Experimental benchmarking of in silico annotations at prostate cancer risk loci and hypothesis-generating cross-cancer prioritisation of ovarian risk variants.
4 affiliations
- 1Department of Biology, Faculty of Science, Al-Esraa University, Baghdad, Iraq.
- 2Department of Pharmacology, College of Medicine, Ibn Sina University of Medical and Pharmaceutical Sciences, Baghdad, Iraq.
- 3Department of Biology, Education Faculty, University of Al-Hamdaniya, Mosul, Iraq.
- 4Department of Biotechnology, College of Science, University of Anbar, Anbar, Iraq. [email protected].
Abstract
Genome-wide association studies (GWAS) have identified numerous non-coding risk variants for prostate and ovarian cancers, yet determining which are regulatorily active and which target genes they control remains challenging. We re-analysed a dinucleotide-barcode massively parallel reporter assay (DiR-seq) of 208 bi-allelic prostate cancer risk single-nucleotide polymorphisms (SNPs) in three prostate cancer cell lines under false-discovery-rate (FDR) control, identifying 50 regulatory SNPs at FDR < 0.10 (30 at FDR < 0.05), including 9 shared by at least two cell lines. Benchmarking standard in-silico functional annotations against this experimental ground truth revealed poor predictive performance (cross-validated ROC-AUC = 0.55-0.59), demonstrating that computational predictions cannot reliably substitute for measured allelic activity. We therefore treated the ovarian analysis as hypothesis-generating. Convergent annotation evidence prioritised 44 of 176 ovarian cancer GWAS leads (31 independent loci); a core of 21 SNPs (17 loci) was stable under alternative weights, leave-one-feature-out scoring and threshold changes, and candidates were enriched in ovarian and fallopian-tube regulatory chromatin (OR = 7.9, FDR = 5 × 10⁻5). Copy-number recurrence at candidate genes agreed between two tumour cohorts (Spearman ρ = 0.75, 95% CI 0.46-0.88) but no more than for chromosome-arm-matched control genes, so this observation is exploratory. Formal colocalisation with full summary statistics supported a shared causal variant for prostate cancer risk and TLCD3A expression at 17p13.3 (PP.H4 = 0.92), whereas the ovarian 17q21.31 signal could not be resolved to a single gene. Transcription-factor motifs disrupted in both cancers were over-represented for the interferon-regulatory factor (IRF) and STAT families (FDR = 3 × 10⁻6), a motif-level hypothesis. In an independent MPRA in primary ovarian epithelial cells, variants disrupting interferon-stimulated response elements (ISREs) were depleted, not enriched, for allele-specific activity (4.6% vs 9.2%; OR = 0.47, nominal p = 0.06, FDR = 0.10), so the IRF/STAT hypothesis was not supported; the same assay confirmed allele-specific activity at one prioritised ovarian candidate, rs2976384 (skew = - 0.67, FDR = 3 × 10⁻5). These results provide an audited prostate regulatory-SNP catalogue, quantify the limits of annotation-based fine-mapping, and offer testable cross-cancer hypotheses.
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BibTeX
@article{alamili2026experimental,
title = {{Experimental benchmarking of in silico annotations at prostate cancer risk loci and hypothesis-generating cross-cancer prioritisation of ovarian risk variants.}},
author = {Wiaam Ahmed Al-Amili and Mohammed Ayyed Najm and Shatha Saadi Jumaah and Ahmed AbdulJabbar Suleiman},
journal = {Genomics \& informatics},
year = {2026},
month = oct,
doi = {10.1186/s44342-026-00087-2},
url = {https://europepmc.org/article/MED/42958578},
note = {CC BY},
}
RIS
TY - JOUR
TI - Experimental benchmarking of in silico annotations at prostate cancer risk loci and hypothesis-generating cross-cancer prioritisation of ovarian risk variants.
AU - Wiaam Ahmed Al-Amili
AU - Mohammed Ayyed Najm
AU - Shatha Saadi Jumaah
AU - Ahmed AbdulJabbar Suleiman
PY - 2026
DA - 2026/10/28
JO - Genomics & informatics
DO - 10.1186/s44342-026-00087-2
UR - https://europepmc.org/article/MED/42958578
AB - Genome-wide association studies (GWAS) have identified numerous non-coding risk variants for prostate and ovarian cancers, yet determining which are regulatorily active and which target genes they control remains challenging. We re-analysed a dinucleotide-barcode massively parallel reporter assay (DiR-seq) of 208 bi-allelic prostate cancer risk single-nucleotide polymorphisms (SNPs) in three prostate cancer cell lines under false-discovery-rate (FDR) control, identifying 50 regulatory SNPs at FDR < 0.10 (30 at FDR < 0.05), including 9 shared by at least two cell lines. Benchmarking standard in-silico functional annotations against this experimental ground truth revealed poor predictive performance (cross-validated ROC-AUC = 0.55-0.59), demonstrating that computational predictions cannot reliably substitute for measured allelic activity. We therefore treated the ovarian analysis as hypothesis-generating. Convergent annotation evidence prioritised 44 of 176 ovarian cancer GWAS leads (31 independent loci); a core of 21 SNPs (17 loci) was stable under alternative weights, leave-one-feature-out scoring and threshold changes, and candidates were enriched in ovarian and fallopian-tube regulatory chromatin (OR = 7.9, FDR = 5 × 10⁻5). Copy-number recurrence at candidate genes agreed between two tumour cohorts (Spearman ρ = 0.75, 95% CI 0.46-0.88) but no more than for chromosome-arm-matched control genes, so this observation is exploratory. Formal colocalisation with full summary statistics supported a shared causal variant for prostate cancer risk and TLCD3A expression at 17p13.3 (PP.H4 = 0.92), whereas the ovarian 17q21.31 signal could not be resolved to a single gene. Transcription-factor motifs disrupted in both cancers were over-represented for the interferon-regulatory factor (IRF) and STAT families (FDR = 3 × 10⁻6), a motif-level hypothesis. In an independent MPRA in primary ovarian epithelial cells, variants disrupting interferon-stimulated response elements (ISREs) were depleted, not enriched, for allele-specific activity (4.6% vs 9.2%; OR = 0.47, nominal p = 0.06, FDR = 0.10), so the IRF/STAT hypothesis was not supported; the same assay confirmed allele-specific activity at one prioritised ovarian candidate, rs2976384 (skew = - 0.67, FDR = 3 × 10⁻5). These results provide an audited prostate regulatory-SNP catalogue, quantify the limits of annotation-based fine-mapping, and offer testable cross-cancer hypotheses.
SN - 1598-866X
SN - 2234-0742
ER -