Clinical pharmacogenomic testing of KRAS, BRAF and EGFR mutations by high resolution melting analysis and ultra-deep pyrosequencing
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- 作者：Emma Borràs (1)
Ismael Jurado (2)
Imma Hernan (1)
María José Gamundi (1)
Miguel Dias (1)
Isabel Martí (1)
Bego?a Ma?é (1)
àngels Arcusa (3)
José AG Agúndez (4)
Miguel Blanca (5)
Miguel Carballo (1) - 刊名：BMC Cancer
- 出版年：2011
- 出版时间：December 2011
- 年：2011
- 卷：11
- 期：1
- 全文大小：454KB
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36. The pre-publication history for this paper can be accessed here:medcentral.com/1471-2407/11/406/prepub" class="a-plus-plus">http://www.biomedcentral.com/1471-2407/11/406/prepub - 作者单位：Emma Borràs (1)
Ismael Jurado (2)
Imma Hernan (1)
María José Gamundi (1)
Miguel Dias (1)
Isabel Martí (1)
Bego?a Ma?é (1)
àngels Arcusa (3)
José AG Agúndez (4)
Miguel Blanca (5)
Miguel Carballo (1)
1. Molecular Genetics Unit, Hospital de Terrassa, Ctra. Torrebonica, 08227, Terrassa, Spain
2. Pathology Service, Hospital de Terrassa, Ctra. Torrebonica, 08227, Terrassa, Spain
3. Oncology Service, Hospital de Terrassa, Ctra. Torrebonica, 08227, Terrassa, Spain
4. Department of Pharmacology, Universidad de Extremadura, Av. Elvas, 06071, Badajoz, Spain
5. Allergy Service, Hospital Carlos Haya, Pl. Hospital Civil, 29009, Málaga, Spain - ISSN：1471-2407
文摘
Background Epidermal growth factor receptor (EGFR) and its downstream factors KRAS and BRAF are mutated in several types of cancer, affecting the clinical response to EGFR inhibitors. Mutations in the EGFR kinase domain predict sensitivity to the tyrosine kinase inhibitors gefitinib and erlotinib in lung adenocarcinoma, while activating point mutations in KRAS and BRAF confer resistance to the anti-EGFR monoclonal antibody cetuximab in colorectal cancer. The development of new generation methods for systematic mutation screening of these genes will allow more appropriate therapeutic choices. Methods We describe a high resolution melting (HRM) assay for mutation detection in EGFR exons 19-21, KRAS codon 12/13 and BRAF V600 using formalin-fixed paraffin-embedded samples. Somatic variation of KRAS exon 2 was also analysed by massively parallel pyrosequencing of amplicons with the GS Junior 454 platform. Results We tested 120 routine diagnostic specimens from patients with colorectal or lung cancer. Mutations in KRAS, BRAF and EGFR were observed in 41.9%, 13.0% and 11.1% of the overall samples, respectively, being mutually exclusive. For KRAS, six types of substitutions were detected (17 G12D, 9 G13D, 7 G12C, 2 G12A, 2 G12V, 2 G12S), while V600E accounted for all the BRAF activating mutations. Regarding EGFR, two cases showed exon 19 deletions (delE746-A750 and delE746-T751insA) and another two substitutions in exon 21 (one showed L858R with the resistance mutation T590M in exon 20, and the other had P848L mutation). Consistent with earlier reports, our results show that KRAS and BRAF mutation frequencies in colorectal cancer were 44.3% and 13.0%, respectively, while EGFR mutations were detected in 11.1% of the lung cancer specimens. Ultra-deep amplicon pyrosequencing successfully validated the HRM results and allowed detection and quantitation of KRAS somatic mutations. Conclusions HRM is a rapid and sensitive method for moderate-throughput cost-effective screening of oncogene mutations in clinical samples. Rather than Sanger sequence validation, next-generation sequencing technology results in more accurate quantitative results in somatic variation and can be achieved at a higher throughput scale.