Whole genome BAC array detects described and novel regions of alteration in oral tumors
Bibliographic record
Abstract
Proc Amer Assoc Cancer Res, Volume 45, 2004 1690 Each year, there are ∼300,000 cases of oral squamous cell carcinoma (OSCC) world-wide. Most cases are not diagnosed or treated until the advanced stages of disease. As a result, patients have a poor prognosis with a 5-year survival rate of just 50%. However, if diagnosed at the pre-malignant stages, prognosis and survival rates improve. Identification of novel genetic alterations in oral dysplasias and tumors will provide novel targets for early diagnosis and treatment. LOH studies on OSCC have identified the earliest genetic alterations to occur on chromosome 9p, followed by 3p and than 17p. However, LOH is not designed to distinguish copy number amplifications from deletions and the resolution is limited. Similarly, conventional CGH, although able to distinguish between copy number increases and decreases, also provides limited resolution. Here, we present a new genome-wide approach to fine-map these alterations with ∼80kb resolution in order to identify novel genes involved in OSCC. OBJECTIVE : The objective of this study is to detect novel regions of alteration in OSCCs using our high resolution human whole genome BAC array CGH technology in order to elucidate the genetic mechanisms underlying OSCC. METHODS: In this study we utilized a BAC array comprised of 32,433 mostly over-lapping BAC clones spanning the entire human genome. DNA from each BAC clone was PCR-amplified and spotted in triplicate onto two glass slides. Tumor DNA, extracted from OSCC specimens and normal reference DNA was labeled with cyanine-dyes, co-hybridized onto whole genome BAC array slides, and scanned for each dye to determine the hybridization signal intensity ratios for each loci. The data was plotted to reveal copy number amplification and deletions across all chromosomes in the human genome. RESULTS: We profiled OSCC using our human whole genome BAC arrays. Alignment of the profiles from each sample revealed recurrent alterations on multiple chromosome arms. Previously reported alterations such as those on 3p and 8q and novel genetic alterations were identified. CONCLUSION : Genome profiling OSCCs using our human whole genome BAC array revealed copy number alterations of novel and known regions. Further expression analysis will elucidate the biological mechanisms underlying OSCC progression. This work was supported by funds from Genome Canada/BC, CIHR and NICDR.
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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 | 0.001 |
| 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) | 0.003 | 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".