Abstract 4361: Retinoblastoma (RB) genomic progression analysis using Tissue Microarrays (TMA) comprising 121 RB patient tumors
Bibliographic record
Abstract
Abstract Retinoblastoma is the second most common childhood intraocular malignancy and development of the tumor is initiated by bi-allelic loss of the RB1 gene. Bi-allelic RB1 loss may not always directly lead to malignant retinoblastoma, rather other genetic changes are likely involved. Subsequent mutational events, specifically gain and loss of chromosomal regions harboring key oncogenes and tumor suppressor genes, appear to underlie the progression of precursor lesions such as retinoma to retinoblastoma. Research thus far has implicated several cytogenetic aberrations in this sequence of molecular events, the two most recurrent and notable being the augmented copy number status of KIF14 and MDM4 on 1q and of DEK and E2F3 on 6p. A small subset of retinoblastoma also exhibits high-level amplification of the MYCN gene on chromosome 2p. KIF14, MDM4, DEK, E2F3 and MYCN have been widely characterized as oncogenes in a variety of cancers. The functional roles of the proteins encoded by these genes would also confer tumor cells manifesting these genomic changes with a selective survival and proliferative advantage. Our project is testing the hypothesis that 1q and 6p gain and 2p amplification - defined by extra copies of KIF14 and MDM4, DEK and E2F3 and MYCN respectively - are associated with clinical parameters of progression. The study comprises formalin-fixed paraffin-embedded fluorescence in situ hybridization (FFPE-FISH) analysis of pre-constructed tissue microarrays comprising 121 patient tumours, in order to determine the genomic copy number status of the five aforementioned genes. Results show 1q gain (3-10 copies) in 102/121 (84%), 6p gain in 115/121 (95%), MYCN gain in 14/121 (12%) and MYCN amplification (>10 copies) in 16/121 (14%) patient tumors. Assessment of potential correlations between the copy number status of these genes and clinical variables of disease progression include patient age, pathology at the time of diagnosis, optic nerve invasion, choroid involvement, laterality of the disease, number of tumor foci present at the time of diagnosis and histopathological parameters. To our knowledge, there has been no recent study associating genomic change of these five genes with clinical parameters of progression in a sample size of statistical significance. The large cohort and consequent statistical power of our results will facilitate a better understanding of the biological role of these genes in the progression from retinoma to retinoblastoma. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4361.
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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 | 0.000 |
| 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 | 0.001 |
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".