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M. Varella-Garcia
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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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P3.02-057 - Comparison of Molecular Testing Modalities for Detection of ROS1 Rearrangements in a Cohort of Positive Patient Samples (ID 10110)
09:30 - 09:30 | Author(s): M. Varella-Garcia
- Abstract
Background:
Targeting oncogenic gene fusions with small molecules has proven to be a highly successful treatment strategy in lung cancer. For ALK and ROS1 rearrangement/fusion positive cases, fusion directed therapy is now considered standard of care for advanced disease. Consequently, the accurate clinical detection of rearrangements/fusions is of critical clinical importance. Multiple distinct methodologies are employed in the clinical setting for rearrangement/fusion detection. In this study, we compare the performance of several of these methodologies on a large cohort of ROS1 rearrangement/fusion-positive patient samples.
Method:
Eighteen ROS1 rearrangement/fusion-positive clinical samples were assessed by at least two of the following molecular testing methodologies: break-apart fluorescence in situ hybridization (FISH), DNA-based hybrid capture library preparation followed by next-generation sequencing (NGS), and RNA-based anchored multiplex PCR library preparation followed by NGS.
Result:
None of the testing methodologies demonstrated 100% sensitivity in detection of ROS1 rearrangements/fusions. FISH results were negative in 2/18 tested clinical samples. One of these demonstrated an atypical staining pattern, suggestive of a complex rearrangement. The other occurred in a case of GOPC-ROS1 fusion in which the genes are in close proximity on chromosome 6. The DNA-based NGS assay was negative in 3/11 tested clinical samples. This assay suffered from poor bait coverage in intronic regions containing repetitive sequences, and false negatives were likely due to this deficiency. The RNA-based NGS assay did not identify ROS1 fusions in 3/15 tested clinical samples. However, this assay is highly reliant on RNA quality, and missed calls were associated with metrics derived from the assay suggestive of degraded RNA (and thus the results would have been deemed uninformative). Additionally, we report cases in which the detected fusion at the transcript level (via RNA-based NGS) occurred between exons not predicted by proximal exons bordering the detected genomic breakpoint (via DNA-based NGS), likely due to exon removal via mRNA splicing. For these cases, the detected genomic DNA breakpoint may have resulted in a non-call due to the prediction of an out-of-frame fusion transcript.
Conclusion:
Rearrangement/fusion detection in the clinical setting is complex and all methodologies have inherent limitations that users must be aware of. Consequently, careful scrutiny of negative results must be performed, particularly in cases negative for other known oncogenic drivers (pan-negative cases). Ideally, orthogonal rearrangement/fusion testing methodologies should be employed for such cases.
