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 language | English |
|---|---|
| Article number | e0158125 |
| Journal | PloS one |
| Volume | 11 |
| Issue number | 6 |
| DOIs | |
| Publication status | Published - 2016 Jun |
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All Science Journal Classification (ASJC) codes
- Biochemistry, Genetics and Molecular Biology(all)
- Agricultural and Biological Sciences(all)
- General
Cite this
}
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 journal › Article
TY - JOUR
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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84978154339&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84978154339&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0158125
DO - 10.1371/journal.pone.0158125
M3 - Article
C2 - 27352172
AN - SCOPUS:84978154339
VL - 11
JO - PLoS One
JF - PLoS One
SN - 1932-6203
IS - 6
M1 - e0158125
ER -