NBBC: a non-B DNA burden explorer in cancer

Alternate (non-B) DNA-forming structures, such as Z-DNA, G-quadruplex, triplex have demonstrated a potential role in cancer etiology. It has been found that non-B DNA-forming sequences can stimulate genetic instability in human cancer genomes, implicating them in the development of cancer and other genetic diseases. While there exist several non-B prediction tools and databases, they lack the ability to both analyze and visualize non-B data within a cancer context. Herein, we introduce NBBC, a non-B DNA burden explorer in cancer, that offers analyses and visualizations for non-B DNA forming motifs. To do so, we introduce 'non-B burden' as a metric to summarize the prevalence of non-B DNA motifs at the gene-, signature- and genomic site-levels. Using our non-B burden metric, we developed two analyses modules within a cancer context to assist in exploring both gene- and motif-level non-B type heterogeneity among gene signatures. NBBC is designed to serve as a new analysis and visualization platform for the exploration of non-B DNA, guided by non-B burden as a novel marker.

Automated summary

Alternate forms of DNA, such as Z-DNA, G-quadruplex, and triplex, have shown potential roles in cancer development. Non-B DNA-forming sequences have been found to induce genetic instability in human cancer genomes, implicating their involvement in cancer and other genetic diseases. However, existing non-B prediction tools and databases lack the capability to analyze and visualize non-B data in a cancer context. In this study, we present NBBC, a non-B DNA burden explorer in cancer, which provides analysis and visualization for non-B DNA forming motifs. We introduce the concept of 'non-B burden' as a metric to summarize the prevalence of non-B DNA motifs at different levels. With the non-B burden metric, we develop two analysis modules within a cancer context, aiming to explore both gene- and motif-level heterogeneity of non-B DNA. NBBC is designed as a novel analysis and visualization platform guided by non-B burden as a marker.