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Dittapol Muntham
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P3.09 - Pathology (Not CME Accredited Session) (ID 975)
- Event: WCLC 2018
- Type: Poster Viewing in the Exhibit Hall
- Track:
- Presentations: 1
- Moderators:
- Coordinates: 9/26/2018, 12:00 - 13:30, Exhibit Hall
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P3.09-19 - Matched Thai Lung Cancer Patients Tissue and cfDNA Molecular Profile by NGS (ID 14341)
12:00 - 13:30 | Author(s): Dittapol Muntham
- Abstract
Background
Liquid biopsy is the new non-invasive technology to explore the molecular profile. We evaluate molecular alteration from matched tissue and liquid specimen in NSCLC patients using NGS.
a9ded1e5ce5d75814730bb4caaf49419 Method
A total 61 matched tumors and cfDNA in NSCLC patients were retrieved for DNA extraction. All qualified samples were analyzed by using Next Generation Sequencing (NGS) with Gene read Qiagen Lung Cancer Panel sequencing 45 Genes on Ion Torrent system.Variants from NGS with coverage of higher than 1000X of tissues and 10000X of liquid biopsy, cutoff at 3% variant frequency were considered positive. Each detected mutation was validated by the different method. EGFR-mutation detected at this cutoff was validated by Real-time PCR technique using the ARMS-PCR (Amoy DX Kit) for tissue samples and droplet-digital PCR (ddPCR) for blood samples in all samples.
4c3880bb027f159e801041b1021e88e8 Result
This study found 59.0% and 19.7% of EGFR mutation, 14.75% and 8.20% of KRAS mutation in tissues and cfDNA, respectively. Moreover, we found 3.29% of BRAF V600E, 1.64% of MET exon14 splice site, and 1.64% of ROS1 mutation in tissue NGS and also confirmed by the other techniques, but there was none of these mutations in the blood sample. Looking at EGFR-mutation detected by different techniques, higher sensitivity, specificity, positive-predictive value, negative-predictive values, and concordant rate were found in tissue NGS and liquid ddPCR compared with liquid NGS at cutoff 3% of variant frequency detection, when the gold standard for validation was ARMS-PCR in tissue testing (Table1).
Table1. Performance of NGS, ARMS and ddPCR for EGFR mutation detection in matched tissue and cfDNA in lung cancer patients. Tissue by ARMS PCR
Result
Tissues by NGS
negative
positive
total
Sensitivity= 87.7%
negative
14
11
25
Specificity= 100%
positive
0
36
36
Positive predictive value= 100%
Total
14
47
61
Negative predictive value= 75.6%
Concordance = 82%
Tissue by ARMS PCR
cfDNA by NGS
negative
positive
total
Sensitivity= 35.7%
negative
12
37
49
Specificity= 98.2%
positive
2
10
12
Positive predictive value= 97.9%
Total
14
47
61
Negative predictive value= 38.9%
Concordance = 42.6%
Tissue by ARMS PCR
cfDNA by ddPCR
negative
positive
total
Sensitivity= 82.7%
negative
14
14
28
Specificity= 100%
positive
0
33
33
Positive predictive value= 100%
Total
14
47
61
Negative predictive value= 69.4%
Concordance = 77.05%
Tissue by NGS
cfDNA by NGS
negative
positive
total
Sensitivity= 36%
negative
20
29
49
Specificity= 93.2%
positive
5
7
12
Positive predictive value= 84.8%
Total
25
36
61
Negative predictive value= 55.8%
Concordance = 60.66%
cfDNA by ddPCR
cfDNA by NGS
negative
positive
total
Sensitivity= 45.5%
negative
25
24
49
Specificity= 97.7%
positive
3
9
12
Positive predictive value= 94.5%
Total
28
33
61
Negative predictive value= 65.6%
Concordance = 65.58%
Using tissue for molecular profile testing is still being the gold standard testing. Liquid biopsy is less invasive, but in our study, liquid NGS performed less sensitivity, specificity, PPV, NPV, and concordance rate compared with tissue NGS. We need to explore more for proper cutoff of variant allele frequency to develop more sensitivity and specificity of liquid NGS.
6f8b794f3246b0c1e1780bb4d4d5dc53