Differential strand separation at critical temperature: A minimally disruptive enrichment method for low-abundance unknown DNA mutations

Nucleic Acids Research

Volumn 41, Issue 3, 2013, Pages

  Guha, Minakshi ^a   Castellanos Rizaldos, Elena ^a   Liu, Pingfang ^a   Mamon, Harvey ^b   Makrigiorgos, G Mike ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; HETERODUPLEX; K RAS PROTEIN; PROTEIN P53;

ANALYTIC METHOD; ARTICLE; DIFFERENTIAL STRAND SEPARATION AT CRITICAL TEMPERATURE; DNA DENATURATION; DNA DETERMINATION; DNA HYBRIDIZATION; DNA SEQUENCE; DNA TEMPLATE; ENZYME MECHANISM; GENE AMPLIFICATION; GENE MUTATION; HIGH RESOLUTION MELTING ANALYSIS; HUMAN; HUMAN CELL; MALE; MUTATIONAL ANALYSIS; ONCOGENE K RAS; POPULATION GENETICS; PRIORITY JOURNAL; RELIABILITY; TEMPERATURE;

CELL LINE, TUMOR; DNA MUTATIONAL ANALYSIS; DNA, NEOPLASM; GENES, P53; HUMANS; MALE; MUTATION; NEOPLASMS; PROTO-ONCOGENE PROTEINS; RAS PROTEINS; TEMPERATURE;

EID: 84873689810     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1250     Document Type: Article

References (28)

1. Sadowska,A.M., Nowe,V., Janssens,A., Boeykens,E., De Backer,W.A. and Germonpre,P.R. (2011) Customizing systemic therapy in patients with advanced non-small cell lung cancer. Ther. Adv. Med. Oncol., 3, 207-218.
2. Milbury,C.A., Li,J. and Makrigiorgos,G.M. (2009) PCR-based methods for the enrichment of minority alleles and mutations. Clin. Chem., 55, 632-640.
3. Sidransky,D., Von Eschenbach,A., Tsai,Y.C., Jones,P., Summerhayes,I., Marshall,F., Paul,M., Green,P., Hamilton,S.R., Frost,P. et al. (1991) Identification of p53 gene mutations in bladder cancers and urine samples. Science, 252, 706-709.
4. Tada,M., Omata,M., Kawai,S., Saisho,H., Ohto,M., Saiki,R.K. and Sninsky,J.J. (1993) Detection of ras gene mutations in pancreatic juice and peripheral blood of patients with pancreatic adenocarcinoma. Cancer Res., 53, 2472-2474.
5. Li,J., Wang,L., Mamon,H., Kulke,M.H., Berbeco,R. and Makrigiorgos,G.M. (2008) Replacing PCR with COLD-PCR enriches variant DNA sequences and redefines the sensitivity of genetic testing. Nat. Med., 14, 579-584.
6. Milbury,C.A., Li,J. and Makrigiorgos,G.M. (2010) Ice-COLDPCR enables rapid amplification and robust enrichment for low-abundance unknown DNA mutations. Nucleic Acids Res., 39, e2.
7. Milbury,C.A., Correll,M., Quackenbush,J., Rubio,R. and Makrigiorgos,G.M. (2011) COLD-PCR enrichment of rare cancer mutations prior to targeted amplicon resequencing. Clin. Chem., 58, 580-589.
8. Li,J., Milbury,C.A., Li,C. and Makrigiorgos,G.M. (2009) 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, 1583-1590.
9. Milbury,C.A., Li,J. and Makrigiorgos,G.M. (2009) COLD-PCR-enhanced high-resolution melting enables rapid and selective identification of low-level unknown mutations. Clin. Chem., 55, 2130-2143.
10. Li,J., Wang,L., Janne,P.A. and Makrigiorgos,G.M. (2009) Coamplification at lower denaturation temperature-PCR increases mutation-detection selectivity of TaqMan-based real-time PCR. Clin. Chem., 55, 748-756.
11. Boisselier,B., Marie,Y., Labussiere,M., Ciccarino,P., Desestret,V., Wang,X., Capelle,L., Delattre,J.Y. and Sanson,M. (2010) COLD PCR HRM: A highly sensitive detection method for IDH1 mutations. Hum. Mutat., 31, 1360-1365.
12. Jeffreys,A.J. and May,C.A. (2003) DNA enrichment by allele-specific hybridization (DEASH): A novel method for haplotyping and for detecting low-frequency base substitutional variants and recombinant DNA molecules. Genome Res., 13, 2316-2324.
13. Song,C., Milbury,C.A., Li,J., Liu,P., Zhao,M. and Makrigiorgos,G.M. (2011) Rapid and sensitive detection of KRAS mutation after fast-COLD-PCR enrichment and high-resolution melting analysis. Diagn. Mol. Pathol., 20, 81-89.
14. Milbury,C.A., Chen,C.C., Mamon,H., Liu,P., Santagata,S. and Makrigiorgos,G.M. (2011) Multiplex amplification coupled with COLD-PCR and high resolution melting enables identification of low-abundance mutations in cancer samples with low DNA content. J. Mol. Diagn., 13, 220-232.
15. Castellanos-Rizaldos,E., Liu,P., Milbury,C.A., Guha,M., Brisci,A., Cremonesi,L., Ferrari,M., Mamon,H. and Makrigiorgos,G.M. (2012) Temperature-tolerant COLD-PCr reduces temperature stringency and enables robust mutation enrichment. Clin. Chem., 58, 1130-1138.
16. Forbes,S.A., Bhamra,G., Bamford,S., Dawson,E., Kok,C., Clements,J., Menzies,A., Teague,J.W., Futreal,P.A. and Stratton,M.R. (2008) The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr. Protoc. Hum. Genet., Chapter 10, Unit 10.11.
17. Efrati,E., Elkin,H., Peerless,Y., Sabo,E., Ben-Izhak,O. and Hershkovitz,D. (2010) LNA-based PCR clamping enrichment assay for the identification of KRAS mutations. Cancer Biomark., 8, 89-94.
18. Huang,Q., Wang,G.Y., Huang,J.F., Zhang,B. and Fu,W.L. (2010) High sensitive mutation analysis on KRAS gene using LNA/ DNA chimeras as PCR amplification blockers of wild-type alleles. Mol. Cell. Probes, 24, 376-380.
19. Diehl,F., Li,M., He,Y., Kinzler,K.W., Vogelstein,B. and Dressman,D. (2006) BEAMing: Single-molecule PCR on microparticles in water-in-oil emulsions. Nat. Methods, 3, 551-559.
20. Suzuki,Y., Orita,M., Shiraishi,M., Hayashi,K. and Sekiya,T. (1990) Detection of ras gene mutations in human lung cancers by single-strand conformation polymorphism analysis of polymerase chain reaction products. Oncogene, 5, 1037-1043.
21. Wistuba,I.I., Gazdar,A.F. and Minna,J.D. (2001) Molecular genetics of small cell lung carcinoma. Semin. Oncol., 28, 3-13.
22. Ding,L., Getz,G., Wheeler,D.A., Mardis,E.R., McLellan,M.D., Cibulskis,K., Sougnez,C., Greulich,H., Muzny,D.M., Morgan,M.B. et al. (2008) Somatic mutations affect key pathways in lung adenocarcinoma. Nature, 455, 1069-1075.
23. Kuang,Y., Rogers,A., Yeap,B.Y., Wang,L., Makrigiorgos,M., Vetrand,K., Thiede,S., Distel,R.J. and Janne,P.A. (2009) Noninvasive detection of EGFR T790M in gefitinib or erlotinib resistant non-small cell lung cancer. Clin. Cancer Res., 15, 2630-2636.
24. Molinari,F., Felicioni,L., Buscarino,M., De Dosso,S., Buttitta,F., Malatesta,S., Movilia,A., Luoni,M., Boldorini,R., Alabiso,O. et al. (2011) Increased detection sensitivity for KRAS mutations enhances the prediction of anti-EGFR monoclonal antibody resistance in metastatic colorectal cancer. Clin. Cancer Res., 17, 4901-4914.
25. Molinari,F. and Frattini,M. (2012) KRAS mutational test for metastatic colorectal cancer patients: not just a technical problem. Expert Rev. Mol. Diagn., 12, 123-126.
26. Araki,T., Shimizu,K., Nakamura,K., Nakamura,T., Mitani,Y., Obayashi,K., Fujita,Y., Kakegawa,S., Miyamae,Y., Kaira,K. et al. (2010) Usefulness of peptide nucleic acid (PNA)-clamp smart amplification process version 2 (SmartAmp2) for clinical diagnosis of KRAS codon 12 mutations in lung adenocarcinoma: Comparison of PNA-clamp SmartAmp2 and PCR-related methods. J. Mol. Diagn., 12, 118-124.
27. Misale,S., Yaeger,R., Hobor,S., Scala,E., Janakiraman,M., Liska,D., Valtorta,E., Schiavo,R., Buscarino,M., Siravegna,G. et al. (2012) Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer. Nature, 486, 532-536.
28. Diaz,L.A. Jr, Williams,R.T., Wu,J., Kinde,I., Hecht,J.R., Berlin,J., Allen,B., Bozic,I., Reiter,J.G., Nowak,M.A. et al. (2012) The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature, 486, 537-540.