Abstract 4704: Prognostic significance of T gene SNP s2305089 in individuals with spinal column chordoma
Bibliographic record
Abstract
Abstract Chordoma is the most common primary spinal column tumor with a median survival of only 6-7 years, with extremely high recurrence rates. Radical surgical resection remains the mainstay of treatment for these tumors, with radiation often utilized to enhance local disease control. There are no approved chemotherapeutic agents for chordomas. Recently, Pillay and colleagues found that the single nucleotide polymorphism (SNP) rs2305089 in the T gene was strongly associated with chordoma development1. The variant A allele at rs2305089 results in a p.GLy177Asp alteration in brachyury, the protein encoded by the T gene. Brachyury has been implicated in the pathogenesis of chordomas and is highly expressed in most of these tumors. Given the rarity of this disease, with an incidence of 0.08 per 100,000 individuals, determining the clinical significance of this SNP has been challenging. In order to address whether the rs2305089 SNP was associated with altered prognosis in individuals with spinal column chordomas, we performed a retrospective analysis on 82 chordomas from 5 different high volume centers in Europe and North America. Each sample was linked to well curated clinical outcomes data that were collected after receiving institutional review board approval. The A variant at rs2305089 was present in 74 of 82 cases analyzed. In our cohort, there were no differences in gender, age, location, ethnicity, histologic subtype or time to local recurrence based on the presence of the A variant. However, overall survival was significantly worse (log-rank = 0.003) in individuals who lacked the A variant. To our knowledge, this is the first time the rs2305089 SNP has been implicated in the prognosis and survival of individuals with chordoma. This finding warrants further investigation and may have important implications on clinical decision-making. 1Nature Genetics. 2012 Nov;44(11):1185-7 Note: This abstract was not presented at the meeting. Citation Format: Peter Varga, Charles Fisher, Lawrence Rhines, Ziya Gokaslan, Stefano Boriani, Áron Lazary, Wei-Lien Wang, Niccole Germscheid, Stephen Yip, Chetan Bettegowda. Prognostic significance of T gene SNP s2305089 in individuals with spinal column chordoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4704. doi:10.1158/1538-7445.AM2014-4704
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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 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
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".