Next Generation Sequencing in Clinical Medicine
Next-generation sequencing (NGS) was developed more than a decade ago to facilitate sequencing of large amounts of genomic data. Use of NGS in clinical diagnosis is now widely accepted, with varying roles from gene panel or targeted sequencing, through whole exome sequencing (also termed clinical exome sequencing), to whole genome sequencing. NGS was first applied to clinical diagnosis when clinical exome sequencing was launched in 2012.
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Next Generation Sequencing (NGS) techniques represent the next phase in the evolution of DNA sequencing technology at dramatically reduced cost compared to traditional Sanger sequencing. A single laboratory today can sequence the entire human genome in a few days for a few thousand dollars in reagents and staff time. Routine whole exome or even whole genome sequencing of clinical patients is well within the realm of affordability for many academic institutions across the country. This paper reviews current sequencing technology methods and upcoming advancements in sequencing technology as well as challenges associated with data generation, data manipulation and data storage.
The goal of clinical NGS is the identification of point mutations and potentially larger structural changes such as translocations, rearrangements, inversions, deletions and duplications either in germline samples or in tumor samples paired with normal genomes for cancer diagnostics. While there are few NGS instruments lending to standardization of some sort, the same cannot be said for the software used to analyse the data.
Cancer is a genetic disease. Decades of research has led to this knowledge, showing that it is the accumulation of molecular alterations that is the key element of tumorigenesis, directing the acquisition of the malignant phenotype. Genes involved in oncogenesis are classified in “oncogenes,” whose activation is responsible for tumor transformation and oncosuppressors, whose inactivation leads to cellular proliferation. Mutations of oncogenes (gain of function) or oncosuppressors (loss of function) can be genetically inherited (germline), but they are mostly acquired and caused by DNA replication errors and/or exposure to carcinogens.
Microbiology
The main utility of NGS in microbiology is to replace conventional characterisation of pathogens by morphology, staining properties and metabolic criteria with a genomic definition of pathogens. The genomes of pathogens define what they are, may harbour information about drug sensitivity and inform the relationship of different pathogens with each other which can be used to trace sources of infection outbreaks.
Oncology
The fundamental premise of cancer genomics is that cancer is caused by somatically acquired mutations, and consequently it is a disease of the genome. Although capillary-based cancer sequencing has been ongoing for over a decade, these investigations were limited to relatively few samples and small numbers of candidate genes. With the advent of NGS, cancer genomes can now be systemically studied in their entirety, an endeavour ongoing via several large scale cancer genome projects.
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