Next-Generation Sequencing (NGS) Basics for Cancer Research

  • Traditional diagnosis and therapies of cancer were heavily dependent on the histological classification of the tumor. With an emphasis on integrating molecular characteristics into diagnosis and the development of potential cancer therapies, increasing prominence is given to the molecular and genetic properties of tumors in cancer research. Recognition of remarkable genetic heterogeneity in cancers with ongoing genomics research, including cancer types, mutation rate, and the number of target mutations, has given impetus to cancer diagnosis and treatment development.


    The introduction of Next-Generation Sequencing


    To speed up the sequencing process, the next-generation sequencing (NGS) based on traditional Sanger sequencing, then was introduced in 2005 to assay multiple genomic variants simultaneously to determine the sequence of DNA or RNA and study genetic variation related diseases. It's a high-throughput DNA sequencing technology that allows sequencing an entire human diploid genome with less time at a lower cost. NGS for cancer detection has greatly advanced the development of cancer research, including clinical diagnostics and treatment.


    NGS analysis of tumor genomics, transcriptomics, and epigenomics contributes to the discovery of biomarkers that can be used to determine if an individual is confirmed with cancer in diagnostics, to predict how cancer will develop without the interfere of treatment in prognostics, and to estimate how a cancer patient will respond to therapy. On the other hand, next-generation sequencing is driving the growth of precision medicine, aiming at matching the molecular characteristics of tumors with targeted drugs.


    NGS Methods


    NGS is a collective name for various modern high-throughput DNA and RNA sequencing technologies, such as whole genome sequencing (WGS), whole exome sequencing (WES), target sequencing, whole transcriptome sequencing (WTS), and immune repertoire sequencing.


    • Whole Genome Sequencing


    Suggested by its name, WGS can sequence the whole genome, including chromosomal and mitochondrial DNA (or chloroplast DNA in plants) as well as the genome of microorganisms. Thus, whole genome sequencing takes the longest time to sequence compared with other NGS technologies.


    Applications of WGS in cancer research can comprehensively explore all types of genomic changes in cancer, helping better understand the overall situation of the driver of mutations and mutation characteristics in the cancer genome, and further clarifying the functional or clinical significance of these unexplored genomic regions and mutation characteristics.


    • Whole Exome Sequencing


    Exome sequencing or whole exome sequencing limits sequencing in the protein coding regions called exons. Although the human exome only accounts for less than 2% of the human genome, about 85% of disease-related mutations occur within the exome. WES is often used to efficiently identify coding variants in exons across a wide range of applications, including population genetics, genetic diseases, and cancer studies.


    • Whole Transcriptome Sequencing


    The transcriptome is the entire set of RNA transcripts in a given cell for a specific developmental stage or physiological condition. Thus, transcriptome sequencing is also known as RNA sequencing (RNA-seq) that can analyze the number and sequence of the transcriptome. Moreover, RNA sequencing technology can identify and analyze single nucleotide polymorphism (SNP), transcription profile, RNA editing, and gene differential expression, helping understand molecular mechanisms of many diseases, including human cancers.