Next-Generation Sequencing options for molecular diagnostics
The development of new techniques of genomic sequencing and bioinformatics analysis in the last decade has led to transcendental advances in the diagnosis, prognosis and treatment of genetic diseases. Next Generation Sequencing (NGS) has demonstrated its cost-effectiveness and it has been integrated in the diagnostic routines in an unstoppable way. However, the NGS irruption has also troubled many health professionals who are now faced with a dilemma when choosing the most appropriate genomic test for each patient. The complexity of the obtained information and the different pricing schemes are key points when making this decision.
In general, there are three strategies to approach molecular diagnosis using NGS. Below are some of its indications, advantages and disadvantages.
Gene panels and / or regions of interest
Panels analyze a limited number of genes associated with a specific group of diseases or phenotypes. These tests are especially indicated for well genetically described mendelian diseases comprising genes and mutations well described in the literature.
Among its advantages, panels have high read depth coverage, which allows the detection of variants at low frequencies. In addition, its design guarantees the sequencing of regions of interest, thus facilitating the subsequent analysis of the data. The main limitation of this technique is that it does not allow to detect mutations in genes and / or regions that have not previously been associated with a pathology. Due to its low cost and thoroughness, it is the most rapid genomic study integrated in diagnostic laboratories.
Whole Exome Sequencing (WES) includes coding regions (exons) of all genes, corresponding to approximately 2% of the genome. It is an adequate methodology when a panel cannot identify the cause of the disease, since it allows the detection of variants in candidate genes not covered by the panel. It is also indicated for polygenic phenotypes with several genes involved or those that are not associated with any previously described disease.
WES constitutes a faster approach compared to genome sequencing with also lower analysis and storage costs. Its main disadvantages are that it offers a non-uniform coverage, does not include intronic or regulatory regions, and in many cases does not detect structural variants.
Whole genome sequencing (WGS) covers almost completely all the information encoded in an individual’s DNA, including intronic and regulatory regions.
One of the main advantages of WGS is identification of complex structural variations, such as copy number variations and chromosomal translocations at a nucleotide base resolution. In addition, it allows detecting mutations in genes previously not associated with the disease, even in non-coding regions. Although the cost of genome sequencing has gone down from hundreds of millions to about 1,000 euros, this price, along with the complexity of data analysis hinder for now its integration to the diagnostic routines.
In addition to understanding the advantages and disadvantages of each of the above methodologies, correct identification and characterization of variants with clinical significance is essential. The development of bioinformatics tools is fundamental for the application of NGS in genetic diagnosis and to ensure the success of precision medicine.
In the next 5 years, we will see sequencing and analysis of a human genome to be available for less than 100 euros. WGS will become the most profitable genomic test, without neglecting the advantages of WES and gene panels for specific cases.