| Literature DB >> 24133623 |
Anne-Sophie Chretien1, Alexandre Harlé, Magali Meyer-Lefebvre, Marie Rouyer, Marie Husson, Carole Ramacci, Valentin Harter, Pascal Genin, Agnès Leroux, Jean-Louis Merlin.
Abstract
KRAS mutation detection represents a crucial issue in metastatic colorectal cancer (mCRC). The optimization of KRAS mutation detection delay enabling rational prescription of first-line treatment in mCRC including anti-EGFR-targeted therapy requires robust and rapid molecular biology techniques. Routine analysis of mutations in codons 12 and 13 on 674 paraffin-embedded tissue specimens of mCRC has been performed for KRAS mutations detection using three molecular biology techniques, that is, high-resolution melting (HRM), polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP), and allelic discrimination PCR (TaqMan PCR). Discordant cases were assessed with COBAS 4800 KRAS CE-IVD assay. Among the 674 tumor specimens, 1.5% (10/674) had excessive DNA degradation and could not be analyzed. KRAS mutations were detected in 38.0% (256/674) of the analysable specimens (82.4% in codon 12 and 17.6% in codon 13). Among 613 specimens in whom all three techniques were used, 12 (2.0%) cases of discordance between the three techniques were observed. 83.3% (10/12) of the discordances were due to PCR-RFLP as confirmed by COBAS 4800 retrospective analysis. The three techniques were statistically comparable (κ > 0.9; P < 0.001). From these results, optimization of the routine procedure consisted of proceeding to systematic KRAS detection using HRM and TaqMan and PCR-RFLP in case of discordance and allowed significant decrease in delays. The results showed an excellent correlation between the three techniques. Using HRM and TaqMan warrants high-quality and rapid-routine KRAS mutation detection in paraffin-embedded tumor specimens. The new procedure allowed a significant decrease in delays for reporting results, enabling rational prescription of first-line-targeted therapy in mCRC.Entities:
Keywords: Colorectal cancer; HRM; KRAS; PCR-RFLP; TaqMan PCR
Mesh:
Substances:
Year: 2013 PMID: 24133623 PMCID: PMC3797557 DOI: 10.1002/cam4.47
Source DB: PubMed Journal: Cancer Med ISSN: 2045-7634 Impact factor: 4.452
Figure 1Macrodissection step to ensure a minimum of 20% tumor tissue content. The hematoxylin–eosin slide with selected area contains more than 20% tumor cells.
Figure 2(A) KRAS mutation analysis using PCR-RFLP. DNA extracts from tumor samples were submitted to double PCR amplification after BstXI and XcmI enzymatic digestion allowing discrimination of codons 12 and 13 mutations. Codons 12 and 13 mutated DNA were used as positive control. Wild-type KRAS DNA and water were used as negative controls. (B) Example of codon 12 KRAS mutation detection using TaqMan PCR. Left panel represents amplification control (VIC). Right panel represents G12S mutation detection (FAM). (C) Example of codon 12 KRAS mutation detection using HRM. Depending on the presence or the absence of mutation, the melting temperature is different (left panel). The plot of the relative signal difference against the temperature allows to evidence the presence or the absence of KRAS mutation (right panel).
Interpretable, noninterpretable (NI) results and discordances for polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP), TaqMan PCR, and HRM PCR. TaqMan PCR showed less NI results than the two other assays
| PCR-RFLP | TaqMan PCR | HRM PCR | ||||
|---|---|---|---|---|---|---|
| Interpretable | 640 | (94.96%) | 650 | (96.44%) | 635 | (94.21%) |
| NI | 32 | (4.75%) | 22 | (3.26%) | 37 | (5.49%) |
| False positive | 4 | (0.62%) | 0 | (0.00%) | 0 | (0.00%) |
| False negative | 6 | (0.93%) | 2 | (0.31%) | 2 | (0.31%) |
Figure 3Comparison of mutation frequency as determined by the different detection methods. Overall as well as for each technique, all mutations frequencies were compared with average data from the Sanger Cosmic data base and were found to be fully consistent with the theoretical frequencies (chi-square test nonsignificant for all the data).
Crossover comparison of mutation frequency as determined by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP), PCR Taqman, and HRM PCR: κ values exceed 0.9 (P < 0.001), showing an excellent correlation between the three techniques
| PCR-RFLP | HRM PCR | |
| TaqMan PCR | ||
| κ = 0.960 | κ = 0.987 | |
| HRM PCR | ||
| κ = 0.973 | ||
Sensitivity of RFLP, PCR TaqMan, HRM, and COBAS assays. The sensitivity was evaluated by mixing codon 12 or codon 13 mutated and wild-type DNA from cell lines at 100%, 50%, 25%, 10%, 5%, 2.5%, and 1% ratios
| Codon 12 | Codon 13 | ||||||
| G12D | G12V | G12C | G12S | G12A | G12R | G13D | |
| RFLP | 2.5% | 5.0% | |||||
| TaqMan PCR | <1.0% | <1.0% | <1.0% | 5.0% | 2.5% | 5.0% | 2.5% |
| HRM PCR | 5.0% | 5.0% | |||||
| COBAS | <1.0% | <1.0% | |||||