The human genome contains over 3 billion base pairs. Therefore, reading the genetic information contained in them using the classic sequencing method is extremely labour-intensive and expensive. Prestigious research centres have undertaken this task as part of the Human Genome Project. It lasted as long as 13 years. It took so long to analyze such a large number of principles using the classic Senger method. This technique is now widely used in genetics but is primarily applied when the mutation load in a specific gene is verified. Otherwise, it can be very ineffective and, at the same time, very costly if it is necessary to analyze the entire genome. (Source: Paragon Genomics)
What is Next Generation Sequencing?
Next-Generation Sequencing is a method that allows you to read the entire genome sequence of a tested organism during a single procedure. This technique is based on the copying of previously isolated DNA.
WES Analysis – the most extensive test using NGS
The WES (Whole Exome sequencing) analysis is the broadest possible genetic test for children and adults.
The WES test is performed mainly to detect changes in genes responsible for the development of specific diseases and symptoms. Therefore, it is a tool that allows in many cases to make a final diagnosis of a given congenital disease and the causes of the patient’s health problems. The WES test is explicitly recommended in patients with a “Diagnostic Odyssey” – when, despite many examinations, the cause of health problems (for instance, symptoms of autism, epilepsy, neurological disorders, and others) has not been established so far.
The WES analysis, thanks to the use of NGS technology, enables the full range of all genes to be tested in one study. This means that every gene that is present in our body, and there are over 23,000 of them, is thoroughly analyzed.
The preparation of NGS libraries is the first critical step in working with Next Generation Sequencing. The DNA or RNA samples are first fragmented (either mechanically or enzymatically), and then adaptations to the specifications for the sequencing platforms are added.
What is Target Enrichment?
Target enrichment technology provides a more precise sequencing by targeting and analyzing particular regions of the genome instead of focusing on the entire genome. The method is applied after library preparation and, through the processes of hybridization or amplicon-based enrichment, allows for more sensitive mutation detection. Besides efficient sequencing and certainty it provides, target enrichment has other dominant aspects over Whole-Genome Sequencing:
- Reduced cost of analysis
- Less sample input
- High throughput
- Simplified process of sequencing due to focusing on specific regions of interest
- Prevents invalid or misleading interpretations of sequencing elements due to in-depth sequencing
Applied Methods of Target Enrichment Sequencing
The two fundamental techniques applied to target enrichment sequencing are hybridization capture and amplicon-based sequencing.
- The hybridization capture is a process based on the hybridization of a given molecule to an oligonucleotide system. Hybridization of the tested molecule to a given oligonucleotide means that the given sequence is inside that DNA molecule. The complete sequence of the tested DNA is determined by analyzing all oligonucleotide sequences for which hybridization has occurred. The method is frequently used for genotyping and identifying rare variants, widely employed in oncology research.
- Amplicon sequencing is another profoundly targeted strategy permitting clinicians and researchers to identify genetic abnormalities in specific genomic regions of interest. The technique provides in-depth sequencing of PCR (Polymerase Chain Reaction) elements by using oligonucleotide probes to target and capture the particular genome.
Current Clinical Applications of Targeted Genomic Regions
The existence of point mutations and chromosomal aberrations of prognostic and predictive significance made genetic analysis an indispensable tool in the field of oncology diagnostics. Unfortunately, the classical analytical techniques currently used on a large scale show many limitations and imperfections – they are relatively time-consuming and inefficient, and at the same time, do not allow obtaining complete information about a given disease case. The progressive development of technology has contributed to the development of many new, highly advanced solutions, such as modern DNA and RNA sequencing mechanisms.
Next-Generation Sequencing enables a more accurate and dynamic analysis of genetic material. Their application allows not only to identify the occurrence of previously undetectable genetic changes but also to conduct research in new areas of oncogenetic, such as fluctuations in gene expression or the influence of epigenetic factors on the activity of particular regions of the genome. Moreover, it has become possible to conduct efficient association studies revealing correlations between the occurrence of specific mutations or polymorphisms and the appearance of one particular form of cancer.
Target enrichment sequencing and other methods of NGS are not limited to the field of oncology and its research. The application of modern techniques for genome analysis is also widely used in cardiology or neurology for the occurrence of heart disease or neurological disorders. Next-Generation Sequencing shows promising applications in research, diagnostics, and the potential treatment of many misunderstood ailments.