Next-Generation Sequencing in Cancer
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REVIEW PAPER
Next-Generation Sequencing in Cancer S. Vinod Nair1
•
Madhulaxmi2 • Gigi Thomas3 • Ravindran Ankathil4
Received: 19 December 2019 / Accepted: 28 September 2020 Ó The Association of Oral and Maxillofacial Surgeons of India 2020
Abstract Objective In this article, we provide a gestalt idea about NGS technologies and their applications in cancer research and molecular diagnosis. Background Next-generation sequencing (NGS) advancements like DNA sequencing and RNA sequencing allow uncovering of genomic, transcriptomic, and epigenomic scenes of individual malignant growths. An assortment of genomic abnormalities can be screened at the same time, for example common and uncommon variations, auxiliary variations like insertions and deletions, copy-number variation, and fusion transcripts. Conclusion NGS innovations together with bioinformatics investigation, which extend our insight, are progressively used to analyze multiple genes in a cost-effective way and have been applied in examining clinical cancer samples and offering NGS-based molecular diagnosis. Application NGS is progressively significant as a device for the diagnosis of cancers. Keywords NGS Next generation sequencing Cancer Cancer research Molecular diagnosis
& S. Vinod Nair [email protected] 1
Department of Oral and Maxillofacial Surgery, P.M.S Dental College, Vattapara, Trivandrum, India
2
Department of Oral and Maxillofacial Surgery, Saveetha Dental College, Chennai, India
3
Community Medicine, Regional Cancer Centre, Trivandrum, India
4
Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, George Town, Malaysia
Abbreviations NGS Next generation sequencing DNA Deoxy ribonucleic acid RNA Ribonucleic acid WES Whole exome sequencing WGS Whole genome sequencing NCDs Non-communicable diseases WHO World Health Organization HNCs Head and neck cancers SCC Squamous cell carcinoma GWAS Genome-wide association study SBS Sequencing by synthesis SMRT Single-molecule real-time CNV Copy number variations SNPs Single-nucleotide polymorphisms TCGA The cancer genome atlas WGBS Whole genome bisulphite sequencing RRBS Reduced representation bisulfite sequencing PC Prostrate cancer BC Breast cancer HNSCC Head and neck squamous cell carcinoma
Introduction Historically, NGS technology helps in investigating mutations in those genes that have known or suspected associations with a particular disease or phenotype. For example, targeted gene sequencing panels have helped clinical scientists establish diagnoses, guide treatments, and produce disease risk assessments for individuals and families. More recently, NGS technology has been used to conduct comprehensive surveys of genetic material.
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J. Maxillofac. Oral Surg.
Besides employing targeted sequencing panels, clinical scientists may use whole-exome sequencing (WES) and whole-genome sequencing (WGS). The Sanger DNA sequencing technique was developed in 1997, later automated with some modifications, and formed sequencing gold standard until the lat
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