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Analytical and Bioanalytical Chemistry

, Volume 406, Issue 22, pp 5513–5520 | Cite as

Ultrasensitive detection and identification of BRAF V600 mutations in fresh frozen, FFPE, and plasma samples of melanoma patients by E-ice-COLD-PCR

  • Alexandre How-Kit
  • Céleste Lebbé
  • Aurélie Bousard
  • Antoine Daunay
  • Nicolas Mazaleyrat
  • Christian Daviaud
  • Samia Mourah
  • Jörg Tost
Note

Abstract

A number of molecular diagnostic methods have been developed for the detection and identification of mutations in tumor samples, which are important for the choice of treatment in the context of personalized medicine. For the treatment of metastatic melanoma, Vemurafenib is recommended for patients with BRAF V600 activating mutations. However, the different assays developed to date for the detection of these mutations lack sensitivity or specificity or do not allow a sequencing-based identification or validation of the mutation. Recently, enhanced improved and complete enrichment co-amplification at lower denaturation temperature-polymerase chain reaction (E-ice-COLD-PCR) has been developed as a sensitive method for the detection and identification of mutations in KRAS codons 12/13. Here, we present the first E-ice-COLD-PCR assay for the detection and identification of BRAF codon 600 mutations, which has a large dynamic range, as 25 pg to 25 ng can be used as DNA input without any reduction in mutation enrichment efficiency, and which can detect down to 0.01 % of mutated alleles in a wild-type background. The assay has been validated on fresh frozen, formalin-fixed paraffin-embedded (FFPE), and plasma samples of melanoma patients and has allowed the detection and identification of BRAF mutations present in samples appearing as wild type using standard pyrosequencing, endpoint genotyping, or Sanger sequencing. Thus, the BRAF V600 E-ice-COLD-PCR assay is currently one of the most powerful molecular diagnostic tools for the ultrasensitive detection and identification of BRAF codon 600 mutations.

Keywords

E-ice-COLD-PCR Melanoma BRAF V600 mutation Vemurafenib Molecular diagnostics 

Notes

Acknowledgments

The authors would like to thank Aurélie Sadoux (AP-HP) and Marie-Pierre Podgorniak (AP-HP) for technical assistance, Leigh Pascoe (CEPH) for his help in statistics, and Steven McGinn (CNG) for the critical reading of the manuscript.

Funding

The work in the presented manuscript was funded through the institutional budget of the CEA and the CEPH.

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

216_2014_7975_MOESM1_ESM.pdf (618 kb)
ESM 1 (PDF 617 kb)
216_2014_7975_MOESM2_ESM.xlsm (110 kb)
ESM 2 (XLSM 110 kb)
216_2014_7975_MOESM3_ESM.txt (95 kb)
ESM 3 (TXT 94 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Alexandre How-Kit
    • 1
  • Céleste Lebbé
    • 2
    • 3
    • 4
  • Aurélie Bousard
    • 5
  • Antoine Daunay
    • 1
  • Nicolas Mazaleyrat
    • 5
  • Christian Daviaud
    • 5
  • Samia Mourah
    • 6
    • 7
  • Jörg Tost
    • 1
    • 5
  1. 1.Laboratory for Functional GenomicsFondation Jean Dausset - CEPHParisFrance
  2. 2.Département de Dermatologie FranceAP-HP - Hôpital Saint-LouisParisFrance
  3. 3.Université Paris-DiderotParisFrance
  4. 4.INSERM U976ParisFrance
  5. 5.Laboratory for Epigenetics and Environment, Centre National de GénotypageCEA-Institut de GénomiqueEvryFrance
  6. 6.Laboratoire de Pharmacologie-GénétiqueAP-HP - Hôpital Saint-LouisParisFrance
  7. 7.INSERM UMR-S 940ParisFrance

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