PMID- 37386758
OWN - NLM
STAT- MEDLINE
DCOM- 20230703
LR  - 20230710
IS  - 1526-2359 (Electronic)
IS  - 1073-2748 (Print)
IS  - 1073-2748 (Linking)
VI  - 30
DP  - 2023 Jan-Dec
TI  - Detection of Nine Oncogenes Amplification in Lung and Colorectal Cancer 
      Formalin-Fixed Paraffin-Embedded Tissue Samples using Combined Next-Generation 
      Sequencing-Based Script and Digital Droplet Polymerase Chain Reaction.
PG  - 10732748231167257
LID - 10.1177/10732748231167257 [doi]
LID - 10732748231167257
AB  - INTRODUCTION: Gene copy number variations have theranostic impact and require 
      reliable methods for their identification. We aimed to evaluate the reliability 
      of combined next-generation sequencing (NGS) and digital droplet PCR (ddPCR) 
      method for gene amplification evaluation. METHODS: We conducted a retrospective 
      multicentric observational study. MET/ERBB2 amplifications were assessed in 
      patients with lung or colorectal carcinoma (cohort A), from 2016 to 2020, by 
      fluorescence in situ hybridization (FISH)/immunohistochemistry (IHC), NGS and 
      ddPCR. NGS-based script and ddPCR were then used to detect amplifications of 7 
      additional oncogenes (EGFR, KRAS, BRAF, FGFR1, FGFR2, FGFR3, PIK3CA) in a cohort 
      of patients (cohort B). RESULTS: 55 patients (9 control, 25 ERBB2-amplified and 
      21 MET-amplified) out of 3779 patients tested were included in cohort A. 
      Correlation coefficient between NGS-based script and FISH/IHC results were .88 
      for MET (P < .001) and .89 (P < .001) for ERBB2. Using a threshold ratio of 1.56 
      with the NGS-based script, the sensitivity was 100% for both genes and the 
      specificity 69% for MET and 90% for ERBB2, respectively. With an alternative 1.76 
      threshold, sensitivity was 94% for MET and 96% for ERBB2, while specificity was 
      85% for MET and 90% for ERBB2. Correlation coefficient between FISH and ddPCR 
      ratio was .90 for MET and .88 for ERBB2. In both cohorts, NGS-based script and 
      ddPCR results were significantly correlated regarding all genes (P < .001). 
      CONCLUSION: Combined NGS-based script and ddPCR method is reliable and easily 
      feasible for the detection of gene amplifications, providing useful data for 
      guided therapy in cancer.
FAU - Bontoux, Christophe
AU  - Bontoux C
AUID- ORCID: 0000-0001-5446-6197
AD  - Laboratory of Clinical and Experimental Pathology, Centre Hospitalier 
      Universitaire de Nice, Universite Cote d'Azur, Hospital-Integrated Biobank, 
      Hopital Pasteur, Nice, France.
AD  - Department of Genetics, University Hospital Bichat-Claude Bernard, AP-HP, Paris 
      University, Paris, France. RINGGOLD: 55076
FAU - Guyard, Alice
AU  - Guyard A
AD  - Department of Genetics, University Hospital Bichat-Claude Bernard, AP-HP, Paris 
      University, Paris, France. RINGGOLD: 55076
FAU - Lupo, Audrey
AU  - Lupo A
AD  - Department of Pathology, University Hospital Bichat-Claude Bernard, AP-HP, 
      University Paris-Diderot, Paris, France. RINGGOLD: 55076
FAU - Diallo, Karim
AU  - Diallo K
AD  - Laboratory of Clinical and Experimental Pathology, Centre Hospitalier 
      Universitaire de Nice, Universite Cote d'Azur, Hospital-Integrated Biobank, 
      Hopital Pasteur, Nice, France.
FAU - Rebah, Khedidja
AU  - Rebah K
AD  - Laboratory of Clinical and Experimental Pathology, Centre Hospitalier 
      Universitaire de Nice, Universite Cote d'Azur, Hospital-Integrated Biobank, 
      Hopital Pasteur, Nice, France.
FAU - Hercent, Agathe
AU  - Hercent A
AD  - Laboratory of Clinical and Experimental Pathology, Centre Hospitalier 
      Universitaire de Nice, Universite Cote d'Azur, Hospital-Integrated Biobank, 
      Hopital Pasteur, Nice, France.
FAU - Guenzi, Edouard
AU  - Guenzi E
AD  - Laboratory of Clinical and Experimental Pathology, Centre Hospitalier 
      Universitaire de Nice, Universite Cote d'Azur, Hospital-Integrated Biobank, 
      Hopital Pasteur, Nice, France.
FAU - Cros, Jerome
AU  - Cros J
AD  - Department of Pathology, Hopitaux Universitaire Paris Centre, Hopital Cochin, 
      AP-HP, Universite de Paris, Paris, France. RINGGOLD: 26935
FAU - Lamoril, Jerome
AU  - Lamoril J
AD  - Laboratory of Clinical and Experimental Pathology, Centre Hospitalier 
      Universitaire de Nice, Universite Cote d'Azur, Hospital-Integrated Biobank, 
      Hopital Pasteur, Nice, France.
FAU - Leroy, Karen
AU  - Leroy K
AD  - Department of Pathology, University Hospital Beaujon, AP-HP, University 
      Paris-Diderot, Paris, France. RINGGOLD: 55100
FAU - Theou-Anton, Nathalie
AU  - Theou-Anton N
AD  - Laboratory of Clinical and Experimental Pathology, Centre Hospitalier 
      Universitaire de Nice, Universite Cote d'Azur, Hospital-Integrated Biobank, 
      Hopital Pasteur, Nice, France.
LA  - eng
PT  - Journal Article
PT  - Observational Study
PL  - United States
TA  - Cancer Control
JT  - Cancer control : journal of the Moffitt Cancer Center
JID - 9438457
RN  - 1HG84L3525 (Formaldehyde)
SB  - IM
MH  - Humans
MH  - *DNA Copy Number Variations
MH  - In Situ Hybridization, Fluorescence
MH  - Paraffin Embedding
MH  - Reproducibility of Results
MH  - Retrospective Studies
MH  - Oncogenes
MH  - Polymerase Chain Reaction
MH  - High-Throughput Nucleotide Sequencing
MH  - Lung
MH  - *Colorectal Neoplasms/genetics
MH  - Formaldehyde
PMC - PMC10328004
OTO - NOTNLM
OT  - amplification
OT  - bioinformatics
OT  - colorectal cancer
OT  - copy number
OT  - digital droplet PCR
OT  - genes
OT  - lung cancer
OT  - sequencing data
COIS- The author(s) declared no potential conflicts of interest with respect to the 
      research, authorship, and/or publication of this article.
EDAT- 2023/06/30 06:42
MHDA- 2023/07/03 06:41
PMCR- 2023/06/29
CRDT- 2023/06/30 01:13
PHST- 2023/07/03 06:41 [medline]
PHST- 2023/06/30 06:42 [pubmed]
PHST- 2023/06/30 01:13 [entrez]
PHST- 2023/06/29 00:00 [pmc-release]
AID - 10.1177_10732748231167257 [pii]
AID - 10.1177/10732748231167257 [doi]
PST - ppublish
SO  - Cancer Control. 2023 Jan-Dec;30:10732748231167257. doi: 
      10.1177/10732748231167257.