Unused Sequencing Data Could be Goldmine for Cancer Research

New research out of Brazil suggests that using unexplored data from next-generation sequencing (NGS) studies could help elucidate carcinogenesis and aid in the discovery of potential biomarkers with clinical applications.

NGS technologies have significantly improved cancer research in recent years and generated an enormous amount of genomic and transcriptomic data. In most cases, the data needed for research goals are used, and unwanted reads are discarded. However, these eliminated data contain potentially useful information.

The team from Instituto Metrópole Digital at the Universidade Federal do Rio Grande do Norte, Núcleo de Pesquisas em Oncologia, and Instituto de Ciências Biológicas at the Universidade Federal do Pará acquired genomic and transcriptomic data from public datasets to test this hypothesis. They used metagenomic tools to explore genomic cancer data, and additional annotations were used to explore differentially expressed ncRNAs from miRNA experiments. Variants in adjacent-to-tumor samples from RNA-seq experiments were also investigated.

The analysis obtained new insights: from DNA-seq data, microbiome taxonomies were characterized with a similar performance of dedicated metagenomic research. Additional differentially expressed sncRNAs were discovered using miRNA-seq data, and somatic variants were found in tumor and adjacent-to-tumor tissue data.

The findings indicate that unexplored data from NGS experiments could help elucidate carcinogenesis and discover clinically relevant biomarkers. Further investigations should be considered for experimental design, providing opportunities to optimize data, saving time and resources while granting access to multiple genomic perspectives from the same sample and experimental run.

“Altogether, our results strengthen the hypothesis that abundant additional and potentially useful information can be extracted from NGS,” according to the authors. “Moreover, the integrated investigation of every available information should provide a broader and more robust interpretation of the molecular scenario from each experiment.”

 The findings were reported in the journal Oncotarget.