Prognostic Significance of T Gene SNP s2305089 in Individuals with Spinal Column Chordoma
Bibliographic record
Abstract
Introduction Chordoma is the most common primary spinal tumor with a median survival of 6 to 7 years, with high recurrence rates. Radical surgical resection remains the mainstay of treatment, with radiation often utilized to enhance local disease control. There are no approved chemotherapeutic agents for chordomas. Brachyury, coded by the T gene, has been implicated in the pathogenesis of chordomas and is highly expressed in most of these tumors. Recently, Pillay et al found that the single nucleotide polymorphism (SNP) rs2305089 in the T gene was associated with chordoma development. The variant A allele at rs2305089 results in a p.Gy177Asp change in Brachyury. 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. Materials and Methods This study included both prospective and retrospective data collected from five high-volume centers within Europe and North America. Data were collected between 1990 and 2013, through the AOSpine Knowledge Forum Tumor (AOSKFT) primary tumor database. Institutional approval was obtained before studying the tumor samples. Results In the overall cohort of 109 patients, survival at last follow-up (mean follow-up: 1,330 ± 1,475 days) was 69.7%. Seven (6.4%) patients had the GG genotype, while 66 (60.6%) and 36 (33.3%) patients had the AA and GA genotypes, respectively. In the 102 cases with the A variant, 75 (73.5%) were alive at the last follow-up compared with only 1 (14.3%) of the 7 patients with the GG genotype. Local recurrence rates were similar between the populations with the A variant and those without, with 40 (39.2%) patients with the A variant experiencing local recurrence compared with 2 (33.3%) patients without the A variant. Conclusions There is a trend toward worse survival in individuals with the GG genotype than with the AA or GA genotypes. To our knowledge, this is the first time the rs2305089 SNP has been considered in the prognosis and survival of individuals with chordoma.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 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) | 0.000 | 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 teacher head, 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".