Genomic landscape of cancer driver genes in Omani breast cancers: a pilot study
Bibliographic record
Abstract
BACKGROUND: The global rise in breast cancer (BC) incidence is mirrored in the Sultanate of Oman, where the median age of diagnosis is strikingly young at 47 years. This pilot study represents the first in the region to examine the genetic alterations of Omani BC biopsies and resected tumors and their correlations with patient characteristics using a targeted pan-cancer panel. METHODS: Utilizing the Oncomine Comprehensive Assay Plus, we profiled 40 BC biopsies alongside 22 matched post-neoadjuvant chemotherapy samples, identifying single-nucleotide variations (SNVs) and copy number variations (CNVs). Chi-Square and Fisher's Exact tests were used for categorical variables. In contrast, the Independent T-test and Levene test were used for continuous variables. Comparative analyses were conducted using the METABRIC and TCGA datasets to place these findings in a global context. RESULTS: The data revealed molecular patterns between early-onset (under 50 years) and late-onset (50 years and older) cases. Notably, SNVs were predominant in late-onset tumors, while CNVs were more frequent in early-onset cases. PIK3CA SNVs emerged as a hallmark of late-onset BC, which persists across pre- and post-treatment stages. NTRK1 mutations were linked to late-onset cases at pre-treatment, while OR6F1 CNV was exclusive to early-onset tumors. The five genes with the highest CNV prevalence in the cohort were CDK12, ERBB2, BRIP1, and BLM, and they closely mirrored those found in global datasets. Correlations with clinical features identified CHEK2 alterations associated with high-grade tumors and luminal and HER2 type, while TP53 mutations were predominantly found in TNBC cases. Mutations in CBFB and GATA3 were predominantly enriched in luminal subtypes, and TSC1 mutations corresponded with smaller tumors, whereas FGFR4 SNVs were linked to nodal (N) status. Additionally, we identified 19 new SNV variants distributed across seven genes that were not recorded in the public databases. CONCLUSION: This study sheds light on the genetic landscape of BC driver genes in Oman and the shared molecular traits with Western populations while uncovering unique regional alterations in NTRK1, OR6F1, and FGFR4. These findings highlight the need for region-specific insights to inform targeted therapies and personalized care, advancing the global understanding of BC biology.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| 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 | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".