High throughput SNP detection system based on magnetic nanoparticles separation

Journal of Biomedical Nanotechnology

Volumn 9, Issue 2, 2013, Pages 247-256

  Liu, Bin ^a   Jia, Yingying ^a   Ma, Man ^a   Li, Zhiyang ^a,c,d   Liu, Hongna ^a,d   Li, Song ^b   Deng, Yan ^a,b   Zhang, Liming ^a,b   Lu, Zhuoxuan ^a,b   Wang, Wei ^d   He, Nongyue ^a,b,d  

^a SOUTHEAST UNIVERSITY   (China)

^b HUNAN UNIVERSITY OF TECHNOLOGY   (China)

^c YANGTZE UNIVERSITY   (China)

^d Nanjing Longliang Biological Science and Technology Limited Company   (China)

Author keywords

High Throughput Nucleic Acid Detection; Magnetic Particles Separation; SNP

Indexed keywords

MAGNETIC NANO-PARTICLES; MAGNETIC NANOPARTI CLES (MNPS); MAGNETIC PARTICLE; NUCLEIC ACID DETECTION; OPTICAL SIGNAL DETECTION; SINGLE-NUCLEOTIDE POLYMORPHISMS; SNP; TEMPERATURE CONTROL UNIT;

DIAGNOSIS; EXPERIMENTS; GENES; MAGNETIC SEPARATION; NANOPARTICLES; POLYMERASE CHAIN REACTION; SEPARATION;

THROUGHPUT;

CYANINE DYE 3; CYCLOOXYGENASE 2; DNA POLYMERASE; GENOMIC DNA; MAGNETIC NANOPARTICLE;

ARTICLE; CONTROLLED STUDY; DNA HYBRIDIZATION; FLUORESCENCE; GENETIC ASSOCIATION; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN TISSUE; LIGHT EMITTING DIODE; MAGNETIC SEPARATION; MEASUREMENT ACCURACY; NUCLEIC ACID ANALYSIS; POLYMERASE CHAIN REACTION; PROMOTER REGION; SIGNAL DETECTION; SIGNAL PROCESSING; SINGLE NUCLEOTIDE POLYMORPHISM;

ADULT; AUTOMATION; DNA; FLUORESCENCE; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MAGNETITE NANOPARTICLES; MICROCHEMISTRY; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SIGNAL PROCESSING, COMPUTER-ASSISTED; TEMPERATURE;

EID: 84876549832     PISSN: 15507033     EISSN: 15507041     Source Type: Journal    
DOI: 10.1166/jbn.2013.1483     Document Type: Article

References (60)

1. R. Sachidanandam, D. Weissman, S. C. Schmidt, J. M. Kakol, L. D. Stein, G. Marth, S. Sherry, J. C. Mullikin, B. J. Mortimore, D. L. Willey, S. E. Hunt, C. G. Cole, P. C. Coggill, C. M. Rice, Z. M. Ning, J. Rogers, D. R. Bentley, P. Y. Kwok, E. R. Mardis, R. T. Yeh, B. Schultz, L. Cook, R. Davenport, M. Dante, L. Fulton, L. Hillier, R. H. Waterston, J. D. McPherson, B. Gilman, S. Schaffner, W. J. Van Etten, D. Reich, J. Higgins, M. J. Daly, B. Blumenstiel, J. Baldwin, N. S. Stange-Thomann, M. C. Zody, L. Linton, E. S. Lander, and D. Altshuler, A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928 (2001).
2. D. G. Wang, J. B. Fan, C. J. Siao, A. Berno, P. Young, R. Sapolsky, G. Ghandour, N. Perkins, E. Winchester, J. Spencer, L. Kruglyak, L. Stein, L. Hsie, T. Topaloglou, E. Hubbell, E. Robinson, M. Mittmann, M. S. Morris, N. P. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, Selecting a maximally informative set of singlenucleotide polymorphisms for association analyses using linkage disequilibrium. Science 74, 106 (2004).
3. G. L. Bond, W. W. Hu, E. E. Bond, H. Robins, S. G. Lutzker, N. C. Arva, J. Bargonetti, F. Bartel, H. Taubert, P. Wuerl, K. Onel, L. Yip, S. J. Hwang, L. C. Strong, G. Lozano, and A. J. Levine, A single nucleotide polymorphism in the MDM2 promoter attenuates the p53 tumor suppressor pathway and accelerates tumor formation in humans. Cell 119, 591 (2004).
4. Y. Nannya, M. Sanada, K. Nakazaki, N. Hosoya, L. L. Wang, A. Hangaishi, M. Kurokawa, S. Chiba, D. K. Bailey, G. C. Kennedy, and S. Ogawa, A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res. 65, 6071 (2005).
5. F. Wang, C. Ma, X. Zeng, C. Y. Li, Y. Deng, and N. Y. He, Chemiluminescence molecular detection of sequence-specific HBVDNA using magnetic nanoparticles. J. Biomed. Nanotechnol. 8, 786 (2012).
6. D. Šponarová, D. Horák, M. Trchová, P. Jendelová, V. Herynek, N. Mitina, A. Zaichenko, R. Stoika, P. Lesný, and E. Syková, The use of oligoperoxide-coated magnetic nanoparticles to label stem cells. J. Biomed. Nanotechnol. 7, 384 (2011).
7. K. R. Loeb, K. R. Jerome, J. Goddard, M. Huang, A. Cent, and L. Corey, High-throughput quantitative analysis of hepatitis B virus DNA in serum using the taqman fluorogenic detection system. Hepatology 32, 626 (2000).
8. S. Tyagi and F. R. Kramer, Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303 (1996).
9. A. Ahmadian, B. Gharizadeh, A. C. Gustafsson, F. Sterky, P. Nyrén, M. Uhlén, and J. Lundeberg, Single-nucleotide polymorphism analysis by pyrosequencing. Anal. Biochem. 280, 103 (2000).
10. D. A. Nickerson, R. Kaiser, S. Lappin, J. Stewart, L. Hood, and U. Landegren, Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay. P. Natl. Acad. Sci. USA 87, 8923 (1990).
11. R. L. Somorjai, B. Dolenko, and R. Baumgartner, Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: Curses, caveats, cautions. Bioinformatics 19, 1484 (2003).
12. S. Li, H. N. Liu, Z. F. Wang, P. Hou, Y. F. Guo, Q. G. He, and N. Y. He, Magnetic-particles-based high-throughput genotyping method with dual-color fluorescence hybridization. Anal. Biochem. 359, 277 (2006).
13. H. N. Liu, S. Li, Z. F. Wang, M. J. Ji, L. B. Nie, and N. Y. He, Highthroughput SNP genotyping based on solid-phase PCR on magnetic nanoparticles with dual-color hybridization. J. Biotechnol. 131, 217 (2007).
14. H. N. Liu, S. Li, L. Tian, L. S. Liu, and N. Y. He, A novel single nucleotide polymorphisms detection sensors based on magnetic nanoparticles array and dual-color single base extension. J. Nanosci. Nanotechnol. 10, 5311 (2010).
15. S. Li, H. N. Liu, L. S. Liu, L. Tian, and N. Y. He, A novel automated assay with dual-color hybridization for single-nucleotide polymorphisms genotyping on gold magnetic nanoparticle array. Anal. Biochem. 405, 141 (2010).
16. H. N. Liu, S. Li, M. J. Ji, L. B. Nie, J. R. Chen, Y. Q. Miao, and N. Y. He, Fabrication and application of single nucleotide polymorphisms library on magnetic nanoparticles using adaptor PCR. J. Nanosci. Nanotechnol. 8, 405 (2008).
17. Z. Y. Li, L. He, N. Y. He, Z. Y. Shi, H. Wang, S. Li, H. N. Liu, Y. B. Dai, and Z. F. Wang, Chemiluminescent detect of E.coli O157:H7 using immunological method based on magnetic nanoparticles. J. Nanosci. Nanotechnol. 10, 696 (2010).
18. 4- nanoparticles and its application in detecting E.coli O157:H7 using chemiluminescent immunological method. J. Biomed. Nanotechnol. 5, 505 (2009).
19. Z. Y. Li, L. He, N. Y. He, Z. Y. Shi, S. Li, H. N. Liu, and Y. B. Dai, An applied approach in detecting E.coil O157:H7 using immunological method based on chemiluminescence and magnetic nanoparticles. Acta. Chim. Sinica 68, 251 (2010).
20. Z. Y. Li, L. He, N. Y. He, Y. Deng, Z. Y. Shi, H. Wang, S. Li, H. N. Liu, Z. F. Wang, and D. X. Wang, Polymerase chain reaction coupling with magnetic nanoparticles-based biotin-avidin system for amplification of chemiluminescent detection signals of nucleic acid. J. Nanosci. Nanotechnol. 11, 1074 (2011).
21. 4 nanoparticles via miniemulsion polymerization. J. Biomed. Nanotechnol. 5, 596 (2009).
22. L. Tian, S. Li, H. N. Liu, Z. F. Wang, and N. Y. He, An automated magStation for high-throughput single nucleotide polymorphism genotyping and the dual-color hybridization. J. Biomed. Nanotechnol. 5, 1 (2009).
23. 4- nanoparticles using linolenic acid as crosslink agent for nucleic acid detection using chemiluminescent method. J. Nanosci. Nanotechnol. 11, 2256 (2011).
24. B. Liu, L. L. Guo, Y. Deng, B. B. Zhang, and N. Y. He (eds.), Bioelectronics and Bioinformatics (ISBB), 2011 International Symposium, Suzhou, China, November (2011), pp. 3-5.
25. H. N. Liu, S. Li, L. S. Liu, L. Tian, and N. Y. He, An integrated and sensitive detection platform for biosensing application based on Fe@Au magnetic nanoparticles as bead array carries. Biosens. Bioelectron. 26, 1442 (2010).
26. Q. L. Wang, L. Xiao, J. Zhang, N. Y. He, X. G. Lu, P. Li, and K. Li, A new assay for CCR5del32 mutation: Genotyping through the number of fragments amplified. J. Biomed. Nanotechnol. 7, 754 (2011).
27. E. Erdal, D. Kavaz, M. Sam, M. Demirbilek, M. E. Demirbilek, N. Saglam, and E. B. Denkbas, Preparation and characterization of magnetically responsive bacterial polyester based nanospheres for cancer therapy. J. Biomed. Nanotechnol. 8, 800 (2012).
28. M. Q. Wang, J. X. Zhang, Z. M. Yuan, W. Z. Yang, Q. Wu, and H. C. Gu, Targeted thrombolysis by using of magnetic mesoporous silica nanoparticles. J. Biomed. Nanotechnol. 8, 624 (2012).
29. H. J. Lee, Y. T. C. Nguyen, M. Muthiah, H. Vu-Quang, R. Namgung, W. J. Kim, M. K. Yu, S. Jon, I. K. Lee, Y. Y. Jeong, and I. K. Park, MR Traceable delivery of p53 tumor suppressor gene by PEI-functionalized superparamagnetic iron oxide nanoparticles. J. Biomed. Nanotechnol. 8, 361 (2012).
30. R. R. Oliveira, F. S. Ferreira, E. R. Cintra, L. C. Branquinho, A. F. Bakuzis, and E. M. Lima, Magnetic nanoparticles and rapamycin encapsulated into polymeric nanocarriers. J. Biomed. Nanotechnol. 8, 193 (2012).
31. L. L. C. Estevanato, L. M. Lacava, L. C. F. Carvalho, R. B. Azevedo, O. Silva, F. Pelegrini, S. N. Báo, P. C. Morais, and Z. G. M. Lacava, Long-term biodistribution and biocompatibility investigation of dextran-coated magnetite nanoparticle using mice as the animal model. J. Biomed. Nanotechnol. 8, 301 (2012).
32. D. de O. C. e Silva, L. L. C. Estevanato, A. R. Simioni, M. M. de A. Rodrigues, B. M. Lacava, Z. G. M. Lacava, A. C. Tedesco, P. C. Morais, and S. N. Báo, Successful strategy for targeting the central nervous system using magnetic albumin nanospheres. J. Biomed. Nanotechnol. 8, 182 (2012).
33. Q. He, L. N. Shao, J. K. Yu, S. X. Ji, H. P. Wang, Y. Y. Mao, and J. H. Chen, Urinary proteome analysis by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry with magnetic beads for identifying the pathologic presentation of clinical early IgA nephropathy. J. Biomed. Nanotechnol. 8, 133 (2012).
34. R. Singh and H. S. Nalwa, Medical applications of nanoparticles in biological imaging, cell labeling, antimicrobial agents, and anticancer nanodrugs. J. Biomed. Nanotechnol. 7, 489 (2011).
35. X. Q. Zhang, L. Jiang, C. L. Zhang, D. Li, C. Wang, F. Gao, and D. X. Cui, A silicon dioxide modified magnetic nanoparticles-labeled lateral flow strips for HBs antigen. J. Biomed. Nanotechnol. 7, 776 (2011).
36. S. Maiti, Nanotoxicity of gold and iron nanoparticles. J. Biomed. Nanotechnol. 7, 65 (2011).
37. H.-X. Ren, L. Liu, C. Liu, S.-Y. He, J. Huang, J.-L. Li, Y. Zhang, X.-J. Huang, and N. Gu, Physiological investigation of magnetic iron oxide nanoparticles towards chinese mung bean. J. Biomed. Nanotechnol. 7, 677 (2011).
38. P. Tallury, S. Santra, P. Sharma, B. M. D. C. Matos, N. Bengtsson, S. Biswas, A. K. Saha, G. A. Walter, E. A. Scott, and B. M. Moudgil, Fluorescent and paramagnetic chitosan nanoparticles that exhibit high magnetic resonance relaxivity: Synthesis, characterization and in vitro studies. J. Biomed. Nanotechnol. 7, 724 (2011).
39. K. W. Huang, S. Y. Yang, C. Y. Yu, J. J. Chieh, C.-C. Yang, H.-E. Horng, C.-Y. Hong, H.-C. Yang, and C.-C. Wu, Exploration of the relationship between the tumor burden and the concentration of vascular endothelial growth factor in liver-cancer-bearing animals using immunomagnetic reduction assay. J. Biomed. Nanotechnol. 7, 535 (2011).
40. M. Naresh, M. Sharma, and A. Mittal, Intracellular magneto-spatial organization of magnetic organelles inside intact bacterial cells. J. Biomed. Nanotechnol. 7, 572 (2011).
41. X. Gao, B. Kan, M. L. Gou, J. Zhang, G. Guo, N. Huang, X. Zhao, and Z. Y. Qian, Preparation of anti-CD40 antibody modified magnetic PCL-PEG-PCL microspheres. J. Biomed. Nanotechnol. 7, 285 (2011).
42. S. P. Singh, Multifunctional magnetic quantum dots for cancer theranostics. J. Biomed. Nanotechnol. 7, 95 (2011).
43. N. Y. He, X. B. Mou, Y. Deng, H. N. Liu, S. Li, L. J. Xu, and X. L. Li, Conditions of PCR amplification by magnetic enrichment and nanoscale detection sensitivity. J. Nanosci. Nanotechnol. 12, 3862 (2012).
44. C. Y. Li, C. Ma, F. Wang, Z. J. Xi, Z. F. Wang, Y. Deng, and N. Y. He, Preparation and biomedical applications of core-shell silica/magnetic nanoparticle composites. J. Nanosci. Nanotechnol. 12, 2964 (2012).
45. 2 magnetic nanoparticles for nucleic acid analysis. J. Nanosci. Nanotechnol. 12, 267 (2012).
46. 4- nanoparticles and micron cubes. J. Nanosci. Nanotechnol. 12, 2939 (2012).
47. 2 core-shell magnetic microspheres for extraction of genomic DNA from human whole blood. J. Nanosci. Nanotechnol. 11, 10295 (2011).
48. M. L. Li, H. S. Kim, L. J. Tian, M. K. Yu, S. Y. Jon, and W. K. Moon, Comparison of two ultrasmall superparamagnetic iron oxides on cytotoxicity and MR imaging of tumors. Theranostics 2, 76 (2012).
49. Q. Zhao, L. N. Wang, R. Cheng, L. D. Mao, R. D. Arnold, E. W. Howerth, Z. G. Chen, and S. Platt, Magnetic nanoparticlebased hyperthermia for head & neck cancer in mouse models. Theranostics 2, 113 (2012).
50. H. L. Shao, C. Min, D. Issadore, M. Liong, T.-J. Yoon, R. Weissleder, and H. Lee, Magnetic nanoparticles and microNMR for diagnostic applications. Theranostics 2, 55 (2012).
51. T. K. Mandal and N. Parvin, Rapid detection of bacteria by carbon quantum dots. J. Biomed. Nanotechnol. 7, 846 (2011).
52. S. L. Sewell, M. M. Higgins, C. S. Bell, and T. D. Giorgio, Quantification of quantum dot concentration using inductively coupled plasma-mass spectrometry (ICP-MS). J. Biomed. Nanotechnol. 7, 685 (2011).
53. R. Wahab, Y. B. Yang, A. Umar, S. Singh, I. H. Hwang, H.-S. Shin, and Y.-S. Kim, Platinum quantum dots and their cytotoxic effect towards myoblast cancer cells (C2C12). J. Biomed. Nanotechnol. 8, 424 (2012).
54. M. Gautam, M. Verma, and G. Misra, Structural and optical properties of ZnO nanocrystals. J. Biomed. Nanotechnol. 7, 161 (2011).
55. V. Sharma, D. Anderson, and A. Dhawan, Zinc oxide nanoparticles induce oxidative stress and genotoxicity in human liver cells (HepG2). J. Biomed. Nanotechnol. 7, 98 (2011).
56. R. D. Umrani and K. M. Paknikar, Ayurvedic medicine Zinc bhasma: Physicochemical evaluation, anti-diabetic activity and safety assessment. J. Biomed. Nanotechnol. 7, 148 (2011).
57. N. Padmavathy and R. Vijayaraghavan, Interaction of ZnO nanoparticles with microbes-a physio and biochemical assay. J. Biomed. Nanotechnol. 7, 813 (2011).
58. K. Choudhari, P. L. Xavier, and T. Pradeep, Size evolution of luminescent lactoferrin protected gold clusters. J. Biomed. Nanotechnol. 7, 70 (2011).
59. A. K. Srivastava, Oxide nanomaterials: Synthesis, microstructure, optical characteristics and bio-applicability. J. Biomed. Nanotechnol. 7, 72 (2011).
60. H. SadAbadi, S. Badilescu, M. Packirisamy, and R. Wüthrich, PDMS-gold nanocomposite platforms with enhanced sensing properties. J. Biomed. Nanotechnol. 8, 539 (2012).