Abstract 5400: Detection of satellite tumor cells in peritumoral edema in myxofibrosarcoma and undifferentiated pleomorphic sarcoma using targeted gene sequencing
Bibliographic record
Abstract
Abstract Myxofibrosarcoma (MFS) and undifferentiated pleomorphic sarcomas (UPS) are soft tissue sarcomas with high local recurrence rates following resection. Common with these cancers is peritumoral edema, termed tumor tails, which our group has found could contain satellite tumor cells. A precise and accurate method of determining the presence of satellite tumor cells in this region is required to improve surgical planning, as the standard morphology-based technique is prone to misclassification. An emerging technology is targeted gene sequencing (t-NGS), a combination of whole genome or exome sequencing (WGS/WXS) comparing primary tumor and patient-matched blood, and digital droplet PCR (ddPCR). The objective of this study was to determine the viability of t-NGS in the detection of satellite tumor cells in the areas of edema surrounding MFS and UPS. A cohort of patients diagnosed with extremity MFS and UPS at Mount Sinai Hospital (Toronto, Canada) who underwent resection were retrospectively studied. Cases with available WGS/WXS data were used (n=8) to identify case-specific tumor-specific variants (TSV) to detect with the QX200 ddPCR platform. (n=4-5/case). Cases with a major TSV-positive droplet population in the tumor tails tissue indicated the presence of satellite tumor cells. Our quality analysis showed DNA above the ddPCR threshold of detection was extracted from the tumor tails of 6 of 8 cases. The ddPCR assay showed that a TSV-positive droplet population was detected within the tumor tails in 5 of 6 cases, while 1 of 6 cases showed no such population in the tumor tails. Overall, our results indicates that t-NGS has potential for TSV detection within tumor tails. A prospective study is underway to further test its validity and compare it with standard histology. The project aims to improve surgical planning by ensuring removal of satellite tumor cells while lowering the risk of wound complications. Targeted gene-sequencing results of all cases within this study Case # Histology Pre-op Radiation DNA Extraction Successful TSV Probes (n) TSV+ Tumor TSV+ Tails TSV+ Normal 1 MFS N Y 5 4 4 0 2 MFS N Y 3 2 2 0 3 MFS Y Y* (normal insufficient) 3 3 0 N/A 4 UPS Y Y 3 2 0 1 5 MFS N Y 4 4 1 0 6 UPS N Y 3 3 3 1 7 MFS Y N N/A N/A N/A N/A 8 MFS Y N N/A N/A N/A N/A Citation Format: Miguel Alfonso V. Principe, Nalan Gokgoz, Patrick Prochazka, Peter C. Ferguson, Simin Dewji, Jay S. Wunder, Irene A. Andrulis, Brendan C. Dickson, Kim M. Tsoi. Detection of satellite tumor cells in peritumoral edema in myxofibrosarcoma and undifferentiated pleomorphic sarcoma using targeted gene sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5400.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".