An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology

Abstract

Next-generation sequencing (NGS) technologies that have advanced rapidly in the past few years possess the potential to classify diseases, decipher the molecular code of related cell processes, identify targets for decision-making on targeted therapy or prevention strategies, and predict clinical treatment response. Thus, NGS is on its way to revolutionize oncology. With the help of NGS, we can draw a finer map for the genetic basis of diseases and can improve our understanding of diagnostic and prognostic applications and therapeutic methods. Despite these advantages and its potential, NGS is facing several critical challenges, including reduction of sequencing cost, enhancement of sequencing quality, improvement of technical simplicity and reliability, and development of semiautomated and integrated analysis workflow. In order to address these challenges, we conducted a literature research and summarized a four-stage NGS workflow for providing a systematic review on NGS-based analysis, explaining the strength and weakness of diverse NGSbased software tools, and elucidating its potential connection to individualized medicine. By presenting this four-stage NGS workflow, we try to provide a minimal structural layout required for NGS data storage and reproducibility.

Pathogenicity and Virulence Factors of Fusarium graminearum Including Factors Discovered Using Next Generation Sequencing Technologies and Proteomics

“…NGS, also termed high-throughput or massively parallel sequencing, is a genre of technologies that allow for thousands to billions of DNA fragments to be sequenced simultaneously and independently [17,18]. Although different platforms are commercially available, the NGS workflow features are generally similar, with four major steps: (i) DNA library preparation, (ii) clonal amplification, (iii) massive parallel sequencing, and (iv) data analysis [19,20]. In just the past five years, a number of instruments have been invented.…”

Application of next-generation sequencing technology to precision medicine in cancer: joint consensus of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology

“…In the present era of personalized oncology therapy, a comprehensive analysis of cancer driver genes and their mutations underlying the pathophysiology of cancer development is crucial for designing the most appropriate treatment strategy for patients using targeted therapies 3 . Although Sanger sequencing 4 is still being used as a gold standard in clinical applications, the more recently developed second-generation technology, namely the next-generation sequencing (NGS) technology, has superseded it owing to simpler usage and functional advantage 5-7 .…”

Methods and novel technology for microRNA quantification in colorectal cancer screening

“…After the addition of each nucleotide, the fluorescent signal is captured. Next, data analysis is performed, including sequence alignment to a reference genome, count generation, data pre-processing, and statistical analysis [ 93 ].…”

“…However, implementing such technology in the clinic poses serious challenges. Like microarray, NGS data analysis is complicated and not standardized [ 93 ]. Several studies have used NGS in blood samples in order to identify candidate miRNA for CRC screening [ 98 – 100 ], but these studies are often validated using another more targeted approach (e.g., qPCR).…”