Detecting Genomes Using Next Generation Sequencing: Introduction, Applications

Posted by Janice on April 29th, 2021

Since the advent of next generation sequencing (NGS) technology three decades ago, enormous progress has been made in the fields of biology and medicine. NGS is a deep, high-throughput, massively parallel or deep sequenced DNA or RNA sequencing technology that has revolutionized genomic research. It is usually used to study genetic variation associated with diseases or other biological phenomena.

NGS can be used to sequence entire genomes or constrained to specific areas of interest, such as a small number of individual genes. NGS involves several major steps in sequencing, such as DNA fragmentation, library preparation, massively parallel sequencing, bioinformatics analysis, and variant/mutation annotation and interpretation.

Currently, NGS technology has been widely used in clinical practice to improve patient care. Compared to traditional Sanger sequencing (first-generation sequencing technology), NGS captures a broader spectrum of mutations and uncovers the human genome without bias. For example, NGS technology unravels the genetic basis of unexplained developmental delays by sequencing affected children and their parents to reveal harmful de novo mutations. Combining these molecular data with detailed clinical phenotypic information, novel genes that mutate in affected children with similar clinical characteristics have been successfully identified.

In recent years, NGS has been used to characterize genomic alterations such as mutations, insertions/deletions, and copy number changes, and the frequency with which they occur in various tumor types. NGS technology allows the detection of gene mutations because of its higher sensitivity. Gene mutations typically occur at variable frequencies in individual cells and tissues, and regular sequencing may miss these variants because they frequently present with a subtlety which falls below the sensitivity of the technology. NGS sequencing provides a far more sensitive read-out and can therefore be used to identify variations that reside in a small number of cells. In addition, NGS has been employed for more sensitive investigations, such as searching for fetal DNA from maternal blood or tracking tumor cells from the circulation of cancer patients.

NGS technology has also been used in the current research of some incurable diseases, changing the way a disease is diagnosed, and providing scientists and physicians with fact-based guidelines for the treatment. Recently, a team of researchers from Singapore demonstrated that the next generation sequencing test can detect HIV drug resistance mutations that cannot be identified by the traditional test. This test may play a critical role in helping clinicians to optimize HIV treatment plans, as well as contributing to public health initiatives to minimize the development of global resistance to antiretroviral drugs. Next generation sequencing technology has opened a broad new area of research with the potential to revolutionize personalized cancer medicine.

NGS test provides a convenient way for genetic screening and diagnosis of complex diseases such as cancer, cardiovascular disease, kidney disease and diabetes. In addition, NGS technology has potential application advantages in multiple fields such as rapid identification of pathogenic microorganisms, targeted drug therapy and prenatal screening. Although NGS has made great progress over the past few years, there are still many challenges remain across the entire NGS workflow, from sample prep through data analysis. The major bottleneck in the implementation and capitalization of this technology remains in the data processing steps, or bioinformatics.