Next Generation Sequencing Analyses in Cancer Research, Diagnosis and Treatment

Dear Colleagues,

Next-generation sequencing has had a huge impact on cancer research in the past decade, accelerating the discovery of unknown culprits and widening the spectrum of what can be investigated and the resolution of the obtainable results. Some of these results have been translated into actionable knowledge, leading to diagnostic and treatment opportunities.

Cancer research benefits from a wide array of NGS-related methods. The Cancer Genome Atlas (TCGA) enables the discovery of novel oncogenic mechanisms, leveraging results from NGS screenings; tumor mutational burden (TMB) is an effective biomarker for immunotherapy response prediction, and this is made possible by the myriad mutations discovered by NGS. When cancers release sufficient cell-free circulating tumor DNA (ctDNA) into the bloodstream or other bodily fluids, it is now detectable with sensitive NGS methods on liquid biopsies, and single-cell sequencing allows us to tackle tumor-infiltrating lymphocytes.

Finally, and more recently, third-generation sequencing (long reads) is increasingly used for clinical research purposes, for instance in structural variation detection, leukemia, or minimal residue disease.

These are examples of an articulated ecosystem of evidence-based resources and methods applied to basic or clinical research in oncology. As can be expected from any powerful new method, the advantages of working with NGS come with initially unforeseeable challenges that need to be addressed now.

In this Special Issue, we want to put a spotlight on recent sequencing achievements, and we invite original contributions leveraging sequencing methods in cancer research, both in basic and clinical research settings. We also encourage contributions reflecting on the current challenges and pitfalls of these methods, such as efficiencies, power, resolution, and practices to lower noise given by the omics nature of the sequencing approach, both on the analytic side (bioinformatics) and the bench lab side (experimental design, libraries preparation).

A look can also be given to the impact of national sequencing initiatives on cancer research: 1000 Genomes, Genomics England, and other nationally sponsored efforts and to their impact on the health system. We welcome studies and/or commentaries at different resolution scales: from single nucleotide polymorphisms to gene panels and from exome to whole genome sequencing, and for all scales, we are interested in the different approaches used: experimental, brute-force sequencing and computational and data-integrative meta-analyses.

Dr. Riccardo Rossi
Guest Editor

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• whole genome sequencing
• exome sequencing
• variant calling
• biomarker discovery
• cell-free DNA sequencing
• polygenic risk scores
• minimal residue disease
• long-read sequencing
• tumor-infiltrating lymphocytes
• sequenced biobanks