PLoS One, 13, e0196334
https://doi.org/10.1371/journal.pone.0196334 pmid: 29698522
77 R. G. Edwards, and R. L. Gardner, (1967) Sexing of live rabbit blastocysts. Nature, 214, 576–577
https://doi.org/10.1038/214576a0 pmid: 6036172
78 A. Hellani, , S. Coskun, , M. Benkhalifa, , A. Tbakhi, , N. Sakati, , A. Al-Odaib, and P. Ozand, (2004) Multiple displacement amplification on single cell and possible PGD applications. Mol. Hum. Reprod., 10, 847–852
https://doi.org/10.1093/molehr/gah114 pmid: 15465849
79 A. Hellani, , S. Coskun, , A. Tbakhi, and S. Al-Hassan, (2005) Clinical application of multiple displacement amplification in preimplantation genetic diagnosis. Reprod. Biomed. Online, 10, 376–380
https://doi.org/10.1016/S1472-6483(10)61799-3 pmid: 15820046
80 Y. Lu, , H. Peng, , Z. Jin, , J. Cheng,, , S. Wang, , M. Ma, , Y. Lu, , D. Han, , Y. Yao, , Y. Li, , et al. (2013) Preimplantation genetic diagnosis for a Chinese family with autosomal recessive Meckel-Gruber syndrome type 3 (MKS3). PLoS One, 8, e73245
https://doi.org/10.1371/journal.pone.0073245 pmid: 24039893
81 X. Shen, , D. Chen, , Y. Xu, , Y. Fu, and C. Zhou, (2019) Preimplantation genetic testing of achondroplasia by two haplotyping systems: short tandem repeats and single nucleotide polymorphism. Biochip J., 13, 165–173.
https://doi.org/10.1007/s13206-018-3207-y
82 L. Chen, , Z. Diao, , Z. Xu, , J. Zhou, , G. Yan, and H. Sun, (2017) The clinical application of NGS-based SNP haplotyping for PGD of Hb H disease. Syst Biol Reprod Med, 63, 212–217
https://doi.org/10.1080/19396368.2017.1296501 pmid: 28340305
83 S. C. Chen, , X. L. Xu, , J. Y. Zhang, , G. L. Ding, , L. Jin, , B. Liu, , D. M. Sun, , C. L. Mei, , X. N. Yang, , H. F. Huang, , et al. (2016) Identification of PKD2 mutations in human preimplantation embryos in vitro using a combination of targeted next-generation sequencing and targeted haplotyping. Sci. Rep., 6, 25488
https://doi.org/10.1038/srep25488 pmid: 27150309
84 M. Konstantinidis, , R. Prates, , N. N. Goodall, , J. Fischer, , V. Tecson, , T. Lemma, , B. Chu, , A. Jordan, , E. Armenti, , D. Wells, , et al. (2015) Live births following Karyomapping of human blastocysts: experience from clinical application of the method. Reprod. Biomed. Online, 31, 394–403
https://doi.org/10.1016/j.rbmo.2015.05.018 pmid: 26206283
85 A. R. Thornhill, , A. H. Handyside, , C. Ottolini, , S. A. Natesan, , J. Taylor, , K. Sage, , G. Harton, , K. Cliffe, , N. Affara, , M. Konstantinidis, , et al. (2015) Karyomapping-a comprehensive means of simultaneous monogenic and cytogenetic PGD: comparison with standard approaches in real time for Marfan syndrome. J. Assist. Reprod. Genet., 32, 347–356
https://doi.org/10.1007/s10815-014-0405-y pmid: 25561157
86 M. Davison, , E. Hall, , R. Zare, and D. Bhaya, (2015) Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity. Photosynth. Res., 126, 135–146
https://doi.org/10.1007/s11120-014-0066-9 pmid: 25515769
87 J. Tu, , L. Chen, , S. Gao, , J. Zhang, , C. Bi, , Y. Tao, , N. Lu, and Z. Lu, (2019) Obtaining genome sequences of mutualistic bacteria in single Microcystis colonies. Int. J. Mol. Sci., 20, 5047
https://doi.org/10.3390/ijms20205047 pmid: 31614621
88 M. Parras-Moltó, , A. Rodríguez-Galet, , P. Suárez-Rodríguez, and A. López-Bueno, (2018) Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses. Microbiome, 6, 119
https://doi.org/10.1186/s40168-018-0507-3 pmid: 29954453
89 N. E. Brinkman, , E. N. Villegas, , J. L. Garland, and S. P. Keely, (2018) Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater. PLoS One, 13, e0195350
https://doi.org/10.1371/journal.pone.0195350 pmid: 29614100
90 M. Hammond, , F. Homa, , H. Andersson-Svahn, , T. J. G. Ettema, and H. N. Joensson, (2016) Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis. Microbiome, 4, 52
https://doi.org/10.1186/s40168-016-0197-7 pmid: 27716450
91 H. W. Veltkamp, , F. Akegawa Monteiro, , R. Sanders, , R. Wiegerink, and J. Lötters, (2020) Disposable DNA amplification chips with integrated low-cost heaters dagger. Micromachines (Basel), 11, 238
https://doi.org/10.3390/mi11030238 pmid: 32106462
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed