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Ion proton next-generation sequencing for identification of clinically relevent mutations in Moroccan colorectal cancer cases

Date

19 Dec 2015

Session

Poster presentation 1

Presenters

Falak Azzam

Citation

Annals of Oncology (2015) 26 (suppl_9): 42-70. 10.1093/annonc/mdv523

Authors

F. Azzam1, F. Jouali2, N. Marchoudi2, M. Karkouri3, J. Fekkak2, D. Squalli Houssaini4, Y. Bakri5, R. Aboukhalid5, S. Amzazi5

Author affiliations

  • 1 Biology, University Mohammed V - Agdal, 11000 - Rabat/MA
  • 2 Genetics, Laboratoire de Radio-Immuno-Analyse Anoual, Casablanca/MA
  • 3 Anatomopathology, IBN ROCHD Casablanca, Casablanca/MA
  • 4 Molecular Biology, Genome Biotechnologies, Casablanca/MA
  • 5 Biology, University Mohammed V - Agdal, Rabat/MA
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Resources

Abstract 345

Aim/Background

The identification of gene variants plays an important role in the diagnosis of genetic diseases. In effect, diagnostic laboratories are confronted with new challenges: costs, turn-around-time and small amount of input DNA for testing will increase with the number of tests performed on a sample using semi conductor sequencing. As other solid tumors, colorectal cancer (CRC) is a genomic disorder in which various types of molecular alterations (MA), such as point mutations, genomic re-arrangements, gene fusions, or chromosomal copy number alterations, can contribute to the initiation and progression of the disease. The aim of this study is to identify mutation variants from CRC Moroccan patients using massive-parallel sequencing for clinical analysis.

Methods

DNA samples were isolated from 80 solid tumors FFPE tissue biopsy specimens using the MagMaxTM FFPE DNA Isolation kit (Invitrogen™, Thermo Fisher Scientific). Ten ng of sample were processed using the Ion AmpliSeq™ Colon and Lung panel v2 developed by OncoNetwork Consortium targeting 87 hotspot regions in 22 genes that are of clinical interest for colorectal and lung cancer following the Ion AmpliSeq™ Library Kit ™ (Ion Torrent™, Thermo Fisher Scientific). After emulsion PCR, spheres were loaded on Ion PI™ Chip v2 for sequencing using Ion Proton system. Results were analyzed using the Ion Reporter™ Software.

Results

The primary results analysis of New Generation Sequencing testing, shown 81% were pre-tested for KRAS. The most frequent currently non-actionable MAs were identified in TP53 and APC. The majority of cases harbored ≥1 actionable MAs and the most commonly are KRAS, BRAF, PIK3CA, SMAD 4 and FBX7. Actionable MAs characterized by gene amplifications were detected in FGFR1, EGFR, and MET.

Conclusions

For the most part, the availability of fast bench top sequencers such as the Ion Proton (Semi conductor sequencing) show that approach to stratify colon and lung cancer patients is feasible in a clinical setting. Results point to the potential of KRAS, BRAF, NRAS, ERBB2 and EGFR targeted therapies for a significant subset of patients.

Clinical trial identification

Disclosure

All authors have declared no conflicts of interest.

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