Epidermal growth factor receptor mutation and anaplastic lymphoma kinase gene fusion: Detection in malignant pleural effusion by RNA or PNA analysis

Yi Lin Chen, Chung Ta Lee, Cheng Chan Lu, Shu Ching Yang, Wan Li Chen, Yang Cheng Lee, Chung Hsien Yang, Shu Ling Peng, Wu Chou Su, Nan Haw Chow, Chung Liang Ho

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Analyzing EGFR mutations and detecting ALK gene fusion are indispensable when planning to treat pulmonary adenocarcinoma. Malignant pleural effusion (MPE) is a devastating complication of lung cancer and sometimes the only source for mutation analysis. The percentage of tumor cells in the pleural effusion may be low; therefore, mutant enrichment is required for a successful analysis. The EGFR mutation status in MPE was determined using three methods: (1) PCR sequencing of genomic DNA (direct sequencing), (2) mutantenriched PCR sequencing of genomic DNA using peptide nucleic acid (PNA-sequencing), and (3) PCR sequencing of cDNA after reverse transcription for cellular RNA (RNAsequencing). RT-PCR was also used to test cases for ALK gene fusion. PNA-sequencing and RNA-sequencing had similar analytical sensitivities (< 1%), which indicates similar enrichment capabilities. The clinical sensitivity in 133 cases when detecting the common EGFR exon 19 and exon 21 mutations was 56.4% (75/133) for direct sequencing, 63.2%(84/133) for PNA-sequencing, and 65.4%(87/133) for RNA-sequencing. RT-PCR and sequencing showed 5 cases (3.8%) with ALK gene fusion. All had wildtype EGFR. For EGFR analysis of MPE, RNA-sequencing is at least as sensitive as PNAsequencing but not limited to specific mutations. Detecting ALK fusion can be incorporated in the same RNA workflow. Therefore, RNA is a better source for comprehensive molecular diagnoses in MPE.

Original languageEnglish
Article numbere0158125
JournalPloS one
Volume11
Issue number6
DOIs
Publication statusPublished - 2016 Jun

Fingerprint

Malignant Pleural Effusion
gene fusion
Gene Fusion
lymphoma
Epidermal Growth Factor Receptor
phosphotransferases (kinases)
RNA Sequence Analysis
Fusion reactions
Genes
RNA
mutation
Polymerase Chain Reaction
Mutation
sequence analysis
DNA Sequence Analysis
exons
Exons
reverse transcriptase polymerase chain reaction
Peptide Nucleic Acids
genomics

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

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title = "Epidermal growth factor receptor mutation and anaplastic lymphoma kinase gene fusion: Detection in malignant pleural effusion by RNA or PNA analysis",
abstract = "Analyzing EGFR mutations and detecting ALK gene fusion are indispensable when planning to treat pulmonary adenocarcinoma. Malignant pleural effusion (MPE) is a devastating complication of lung cancer and sometimes the only source for mutation analysis. The percentage of tumor cells in the pleural effusion may be low; therefore, mutant enrichment is required for a successful analysis. The EGFR mutation status in MPE was determined using three methods: (1) PCR sequencing of genomic DNA (direct sequencing), (2) mutantenriched PCR sequencing of genomic DNA using peptide nucleic acid (PNA-sequencing), and (3) PCR sequencing of cDNA after reverse transcription for cellular RNA (RNAsequencing). RT-PCR was also used to test cases for ALK gene fusion. PNA-sequencing and RNA-sequencing had similar analytical sensitivities (< 1{\%}), which indicates similar enrichment capabilities. The clinical sensitivity in 133 cases when detecting the common EGFR exon 19 and exon 21 mutations was 56.4{\%} (75/133) for direct sequencing, 63.2{\%}(84/133) for PNA-sequencing, and 65.4{\%}(87/133) for RNA-sequencing. RT-PCR and sequencing showed 5 cases (3.8{\%}) with ALK gene fusion. All had wildtype EGFR. For EGFR analysis of MPE, RNA-sequencing is at least as sensitive as PNAsequencing but not limited to specific mutations. Detecting ALK fusion can be incorporated in the same RNA workflow. Therefore, RNA is a better source for comprehensive molecular diagnoses in MPE.",
author = "Chen, {Yi Lin} and Lee, {Chung Ta} and Lu, {Cheng Chan} and Yang, {Shu Ching} and Chen, {Wan Li} and Lee, {Yang Cheng} and Yang, {Chung Hsien} and Peng, {Shu Ling} and Su, {Wu Chou} and Chow, {Nan Haw} and Ho, {Chung Liang}",
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Epidermal growth factor receptor mutation and anaplastic lymphoma kinase gene fusion : Detection in malignant pleural effusion by RNA or PNA analysis. / Chen, Yi Lin; Lee, Chung Ta; Lu, Cheng Chan; Yang, Shu Ching; Chen, Wan Li; Lee, Yang Cheng; Yang, Chung Hsien; Peng, Shu Ling; Su, Wu Chou; Chow, Nan Haw; Ho, Chung Liang.

In: PloS one, Vol. 11, No. 6, e0158125, 06.2016.

Research output: Contribution to journalArticle

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T1 - Epidermal growth factor receptor mutation and anaplastic lymphoma kinase gene fusion

T2 - Detection in malignant pleural effusion by RNA or PNA analysis

AU - Chen, Yi Lin

AU - Lee, Chung Ta

AU - Lu, Cheng Chan

AU - Yang, Shu Ching

AU - Chen, Wan Li

AU - Lee, Yang Cheng

AU - Yang, Chung Hsien

AU - Peng, Shu Ling

AU - Su, Wu Chou

AU - Chow, Nan Haw

AU - Ho, Chung Liang

PY - 2016/6

Y1 - 2016/6

N2 - Analyzing EGFR mutations and detecting ALK gene fusion are indispensable when planning to treat pulmonary adenocarcinoma. Malignant pleural effusion (MPE) is a devastating complication of lung cancer and sometimes the only source for mutation analysis. The percentage of tumor cells in the pleural effusion may be low; therefore, mutant enrichment is required for a successful analysis. The EGFR mutation status in MPE was determined using three methods: (1) PCR sequencing of genomic DNA (direct sequencing), (2) mutantenriched PCR sequencing of genomic DNA using peptide nucleic acid (PNA-sequencing), and (3) PCR sequencing of cDNA after reverse transcription for cellular RNA (RNAsequencing). RT-PCR was also used to test cases for ALK gene fusion. PNA-sequencing and RNA-sequencing had similar analytical sensitivities (< 1%), which indicates similar enrichment capabilities. The clinical sensitivity in 133 cases when detecting the common EGFR exon 19 and exon 21 mutations was 56.4% (75/133) for direct sequencing, 63.2%(84/133) for PNA-sequencing, and 65.4%(87/133) for RNA-sequencing. RT-PCR and sequencing showed 5 cases (3.8%) with ALK gene fusion. All had wildtype EGFR. For EGFR analysis of MPE, RNA-sequencing is at least as sensitive as PNAsequencing but not limited to specific mutations. Detecting ALK fusion can be incorporated in the same RNA workflow. Therefore, RNA is a better source for comprehensive molecular diagnoses in MPE.

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