Next-Generation Sequencing (NGS): Unlocking the Future of Genomics

Today, there are a number of next-generation sequencing (NGS) platforms that use different sequencing technologies. The idea behind all NGS platforms is the same, despite their variations: they sequence millions of brief DNA fragments simultaneously. These reads are then aligned to the human reference genome using bioinformatics tools to reconstruct the entire sequence. The genome's roughly three billion bases are covered several times, guaranteeing a high sequencing depth for increased precision and the identification of unanticipated genetic variations. Whole genomes, all 22,000 protein coding genes (whole exome sequencing), or targeted gene sets can all be sequenced using NGS.

APPLICATIONS OF NGS IN CLINICAL PRACTICE

Medicinal Genetics

There are many chances to improve clinical genetics patient care with next-generation sequencing (NGS).

Compared to Sanger sequencing, NGS finds a wider variety of mutations.

A wide range of DNA variations can be found in the human genome, such as complex rearrangements like inversions and translocations, large-scale deletions involving entire exons or genes, insertions and deletions, and single-nucleotide substitutions. The detection of larger or more complex mutations usually necessitates specialized tests like comparative genomic hybridization (CGH) microarrays or fluorescence in situ hybridization (FISH), whereas traditional Sanger sequencing is restricted to detecting substitutions and minor insertions/deletions. However, NGS eliminates the need for numerous specialized assays by capturing all of these variations in a single sequencing run. The primary obstacles are found in genomic regions that are hard to precisely sequence or align, like those with a high guanine-cytosine (GC) content or repetitive elements, like the repeat expansions associated with Fragile X syndrome or Huntington’s disease.

Unbiased genome analysis

NGS enables an objective, thorough examination of the complete genome or exome, in contrast to capillary (Sanger) sequencing, which necessitates prior knowledge of the gene or region of interest. This makes it possible to identify new mutations and hitherto unknown genes that cause disease. For example, NGS can assist in determining the genetic origins of inexplicable syndromes in pediatric genetics. The Deciphering Developmental Disorders project, a national effort spearheaded by the Wellcome Trust Sanger Institute in partnership with NHS clinical genetics services, is a noteworthy example. To find dangerous de novo mutations, the project sequences parents and children with developmental delays. Researchers have successfully discovered new genes linked to comparable clinical phenotypes in afflicted children by combining genomic data with comprehensive clinical information.

NGS increases the sensitivity of mosaic mutation detection.

Following fertilization, mosaic mutations can occur in a variety of cells and tissues within an individual at different frequencies. Traditional capillary (Sanger) sequencing, which lacks the sensitivity necessary to detect subtle variant signals, frequently misses these mutations because of their low abundance. Next-generation sequencing (NGS), on the other hand, has a far higher sensitivity and can identify variants, such as mosaic alterations, that are found in a very small percentage of cells. NGS is especially useful in applications that require high precision, like the analysis of fetal DNA in maternal blood or the monitoring of circulating tumor DNA in cancer patients. This sensitivity can also be further increased by increasing the sequencing depth.

Microbiology

One of the main uses of next-generation sequencing (NGS) in microbiology is to shift from conventional pathogen identification techniques, which rely on morphology, staining properties, and metabolic traits, to a genomic-based classification. In addition to defining a pathogen's identity, its genome offers vital details regarding antibiotic resistance and its genetic relationships with other strains. Tracking the origin and progression of infectious disease outbreaks can be greatly aided by this genomic insight. One prominent instance that attracted media attention in the United Kingdom concerned a methicillin-resistant Staphylococcus aureus (MRSA) outbreak in a neonatal intensive care unit. NGS allowed for thorough genomic characterization of the isolates and revealed a protracted outbreak that started with a single employee, even though routine microbiological surveillance was unable to connect the individual MRSA cases.

Oncology

The foundation of cancer genomics is the idea that cancer is a disease with a genetic basis because it results from somatic mutations. For more than ten years, capillary-based sequencing has been employed in cancer research; however, these efforts have typically been restricted to small cohorts and a limited number of candidate genes. The field has undergone a revolution with the advent of next-generation sequencing (NGS), which makes it possible to analyze entire cancer genomes in detail. Numerous extensive global initiatives, including those that are especially targeted at pediatric cancers, have been the driving force behind this change.

NGS has several benefits for children with cancer: it can result in a more accurate diagnosis, better disease classification, more informed prognostic evaluations, and the discovery of particular genetic changes that could direct focused treatment approaches. Therefore, the basis for individualized cancer treatment may be the sequencing of a patient's tumor's genome. Pilot studies to incorporate NGS into clinical oncology are currently underway, with the main objective being the identification of tumor mutations that could be addressed by customized treatment strategies.