A garbage treasure in cancer research

"This data, which is considered useless, is mostly treated as garbage and has never been mined
.
However, in some cases, the treasures hidden in this data are discarded
.
”

A new research perspective was published in Volume 13 of Oncotarget on November 17, 2022, titled "Garbage Treasures in Cancer Research.
"

In recent years, there have been significant advances in cancer research, largely thanks to next-generation sequencing (NGS) technology
.
As a result, a large amount of genomic and transcriptome data
is generated.
In most cases, data needed for the research objective is used and unwanted reads are discarded
.
However, the excluded data contains relevant information
.
To test this hypothesis, we acquired genomic and transcriptome data
from public datasets.

In this new research perspective, researchers use metagenomics tools to explore genomic cancer data; We used additional annotations to explore differentially expressed ncRNAs in miRNA experiments and also investigated variation in neighboring tumor samples in RNA-seq experiments
.

"Here, we demonstrate potential strategies
to benefit from non-targeted information obtained from high-throughput cancer investigations.
"

In all the analyses, new data were obtained: from the DNA-seq data, the microbiome classification had similar properties for specialized metagenomic studies; From the miRNA-seq data, additional differentially expressed sncRNAs were found; Somatic variants
are found in the data of tumors and tumor-adjacent tissues.

These findings suggest that unexplored data from NGS experiments can help elucidate the mechanism of carcinogenesis and discover presumptive biomarkers with clinical application
.
The experimental design should consider further research, providing opportunities to optimize data, saving time and resources, while allowing multiple genomic perspectives
to be obtained from the same sample and experimental run.

"Together, our findings reinforce the hypothesis that a large amount of additional, potentially useful information
can be extracted from NGS.
" In addition, a comprehensive investigation of every available piece of information should provide a broader and more reliable interpretation
of the molecular scenario for each experiment.
”