Abstract 4210: Association of the 15q25 and 5p15 lung cancer susceptibility regions with gene expression in lung tumor tissue
Bibliographic record
Abstract
Abstract Lung cancer is one of the most commonly diagnosed cancers worldwide, with 1.6 million new cases reported each year and ranks first in annual global cancer deaths. Genome-wide association studies have identified two independent lung cancer susceptibility loci at chromosome 15q25 and one locus at 5p15. We examined the association of genetic variants in these lung cancer susceptibility regions with gene expression in lung tumor tissue in an effort to elucidate carcinogenic mechanisms by which these variants influence lung cancer risk. We used data from two independent studies: the JBR.10 clinical trial (131 NSCLC patients) and a patient sample from the University Health Network (UHN) in Toronto (181 NSCLC patients). We genotyped seven 15q25 and five 5p15 variants and examined their association with the expression profiles of genes in the corresponding regions measured by Affymetrix HG-U133A. The minor allele (C) of a variant representing one of the two loci at 15q25 (rs2036534) was associated with increased expression of the IREB2 (iron-responsive element binding protein 2) gene in both studies (JBR.10 P=0.042; UHN P=0.002). An FDRα0.05 in the UHN sample increased our confidence in this association. The association appears to be more prominent among patients with lung adenocarcinoma. We did not detect an association between the genotype and expression profile for the other 15q25 locus (represented by rs16969968 and rs1051730). Previous studies suggest that 15q25 variants are associated with risk through an effect on smoking behaviour, indicating risk is modulated through activity of nicotinic acetylcholine receptor genes present in this region. Our results indicate there is a second mechanism through which variants at 15q25 influence risk, operating through modulation of IREB2 gene expression. This finding may have implications for future research on lung cancer chemoprevention strategies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4210. doi:1538-7445.AM2012-4210
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 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 | 0.000 |
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".