329. IMPROVED TUMOUR PURITY AND PLOIDY ESTIMATION FROM LASER CAPTURE MICRODISSECTED ESOPHAGEAL ADENOCARCINOMA SAMPLES
Bibliographic record
Abstract
Abstract Large scale sequencing efforts by The Cancer Genome Atlas (TCGA), among others, have generated detailed genomic data for esophageal adenocarcinoma. However, samples with low cancer purity (i.e. high amounts of normal DNA) will limit accurate inference of copy number aberrations, a genomic hallmark of esophageal adenocarcinoma. This consequently restricts more advanced analysis such as quantifying intratumor heterogeneity or inferring tumor evolution. We have systematically collected biopsies from pre-treatment and post-induction esophageal adenocarcinoma tumors. Laser capture microdissection (LCM) was utilized to enrich for tumor cells for whole genome sequencing. Matching blood was utilized as germline control. Cancer purity and ploidy was estimated using a developed method tailored to the high genomic instability observed in EAC samples. This method uses both sequencing depth and minor allele frequencies to infer ploidy and purity. The esophageal adenocarcinoma dataset from TCGA were used as comparison. We achieved significantly higher tumor cellularity in surgical resection specimens (n = 8) compared to TCGA (71%+/−11 vs. 58%+/−18). Interestingly, tumor cellularity from biopsy specimens (n = 25) remained similar to TCGA despite LCM (65%+/−13), which is likely due to TCGA only using surgical resections that were pre-selected to have at least 60% cellularity, while we applied no histopathological cellular constraints on our samples. Estimated ploidy was similar between biopsy of primary tumors and surgical resection specimens compared to TCGA (2.67+/−0.58, 2.72+/−0.70, 2.64+/−0.75). There was a trend towards higher ploidy (3.07+/− 0.13) in metastatic biopsies (n = 3) but additional specimens are required. Laser capture microdissection of post-induction esophageal adenocarcinoma surgical resection specimens has resulted in significantly higher tumor purity in whole genome sequencing data. This will allow for improved inferences of phylogenetic trees between pre- and post- induction samples and quantification of subclonal copy number aberrations or intratumor heterogeneity.
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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 | 0.001 | 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 | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".