Abstract A53: Genome-wide profile of somatic copy number alterations in Wilms tumor: Comparison between samples derived from patients with and without relapse
Bibliographic record
Abstract
Abstract Wilms tumor (WT) is the most common kidney malignancy of childhood; nevertheless, its pathogenesis remains largely unknown. Although the majority of the WT occur sporadically, a strong genetic component is present at least in the many cases which are related to underlying syndromes. Tumor relapse occurs at a rate of approximately 15%, and molecular studies are focused in identifying markers to define the minimal therapy for limiting the late effects of treatment while maintaining high survival rate. Loss of heterozygosity of both 1p and 16q was already associated to an increased risk of relapse and death although detected in a very small subset of WT patients, making this feature a less sensitive prognostic factor. Somatic DNA copy number alterations (CNAs) are common genetic mutations in cancer, and often define key pathogenic events. This study was designed to assess the genome profile of CNAs in WT, aiming to identify genetic markers associated to relapse that could be of clinical and prognostic importance. We performed an array-CGH based survey of 48 WT samples, mainly tumors in stages III and IV, derived from patients with (17) and without (31) relapse in at least three years. Data was obtained using a high resolution oligoarray platform (180K - Agilent), with an average resolution >70 Kb, and analysis was performed on the software Nexus 6 (Biodiscovery). The analysis revealed high frequency of arm/whole chromosome alterations at 1q, 7q, and chromosomes 6 and 12 (gains), while losses were recurrent at 7p, 11 q, and 16q chromosome regions. WT derived from patients with relapse exhibited a distinctive pattern of genomic alterations, mainly characterized for an increased frequency of proximal 1q gain and low amplitude gain of chromosome 6. Additionally, analysis of small regions affected by recurrent focal alterations disclosed new genes that can be relevant for Wilms tumorigenesis and relapse. Financial support: FAPESP/CNPq Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A53.
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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) | 0.002 | 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".