HiFIseek: Gene-specific enrichment of high-impact mutations in associated genomic regions

Transcription is regulated through the sequence-specific binding of transcription factors (TFs) to cis-regulatory regions (CRRs); DNA variants in CRRs can disrupt TF-DNA interactions and gene regulatory networks through a cascading effect. Despite a few cases of reported recurrent cis-regulatory variants (CRVs), another approach for detecting non-coding functional events relies on combining gene-CRR associations capturing the regulatory elements controlling gene transcription, and functional impact (FI) scores quantifying the deleterious effect of variants. While many methods exist for each, how much they agree and how strongly the choice of CRR-FI score combination impacts the prediction of cis-regulatory altered genes has not been systematically assessed. Here, we demonstrate that gene-CRR associations and FI scoring methods exhibit little consensus, highlighting the impact of the choice of a specific CRR-FI score combination in a given analysis. These observations point to the need for a systematic approach to evaluate several gene-CRR and FI scoring methods in a unified framework. To address this gap, we developed HiFIseek, a Snakemake pipeline of two enrichment detection methods exploring the enrichment of high FI variants in CRRs associated with a gene using all region-score combinations. We applied HiFIseek to detect genes exhibiting high functional impact CRVs in eight cancer cohorts and a set of breast cancer risk-associated single-nucleotide polymorphisms (SNPs). We demonstrate that cancer driver genes exhibit a higher frequency of FI CRVs compared to non-cancer genes. In the cancer cohorts, HiFIseek detected genes pointing to cancer-related pathways with enrichment for high FI CRVs despite a small degree of agreement across CRR-FI score combinations. In the SNP cohort, HiFIseek found again small consensus across CRR-score combinations, one of which returned 18 known cancer-related genes, including BRCA1, showing an enrichment of high-impact CRVs.