Comparison study of the performance of the QIAGEN EGFR RGQ and EGFR pyro assays for mutation analysis in non-small cell lung cancer

Allison M Cushman-Vokoun, Ann M. Crowley, Sharleen A. Rapp, Timothy Charles Greiner

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Objectives: To compare 2 laboratory assays commonly used in the evaluation of epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC). Methods: Fifty-three formalin-fixed, paraffinembedded NSCLC specimens were selected. Extracted DNA was analyzed using the EGFR RGQ Amplification Refractory Mutation System Scorpions probe-based real-time polymerase chain reaction (PCR) assay and the EGFR Pyro pyrosequencing assay. Results: Fourteen EGFR mutations were identified in 13 specimens using at least 1 of the assays, with a mutation concordance rate of 92.9%. Using dideoxy sequencing as the gold standard, clinical sensitivity was 73.7% and 68.4% by the RGQ and Pyro assays, respectively, but 100% by both for common drug sensitivity mutations. Performance observations included the following: the RGQ system requires higher DNA input, the RGQ system is a single-step procedure, the EGFR Pyro assay is a 2-step procedure, only the RGQ system can identify exon 20 insertions, the RGQ system is more sensitive, and the Pyro system can specify exact mutations for all interrogated sites. Conclusions: Both the RGQ real-time PCR and Pyro assays adequately detect common EGFR mutations; however, the RGQ system is more clinically and analytically sensitive. Performance characteristics should be considered when evaluating these EGFR mutation assays for clinical adoption.

Original languageEnglish (US)
Pages (from-to)7-19
Number of pages13
JournalAmerican Journal of Clinical Pathology
Volume140
Issue number1
DOIs
StatePublished - Jul 1 2013

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Epidermal Growth Factor Receptor
Non-Small Cell Lung Carcinoma
Mutation
Real-Time Polymerase Chain Reaction
Scorpions
DNA
Mutation Rate
Formaldehyde
Exons
Pharmaceutical Preparations

Keywords

  • ARMS
  • Amplification Refractory Mutation System
  • Epidermal growth factor receptor
  • Non-small cell lung cancer
  • Pyrosequencing
  • Real-time PCR

ASJC Scopus subject areas

  • Pathology and Forensic Medicine

Cite this

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title = "Comparison study of the performance of the QIAGEN EGFR RGQ and EGFR pyro assays for mutation analysis in non-small cell lung cancer",
abstract = "Objectives: To compare 2 laboratory assays commonly used in the evaluation of epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC). Methods: Fifty-three formalin-fixed, paraffinembedded NSCLC specimens were selected. Extracted DNA was analyzed using the EGFR RGQ Amplification Refractory Mutation System Scorpions probe-based real-time polymerase chain reaction (PCR) assay and the EGFR Pyro pyrosequencing assay. Results: Fourteen EGFR mutations were identified in 13 specimens using at least 1 of the assays, with a mutation concordance rate of 92.9{\%}. Using dideoxy sequencing as the gold standard, clinical sensitivity was 73.7{\%} and 68.4{\%} by the RGQ and Pyro assays, respectively, but 100{\%} by both for common drug sensitivity mutations. Performance observations included the following: the RGQ system requires higher DNA input, the RGQ system is a single-step procedure, the EGFR Pyro assay is a 2-step procedure, only the RGQ system can identify exon 20 insertions, the RGQ system is more sensitive, and the Pyro system can specify exact mutations for all interrogated sites. Conclusions: Both the RGQ real-time PCR and Pyro assays adequately detect common EGFR mutations; however, the RGQ system is more clinically and analytically sensitive. Performance characteristics should be considered when evaluating these EGFR mutation assays for clinical adoption.",
keywords = "ARMS, Amplification Refractory Mutation System, Epidermal growth factor receptor, Non-small cell lung cancer, Pyrosequencing, Real-time PCR",
author = "Cushman-Vokoun, {Allison M} and Crowley, {Ann M.} and Rapp, {Sharleen A.} and Greiner, {Timothy Charles}",
year = "2013",
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AU - Cushman-Vokoun, Allison M

AU - Crowley, Ann M.

AU - Rapp, Sharleen A.

AU - Greiner, Timothy Charles

PY - 2013/7/1

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N2 - Objectives: To compare 2 laboratory assays commonly used in the evaluation of epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC). Methods: Fifty-three formalin-fixed, paraffinembedded NSCLC specimens were selected. Extracted DNA was analyzed using the EGFR RGQ Amplification Refractory Mutation System Scorpions probe-based real-time polymerase chain reaction (PCR) assay and the EGFR Pyro pyrosequencing assay. Results: Fourteen EGFR mutations were identified in 13 specimens using at least 1 of the assays, with a mutation concordance rate of 92.9%. Using dideoxy sequencing as the gold standard, clinical sensitivity was 73.7% and 68.4% by the RGQ and Pyro assays, respectively, but 100% by both for common drug sensitivity mutations. Performance observations included the following: the RGQ system requires higher DNA input, the RGQ system is a single-step procedure, the EGFR Pyro assay is a 2-step procedure, only the RGQ system can identify exon 20 insertions, the RGQ system is more sensitive, and the Pyro system can specify exact mutations for all interrogated sites. Conclusions: Both the RGQ real-time PCR and Pyro assays adequately detect common EGFR mutations; however, the RGQ system is more clinically and analytically sensitive. Performance characteristics should be considered when evaluating these EGFR mutation assays for clinical adoption.

AB - Objectives: To compare 2 laboratory assays commonly used in the evaluation of epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC). Methods: Fifty-three formalin-fixed, paraffinembedded NSCLC specimens were selected. Extracted DNA was analyzed using the EGFR RGQ Amplification Refractory Mutation System Scorpions probe-based real-time polymerase chain reaction (PCR) assay and the EGFR Pyro pyrosequencing assay. Results: Fourteen EGFR mutations were identified in 13 specimens using at least 1 of the assays, with a mutation concordance rate of 92.9%. Using dideoxy sequencing as the gold standard, clinical sensitivity was 73.7% and 68.4% by the RGQ and Pyro assays, respectively, but 100% by both for common drug sensitivity mutations. Performance observations included the following: the RGQ system requires higher DNA input, the RGQ system is a single-step procedure, the EGFR Pyro assay is a 2-step procedure, only the RGQ system can identify exon 20 insertions, the RGQ system is more sensitive, and the Pyro system can specify exact mutations for all interrogated sites. Conclusions: Both the RGQ real-time PCR and Pyro assays adequately detect common EGFR mutations; however, the RGQ system is more clinically and analytically sensitive. Performance characteristics should be considered when evaluating these EGFR mutation assays for clinical adoption.

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