Enhanced ratio of signals enables digital mutation scanning for rare allele detection

Journal of Molecular Diagnostics

Volumn 17, Issue 3, 2015, Pages 284-292

  Castellanos Rizaldos, Elena ^a   Paweletz, Cloud ^b   Song, Chen ^a   Oxnard, Geoffrey R ^b   Mamon, Harvey ^c   Jänne, Pasi A ^b   Mike Makrigiorgos, G ^a,c  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPLICON; ARTICLE; COAMPLIFICATION AT LOWER DENATURATION TEMPERATURE PCR; CONTROLLED STUDY; DILUTION; DROPLET DIGITAL PCR; EXON; GENE FREQUENCY; GENE MUTATION; GENE SEQUENCE; GENE TARGETING; HUMAN; HUMAN CELL; HYDROLYSIS; MUTATIONAL ANALYSIS; POLYMERASE CHAIN REACTION; VALIDATION STUDY; WILD TYPE; ALLELE; DEVICES; DNA DENATURATION; DNA MUTATIONAL ANALYSIS; ECONOMICS; EQUIPMENT DESIGN; EVALUATION STUDY; GENETICS; MUTATION; NEOPLASM; PROCEDURES; TUMOR CELL LINE;

DNA; EPIDERMAL GROWTH FACTOR RECEPTOR; PROTEIN P53;

ALLELES; CELL LINE, TUMOR; DNA; DNA MUTATIONAL ANALYSIS; EQUIPMENT DESIGN; HUMANS; MUTATION; NEOPLASMS; NUCLEIC ACID DENATURATION; POLYMERASE CHAIN REACTION; RECEPTOR, EPIDERMAL GROWTH FACTOR; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84928168931     PISSN: 15251578     EISSN: 19437811     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2014.12.003     Document Type: Article

References (37)

1. P.S. Bernard, and C.T. Wittwer Real-time PCR technology for cancer diagnostics Clin Chem 48 2002 1178 1185
2. S. Tyagi, and F.R. Kramer Molecular beacons: probes that fluoresce upon hybridization Nat Biotechnol 14 1996 303 308
3. J. Li, F. Wang, H. Mamon, M.H. Kulke, L. Harris, E. Maher, L. Wang, and G.M. Makrigiorgos Antiprimer quenching-based real-time PCR and its application to the analysis of clinical cancer samples Clin Chem 52 2006 624 633
4. G. Amicarelli, E. Shehi, G.M. Makrigiorgos, and D. Adlerstein FLAG assay as a novel method for real-time signal generation during PCR: application to detection and genotyping of KRAS codon 12 mutations Nucleic Acids Res 35 2007 e131
5. B. Vogelstein, and K.W. Kinzler Digital PCR Proc Natl Acad Sci U S A 96 1999 9236 9241
6. V. Taly, D. Pekin, L. Benhaim, S.K. Kotsopoulos, D. Le Corre, X. Li, I. Atochin, D.R. Link, A.D. Griffiths, K. Pallier, H. Blons, O. Bouche, B. Landi, J.B. Hutchison, and P. Laurent-Puig Multiplex picodroplet digital PCR to detect KRAS mutations in circulating DNA from the plasma of colorectal cancer patients Clin Chem 59 2013 1722 1731
7. E. Day, P.H. Dear, and F. McCaughan Digital PCR strategies in the development and analysis of molecular biomarkers for personalized medicine Methods 59 2013 101 107
8. C.M. Hindson, J.R. Chevillet, H.A. Briggs, E.N. Gallichotte, I.K. Ruf, B.J. Hindson, R.L. Vessella, and M. Tewari Absolute quantification by droplet digital PCR versus analog real-time PCR Nat Methods 10 2013 1003 1005
9. J.F. Huggett, C.A. Foy, V. Benes, K. Emslie, J.A. Garson, R. Haynes, J. Hellemans, M. Kubista, R.D. Mueller, T. Nolan, M.W. Pfaffl, G.L. Shipley, J. Vandesompele, C.T. Wittwer, and S.A. Bustin The digital MIQE guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments Clin Chem 59 2013 892 902
10. F. Diehl, K. Schmidt, M.A. Choti, K. Romans, S. Goodman, M. Li, K. Thornton, N. Agrawal, L. Sokoll, S.A. Szabo, K.W. Kinzler, B. Vogelstein, and L.A. Diaz Jr. Circulating mutant DNA to assess tumor dynamics Nat Med 14 2008 985 990
11. B.J. Hindson, K.D. Ness, D.A. Masquelier, P. Belgrader, N.J. Heredia, and A.J. Makarewicz High-throughput droplet digital PCR system for absolute quantitation of DNA copy number Anal Chem 83 2011 8604 8610
12. D.J. Marsh, G. Theodosopoulos, V. Howell, A.L. Richardson, D.E. Benn, A.L. Proos, C. Eng, and B.G. Robinson Rapid mutation scanning of genes associated with familial cancer syndromes using denaturing high-performance liquid chromatography Neoplasia 3 2001 236 244
13. C.T. Wittwer, G.H. Reed, C.N. Gundry, J.G. Vandersteen, and R.J. Pryor High-resolution genotyping by amplicon melting analysis using LCGreen Clin Chem 49 2003 853 860
14. J. Li, R. Berbeco, R.J. Distel, P.A. Janne, L. Wang, and G.M. Makrigiorgos s-RT-MELT for rapid mutation scanning using enzymatic selection and real time DNA-melting: new potential for multiplex genetic analysis Nucleic Acids Res 35 2007 e84
15. J.E. Rice, A.H. Reis Jr., L.M. Rice, R.K. Carver-Brown, and L.J. Wangh Fluorescent signatures for variable DNA sequences Nucleic Acids Res 40 2012 e164
16. C.A. Milbury, J. Li, and G.M. Makrigiorgos COLD-PCR-enhanced high-resolution melting enables rapid and selective identification of low-level unknown mutations Clin Chem 55 2009 2130 2143
17. P. Carotenuto, C. Roma, S. Cozzolino, F. Fenizia, A.M. Rachiglio, F. Tatangelo, A. Iannaccone, L. Baron, G. Botti, and N. Normanno Detection of KRAS mutations in colorectal cancer with Fast COLD-PCR Int J Oncol 40 2012 378 384
18. C.C. Pritchard, L. Akagi, P.L. Reddy, L. Joseph, and J.F. Tait COLD-PCR enhanced melting curve analysis improves diagnostic accuracy for KRAS mutations in colorectal carcinoma BMC Clin Pathol 10 2010 6
19. L.S. Kristensen, I.L. Daugaard, M. Christensen, S. Hamilton-Dutoit, H. Hager, and L.L. Hansen Increased sensitivity of KRAS mutation detection by high-resolution melting analysis of COLD-PCR products Hum Mutat 31 2010 1366 1373
20. A. How Kit, N. Mazaleyrat, A. Daunay, H.M. Nielsen, B. Terris, and J. Tost Sensitive detection of KRAS mutations using enhanced-ice-COLD-PCR mutation enrichment and direct sequence identification Hum Mutat 34 2013 1568 1580
21. J. Li, L. Wang, H. Mamon, M.H. Kulke, R. Berbeco, and G.M. Makrigiorgos Replacing PCR with COLD-PCR enriches variant DNA sequences and redefines the sensitivity of genetic testing Nat Med 14 2008 579 584
22. J. Li, C.A. Milbury, C. Li, and G.M. Makrigiorgos Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based Sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma Hum Mutat 30 2009 1583 1590
23. M. Guha, E. Castellanos-Rizaldos, P. Liu, H. Mamon, and G.M. Makrigiorgos Differential strand separation at critical temperature: a minimally disruptive enrichment method for low-abundance unknown DNA mutations Nucleic Acids Res 41 2013 e50
24. G.R. Oxnard, C.P. Paweletz, Y. Kuang, S.L. Mach, A. O'Connell, M.M. Messineo, J.J. Luke, M. Butaney, P. Kirschmeier, D.M. Jackman, and P.A. Janne Noninvasive detection of response and resistance in EGFR-mutant lung cancer using quantitative next-generation genotyping of cell-free plasma DNA Clin Cancer Res 20 2014 1698 1705
25. S.T. Sherry, M.H. Ward, M. Kholodov, J. Baker, L. Phan, E.M. Smigielski, and K. Sirotkin dbSNP: the NCBI database of genetic variation Nucleic Acids Res 29 2001 308 311
26. M. Guha, E. Castellanos-Rizaldos, and G.M. Makrigiorgos DISSECT method using PNA-LNA clamp improves detection of T790m mutation PLoS One 8 2013 e67782
27. C. Greenman, P. Stephens, R. Smith, G.L. Dalgliesh, C. Hunter, and G. Bignell Patterns of somatic mutation in human cancer genomes Nature 446 2007 153 158
28. S. Galbiati, A. Brisci, F. Lalatta, M. Seia, G.M. Makrigiorgos, M. Ferrari, and L. Cremonesi Full COLD-PCR protocol for noninvasive prenatal diagnosis of genetic diseases Clin Chem 57 2011 136 138
29. Y. Kuang, A. Rogers, B.Y. Yeap, L. Wang, M. Makrigiorgos, K. Vetrand, S. Thiede, R.J. Distel, and P.A. Janne Noninvasive detection of EGFR T790M in gefitinib or erlotinib resistant non-small cell lung cancer Clin Cancer Res 15 2009 2630 2636
30. E. Castellanos-Rizaldos, P. Liu, C.A. Milbury, M. Guha, A. Brisci, L. Cremonesi, M. Ferrari, H. Mamon, and G.M. Makrigiorgos Temperature-tolerant COLD-PCR reduces temperature stringency and enables robust mutation enrichment Clin Chem 58 2012 1130 1138
31. A. Narayan, N.J. Carriero, S.N. Gettinger, J. Kluytenaar, K.R. Kozak, T.I. Yock, N.E. Muscato, P. Ugarelli, R.H. Decker, and A.A. Patel Ultrasensitive measurement of hotspot mutations in tumor DNA in blood using error-suppressed multiplexed deep sequencing Cancer Res 72 2012 3492 3498
32. I. Kinde, J. Wu, N. Papadopoulos, K.W. Kinzler, and B. Vogelstein Detection and quantification of rare mutations with massively parallel sequencing Proc Natl Acad Sci U S A 108 2011 9530 9535
33. C.A. Milbury, M. Correll, J. Quackenbush, R. Rubio, and G.M. Makrigiorgos COLD-PCR enrichment of rare cancer mutations prior to targeted amplicon resequencing Clin Chem 58 2012 580 589
34. C.A. Milbury, J. Li, and G.M. Makrigiorgos PCR-based methods for the enrichment of minority alleles and mutations Clin Chem 55 2009 4632 4640
35. M.G. Herrmann, J.D. Durtschi, L.K. Bromley, C.T. Wittwer, and K.V. Voelkerding Amplicon DNA melting analysis for mutation scanning and genotyping: cross-platform comparison of instruments and dyes Clin Chem 52 2006 494 503
36. D. Delaney, T.C. Diss, N. Presneau, S. Hing, F. Berisha, B.D. Idowu, P. O'Donnell, J.A. Skinner, R. Tirabosco, and A.M. Flanagan GNAS1 mutations occur more commonly than previously thought in intramuscular myxoma Mod Pathol 22 2009 718 724
37. C.A. Milbury, J. Li, and G.M. Makrigiorgos Ice-COLD-PCR enables rapid amplification and robust enrichment for low-abundance unknown DNA mutations Nucleic Acids Res 39 2011 e2