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Nicolas Marie Guibert
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MA 20 - Recent Advances in Pulmonology/Endoscopy (ID 685)
- Event: WCLC 2017
- Type: Mini Oral
- Track: Pulmonology/Endoscopy
- Presentations: 1
- Moderators:C. Lee, S. Sasada
- Coordinates: 10/18/2017, 14:30 - 16:15, F205 + F206 (Annex Hall)
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MA 20.14 - Genotyping of Lung Cancer Using Cell-Free DNA (cfDNA) from Cytologic Supernatant (CSN) (ID 9057)
14:30 - 16:15 | Presenting Author(s): Nicolas Marie Guibert
- Abstract
- Presentation
Background:
Tumor genotyping is transforming lung cancer care but increasingly requires more tumor tissue. Advances in minimally invasive bronchoscopic techniques increase access to small lesions, but often result in smaller samples. With the advent of new cfDNA (“liquid biopsy”) genotyping technologies, we hypothesized that CSN might increase the yield from small FNAs, facilitating cancer genotyping.
Method:
We studied patients with known or suspected lung cancer undergoing FNAs. CSN, which is usually discarded, was collected under IRB approval. cfDNA was extracted after a hard spin (1600 Gs) and tested by both ddPCR (EGFR, KRAS mutations) and targeted next-generation sequencing (NGS).
Result:
14 patients with suspected or known lung cancer were studied at time of analysis (final diagnosis: 2 non-malignant, 9 adenocarcinomas, 1 small-cell carcinoma, 2 squamous cell carcinomas), including 12 EBUS-TBNAs and 2 CT-guided FNAs. Among 6 known KRAS and EGFR mutations, all could be detected with ddPCR of CSN, with allelic fraction (AF) ranging from 1%-46% (median 8.5%). No ddPCR false positives were seen across 9 cases. NGS analysis was piloted on 7 specimens; 5 failed due to insufficient residual DNA. In one specimen, an EGFR exon 19 deletion was detected at 6% AF (2% AF ddPCR). In the other, a BRAF V600E, PIK3CA E784D and TP53 V274F mutations were detected at 48% (46% AF ddPCR), 18% and 86% AF, respectively.
Conclusion:
Cytology supernatant, usually discarded, may be a rich source of fresh tumor DNA, increasing the yield from FNAs. This widely available biospecimen has potential for aiding resistance genotyping, reducing turnaround time of cancer genotyping, and possibly a future role in clarifying the malignant potential of non-diagnostic biopsies. Enrollment continues in order to optimize this biospecimen for NGS. Figure 1
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P3.02 - Biology/Pathology (ID 620)
- Event: WCLC 2017
- Type: Poster Session with Presenters Present
- Track: Biology/Pathology
- Presentations: 1
- Moderators:
- Coordinates: 10/18/2017, 09:30 - 16:00, Exhibit Hall (Hall B + C)
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P3.02-014 - Amplicon-Based Next-Generation Sequencing (NGS) of Plasma Cell-Free DNA (cfDNA) for Detection of Driver and Resistance Mutations in NSCLC (ID 10551)
09:30 - 16:00 | Presenting Author(s): Nicolas Marie Guibert
- Abstract
Background:
While several studies have evaluated hybrid-capture NGS for cfDNA genotyping, amplicon-based NGS is an attractive alternative with the potential to be faster and less expensive. We performed a blinded evaluation of this approach for the characterization and monitoring of the molecular profile of advanced NSCLC during genotype-directed therapy.
Method:
Plasma samples from patients with advanced NSCLC and a known targetable genotype (EGFR, BRAF, MET, HER2 mutations; ALK, ROS1 rearrangements) were collected and analyzed, blinded to tumor genotype, with IRB approval. Up to 4 specimens were collected for each patient: baseline, initial 2 follow-ups, and progression. Plasma NGS was performed using enhanced tagged amplicon sequencing of hotspots and coding regions from 36 genes. A novel approach was used to detect ALK/ROS1 fusions using amplicon sequencing in cfDNA. Diagnostic accuracy was compared to plasma ddPCR and tumor genotype (including NGS when available).
Result:
A total of 146 specimens from 49 patients were studied. Testing was completed for 115 specimens at the time of analysis. Matched plasma NGS and ddPCR were available across 95 samples and revealed high concordance of allelic fraction (AF). At baseline, sensitivity of plasma NGS for the detection of the driver was 100% (26/26) for EGFR (88.5% ddPCR sensitivity). Sensitivity for the detection of ALK/ROS1 fusions was 89% (6/7 ALK, 2/2 ROS1). Rare instances of plasma NGS-positive/tissue NGS-negative discordance were seen across 13 cases with match tumor NGS (3/442 genes sequenced) and appear related to resistance heterogeneity, clonal hematopoiesis, and low tumor content of biopsy. Among patients with acquired T790M and available specimens at osimertinib resistance (n=21), 11 resistance mechanisms could be detected including tertiary EGFR mutations (e.g. C797S), mutations in BRAF, PIK3CA, or KRAS, and amplification of MET, HER2, or FGFR1. 4 were detected pre-osimertinib.
Conclusion:
This blinded analysis demonstrates for the first time the ability of amplicon-based plasma NGS to detect a full range of targetable genotypes in NSCLC. This approach has attractive sensitivity and specificity and deserves further study as an alternative to better-established hybrid capture approaches. Serial plasma NGS can detect competing resistance mutations in patients with TKIs resistance, highlighting the pitfalls of PCR-based plasma assays in patients with heterogeneous resistance and paving the way towards combination therapies.
