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P1.02 - Poster Session with Presenters Present (ID 454)
- Event: WCLC 2016
- Type: Poster Presenters Present
- Track: Biology/Pathology
- Presentations: 1
- Coordinates: 12/05/2016, 14:30 - 15:45, Hall B (Poster Area)
P1.02-023 - Application of an Amplicon-Based NGS Strategy in the Molecular Diagnosis of NSCLC: Comparable Performance with FISH and ARMS-PCR (ID 4967)
14:30 - 15:45 | Author(s): L. Zhou
Next generation sequencing (NGS) enables us to detect comprehensive genetic aberrations within a tumor sample, which provides potential alternative to well adopted clinical diagnostic approaches such as amplification refractory mutation system PCR (ARMS-PCR) and FISH. However, there is no enough data to illustrate the overall concordance between NGS with traditional clinical diagnostic approaches. This study is aimed to fill in this blank.
We have used 20 cell lines from ATCC and 19 FFPE samples to construct molecular standards and there are 50, 34 and 48 samples for SNV and Indel, CNV and fusion, respectively. All the mutations were verified by Sanger sequencing or QuantStudio 3D digital PCR. To assess the performance of NGS, an amplicon-based NGS strategy was used to detect gene mutations in molecular standards. In order to illustrate the overall concordance between NGS with ARMS-PCR and FISH, we further verified NGS in 2500 retrospective FFPE samples from non-small lung cancer (NSCLC) and breast cancer patients.
So far, we have detected genetic aberrations in 108 FFPE samples. For SNV and Indel, we focused on the mutation profile of EGFR, KRAS, BARF and PIK3CA, which were the most common mutations in NSCLC. In molecular standards, 34 of 50 (68%) were positive for Sanger and 33 of 50 were positive for NGS, thus the sensitivity, specificity and accuracy was 97%, 100% and 98%, respectively. In FFPE samples from 31 lung cancer patients, NGS results were consistent with ARMS-PCR. For CNV, in molecular standards, the copy number of HER2, MET, EGFR and FGFR1 detected by NGS was high consistent with digital PCR and R[2 ]was 0.9673. In FFPE samples from 45 breast cancer patients, 80% of cases (36/45) were HER2 amplification positive and 20% (9/45) were negative for FISH, 34 HER2 positive and 9 HER2 negative for FISH were also classified by NGS. Thus, the overall concordance between NGS and FISH were 95.56%. For ALK and ROS1 gene fusion, the overall concordance were both 100% in 48 molecular standards (NGS versus Sanger sequencing) and 32 FFPE samples (NGS versus FISH).
Our result reveal that the amplicon-based NGS strategy for detecting genetic aberrations is of high accuracy and comparable with standard clinical diagnostic approaches, and therefore provides a promising diagnosis approach for clinical in the future.
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