A vertically stacked, polymer, microfluidic point mutation analyzer: Rapid high accuracy detection of low-abundance K-ras mutations

Analytical Biochemistry

Volumn 417, Issue 2, 2011, Pages 211-219

  Han, Kyudong ^a   Lee, Tae Yoon ^b,c   Nikitopoulos, Dimitris E ^c   Soper, Steven A ^c   Murphy, Michael C ^c  

^a Dankook University   (South Korea)

^b LG Electronics Inc   (South Korea)

^c LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

K ras mutation; Ligase detection reaction; Microfluidic system

Indexed keywords

ADHESIVES; DNA; GENES; MICROFLUIDICS;

CLINICAL MANAGEMENT; FUNCTIONAL DEVICES; INDIVIDUAL DEVICES; LIGASE DETECTION REACTIONS; MICRO FLUIDIC SYSTEM; MODULAR ARCHITECTURES; MOLECULAR ANALYSIS; PROCESS AUTOMATION;

POLYMERASE CHAIN REACTION;

GENOMIC DNA; K RAS PROTEIN; POLYCARBONATE; POLYMER;

ALLELE; ANALYTIC METHOD; ANALYZER; ARTICLE; ASSAY; AUTOMATION; CONTINUOUS FLOW REACTOR; CONTROLLED STUDY; FALSE POSITIVE RESULT; GEL ELECTROPHORESIS; HUMAN; HUMAN CELL; LIGASE DETACTION REACTION; MICROFLUIDIC ANALYSIS; MOLECULAR ASSAY; MUTANT; POINT MUTATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PURIFICATION; QUANTITATIVE ANALYSIS; RELIABILITY; WILD TYPE;

EID: 80051546267     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2011.06.030     Document Type: Article

References (53)

1. J.L. Bos The ras gene family and human carcinogenesis Mutat. Res. 195 1988 255 271
2. C. Almoguera, D. Shibata, K. Forrester, J. Martin, N. Arnheim, and M. Perucho Most human carcinomas of the exocrine pancreas contain mutant c-K-ras genes Cell 53 1988 549 554
3. R.H. Hruban, A.D. van Mansfeld, G.J. Offerhaus, D.H. van Weering, D.C. Allison, S.N. Goodman, T.W. Kensler, K.K. Bose, J.L. Cameron, and J.L. Bos K-ras oncogene activation in adenocarcinoma of the human pancreas: a study of 82 carcinomas using a combination of mutant-enriched polymerase chain reaction analysis and allele-specific oligonucleotide hybridization Am. J. Pathol. 143 1993 545 554 (Pubitemid 24058210)
4. V.T. Smit, A.J. Boot, A.M. Smits, G.J. Fleuren, C.J. Cornelisse, and J.L. Bos KRAS codon 12 mutations occur very frequently in pancreatic adenocarcinomas Nucleic Acids Res. 16 1988 7773 7782
5. M. Tada, M. Omata, and M. Ohto Clinical application of ras gene mutation for diagnosis of pancreatic adenocarcinoma Gastroenterology 100 1991 233 238
6. S.N. Andersen, T. Lovig, J. Breivik, E. Lund, G. Gaudernack, G.I. Meling, and T.O. Rognum K-ras mutations and prognosis in large-bowel carcinomas Scand. J. Gastroenterol. 32 1997 62 69 (Pubitemid 27026469)
7. J.M. Chiang Role of K-ras mutations in colorectal carcinoma Cancer Lett. 126 1998 179 185
8. C.B. Rothschild, C.S. Brewer, B. Loggie, G.A. Beard, and M.X. Triscott Detection of colorectal cancer K-ras mutations using a simplified oligonucleotide ligation assay J. Immunol. Methods 206 1997 11 19 (Pubitemid 27395860)
9. J. Breivik, G.I. Meling, A. Spurkland, T.O. Rognum, and G. Gaudernack K-ras mutation in colorectal cancer: relations to patient age sex and tumour location Br. J. Cancer 69 1994 367 371 (Pubitemid 24046565)
10. G. Capella, S. Cronauer-Mitra, M.A. Pienado, and M. Perucho Frequency and spectrum of mutations at codons 12 and 13 of the c-K-ras gene in human tumors Environ. Health Perspect. 93 1991 125 131
11. S.D. Finkelstein, R. Sayegh, A. Bakker, and P. Swalsky Determination of tumor aggressiveness in colorectal cancer by K-ras-2 analysis Arch. Surg. 128 1993 526 531 (discussion 531-532)
12. K. Forrester, C. Almoguera, K. Han, W.E. Grizzle, and M. Perucho Detection of high incidence of K-ras oncogenes during human colon tumorigenesis Nature 327 1987 298 303 (Pubitemid 17075080)
13. L. Losi, J. Benhattar, and J. Costa Stability of K-ras mutations throughout the natural history of human colorectal cancer Eur. J. Cancer A 28 1992 1115 1120
14. A.J. Smith, H.S. Stern, M. Penner, K. Hay, A. Mitri, B.V. Bapat, and S. Gallinger Somatic APC and K-ras codon 12 mutations in aberrant crypt foci from human colons Cancer Res. 54 1994 5527 5530 (Pubitemid 24346239)
15. S.G. Martinez-Garza, A. Nunez-Salazar, A.L. Calderon-Garciduenas, F.J. Bosques-Padilla, A. Niderhauser-Garcia, and H.A. Barrera-Saldana Frequency and clinicopathology associations of K-ras mutations in colorectal cancer in a northeast Mexican population Dig. Dis. 17 1999 225 229 (Pubitemid 30198256)
16. N. Urosevic, K. Krtolica, A. Skaro-Milic, S. Knezevic-Usaj, and A. Dujic Prevalence of G-to-T transversions among K-ras oncogene mutations in human colorectal tumors in Yugoslavia Intl. J. Cancer 54 1993 249 254 (Pubitemid 23154890)
17. P. Crespo, and J. Leon Ras proteins in the control of the cell cycle and cell differentiation Cell. Mol. Life Sci. 57 2000 1613 1636
18. J.L. Bos Ras oncogenes in human cancer: a review Cancer Res. 49 1989 4682 4689 (Pubitemid 19213607)
19. P.B. McKinzie, and B.L. Parsons Detection of rare K-ras codon 12 mutations using allele-specific competitive blocker PCR Mutat. Res. 517 2002 209 220 (Pubitemid 34597020)
20. M. Schuermann Detection of K-ras and p53 mutations by "mutant-enriched" PCR-RFLP Methods Mol. Med. 75 2003 325 333
21. W. Jiang, S.M. Kahn, J.G. Guillem, S.H. Lu, and I.B. Weinstein Rapid detection of ras oncogenes in human tumors: applications to colon, esophageal, and gastric cancer Oncogene 4 1989 923 928 (Pubitemid 19176982)
22. S. Levi, A. Urbano-Ispizua, R. Gill, D.M. Thomas, J. Gilbertson, C. Foster, and C.J. Marshall Multiple K-ras codon 12 mutations in cholangiocarcinomas demonstrated with a sensitive polymerase chain reaction technique Cancer Res. 51 1991 3497 3502
23. L. Theodor, E. Melzer, M. Sologov, G. Idelman, E. Friedman, and S. Bar-Meir Detection of pancreatic carcinoma: diagnostic value of K-ras mutations in circulating DNA from serum Dig. Dis. Sci. 44 1999 2014 2019 (Pubitemid 29510811)
24. F. Barany Genetic disease detection and DNA amplification using cloned thermostable ligase Proc. Natl. Acad. Sci. USA 88 1991 189 193 (Pubitemid 21914452)
25. M. Khanna, P. Park, M. Zirvi, W. Cao, A. Picon, J. Day, P. Paty, and F. Barany Multiplex PCR/LDR for detection of K-ras mutations in primary colon tumors Oncogene 18 1999 27 38 (Pubitemid 29060576)
26. M. Hashimoto, F. Barany, F. Xu, and S.A. Soper Serial processing of biological reactions using flow-through microfluidic devices: coupled PCR/LDR for the detection of low-abundant DNA point mutations Analyst 132 2007 913 921 (Pubitemid 47283695)
27. M. Hashimoto, F. Barany, and S.A. Soper Polymerase chain reaction/ligase detection reaction/hybridization assays using flow-through microfluidic devices for the detection of low-abundant DNA point mutations Biosens. Bioelectron. 21 2006 1915 1923
28. M. Hashimoto, M.L. Hupert, M.C. Murphy, S.A. Soper, Y.W. Cheng, and F. Barany Ligase detection reaction/hybridization assays using three-dimensional microfluidic networks for the detection of low-abundant DNA point mutations Anal. Chem. 77 2005 3243 3255 (Pubitemid 40695482)
29. D.T. McNamara, J.M. Thomson, L.J. Kasehagen, and P.A. Zimmerman Development of a multiplex PCR-ligase detection reaction assay for diagnosis of infection by the four parasite species causing malaria in humans J. Clin. Microbiol. 42 2004 2403 2410 (Pubitemid 38747481)
30. R. Sinville, J. Coyne, R.J. Meagher, Y.W. Cheng, F. Barany, A. Barron, and S.A. Soper Ligase detection reaction for the analysis of point mutations using free-solution conjugate electrophoresis in a polymer microfluidic device Electrophoresis 29 2008 4751 4760
31. N.P. Gerry, N.E. Witowski, J. Day, R.P. Hammer, G. Barany, and F. Barany Universal DNA microarray method for multiplex detection of low abundance point mutations J. Mol. Biol. 292 1999 251 262 (Pubitemid 29435764)
32. F. Diehl, B. Beckmann, N. Kellner, N.C. Hauser, S. Diehl, and J.D. Hoheisel Manufacturing DNA microarrays from unpurified PCR products Nucleic Acids Res. 30 2002 e79
33. C. Zhang, and D. Xing Miniaturized PCR chips for nucleic acid amplification and analysis: latest advances and future trends Nucleic Acids Res. 35 2007 4223 4237 (Pubitemid 47244579)
34. D.S. Park, M.L. Hupert, M.A. Witek, B.H. You, P. Datta, J. Guy, J.B. Lee, S.A. Soper, D.E. Nikitopoulos, and M.C. Murphy A titer plate-based polymer microfluidic platform for high throughput nucleic acid purification Biomed. Microdevices 10 2008 21 33
35. J. Berger, T. Suzuki, K.A. Senti, J. Stubbs, G. Schaffner, and B.J. Dickson Genetic mapping with SNP markers in Drosophila Nat. Genet. 29 2001 475 481 (Pubitemid 34326701)
36. K.S. Caldwell, J. Dvorak, E.S. Lagudah, E. Akhunov, M.C. Luo, P. Wolters, and W. Powell Sequence polymorphism in polyploid wheat and their D-genome diploid ancestor Genetics 167 2004 941 947 (Pubitemid 38931878)
37. K.A. Dugan, H.S. Lawrence, D.R. Hares, C.L. Fisher, and B. Budowle An improved method for post-PCR purification for mtDNA sequence analysis J. Forensic Sci. 47 2002 811 818 (Pubitemid 34760908)
38. F. Eckhardt, J. Lewin, R. Cortese, V.K. Rakyan, J. Attwood, M. Burger, J. Burton, T.V. Cox, R. Davies, T.A. Down, C. Haefliger, R. Horton, K. Howe, D.K. Jackson, J. Kunde, C. Koenig, J. Liddle, D. Niblett, T. Otto, R. Pettett, S. Seemann, C. Thompson, T. West, J. Rogers, A. Olek, K. Berlin, and S. Beck DNA methylation profiling of human chromosomes 6, 20, and 22 Nat. Genet. 38 2006 1378 1385 (Pubitemid 44837559)
39. J. Mu, J. Duan, K.D. Makova, D.A. Joy, C.Q. Huynh, O.H. Branch, W.H. Li, and X.Z. Su Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum Nature 418 2002 323 326 (Pubitemid 34790682)
40. Y. Watanabe, A. Kinoshita, T. Yamada, T. Ohta, T. Kishino, N. Matsumoto, M. Ishikawa, N. Niikawa, and K. Yoshiura A catalog of 106 single-nucleotide polymorphisms (SNPs) and 11 other types of variations in genes for transforming growth factor-beta1 (TGF-β1) and its signaling pathway J. Hum. Genet. 47 2002 478 483 (Pubitemid 34988284)
41. W.A. Kibbe OligoCalc: an online oligonucleotide properties calculator Nucleic Acids Res. 35 2007 W43 W46
42. F. Sanger, and A.R. Coulson A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase J. Mol. Biol. 94 1975 441 448
43. P.C. Chen, D.E. Nikitopoulos, S.A. Soper, and M.C. Murphy Temperature distribution effects on micro-CFPCR performance Biomed. Microdevices 10 2008 141 152 (Pubitemid 351337917)
44. D.E. Whitney Mechanical Assemblies: Their Design, Manufacture, and Role in Product Development 2004 Oxford University Press New York
45. A. Maha, V. Palaparthy, S.A. Soper, M.C. Murphy, D.E. Nikitopoulos, Optimized high-aspect-ratio diffusional micromixers, in: ASME Conference Proceedings, 2008, pp. 645-646.
46. D.E. Nikitopoulos, A. Maha, in: W. Wang, S.A. Soper (Eds.), Micromixers in Bio-MEMS: Technologies and Applications, Taylor & Frances, Boca Raton, FL, 2007.
47. M. Heule, and A. Manz Sequential DNA hybridisation assays by fast micromixing Lab Chip 4 2004 506 511 (Pubitemid 39468925)
48. T.M. Squires, and S.R. Quake Microfluidics: fluid physics at the nanoliter scale Rev. Mod. Phys. 77 2005 977 1026 (Pubitemid 43272528)
49. F.G. Bessoth, A.J. deMello, and A. Manz Microstructure for efficient continuous flow mixing Anal. Commun. 36 1999 213 215
50. T.Y. Lee, A multi-function, disposable, microfluidic module for mutation detection, Ph.D. Dissertation, Louisiana State University, 2009.
51. G. Thomas, R. Sinville, S. Sutton, H. Farquar, R.P. Hammer, S.A. Soper, Y.W. Cheng, and F. Barany Capillary and microelectrophoretic separations of ligase detection reaction products produced from low-abundant point mutations in genomic DNA Electrophoresis 25 2004 1668 1677 (Pubitemid 38885832)
52. Y. Wang, B. Vaidya, H.D. Farquar, W. Stryjewski, R.P. Hammer, R.L. McCarley, S.A. Soper, Y.W. Cheng, and F. Barany Microarrays assembled in microfluidic chips fabricated from poly(methyl methacrylate) for the detection of low-abundant DNA mutations Anal. Chem. 75 2003 1130 1140 (Pubitemid 36402642)
53. P.M. Holland, R.D. Abramson, R. Watson, and D.H. Gelfand Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase Proc. Natl. Acad. Sci. USA 88 1991 7276 7280 (Pubitemid 21915133)