The discoveries of new genetic markers that help identify and, therefore, to better prevent multiple diseases.
These markers are used to relate certain genetic mutations to the risk of appearance and development of numerous inherited disorders. The use of new genome sequencing techniques will be essential in advancing knowledge of this type of diseases and many others.
In this article we explain what a genetic marker is, what types of markers exist, how the different genetic variants are detected and what are the main techniques used in genomic sequencing.
Genetic markers are segments of DNA located at a known position (a locus) on a given chromosome. Typically, these markers are associated with specific disease phenotypes and are very useful in identifying different genetic variations in specific individuals and populations.
The technology of genetic markers based on DNA has revolutionized the world of genetics, since thanks to them it is possible to detect polymorphisms (responsible for the great variability that exists between individuals of the same species) between different genotypes or alleles of a gene to a certain DNA sequence in a group of genes.
Those markers that confer a high probability of disease occurrence are most useful as diagnostic tools A marker may have functional consequences, such as altering the expression or function of a gene that directly contributes to the development of a disease; and conversely, it may have no functional consequence, but may be located close to a functional variant so that both the marker and the variant tend to be inherited together in the general population.
DNA variations are classified as “neutral” when they do not produce any changes in metabolic or phenotypic traits (the observable traits), and when they are not subject to any evolutionary pressure (whether positive, negative or balancing); Otherwise, the variations are called functional.
Mutations in key nucleotides of a DNA sequence can change the amino acid composition of a protein and lead to new functional variants. Such variants may have greater or lesser metabolic efficiency compared to the original sequence; They can lose their functionality completely or even incorporate a new one.
Polymorphism detection methods
Polymorphisms are defined as genetic variants in the DNA sequence between individuals of the same species These can have consequences on the phenotype if they are found in coding regions of the DNA.
To detect these polymorphisms, there are two main methods: the Southern method, a nucleic acid hybridization technique; and the polymerase chain reaction PCR technique, which allows specific small regions of DNA material to be amplified.
By using these two methods, genetic variations in DNA samples and polymorphisms in a specific region of the DNA sequence can be identified. However, the studies carried out show that in the case of more complex diseases it is more difficult to identify these genetic markers, since they are usually polygenic, that is, caused by defects in multiple genes.
Types of genetic markers
There are two main types of molecular markers s: those of post-transcription-translation, which are carried out by indirect DNA analysis; and those of the pretranscription-translation type, which allow polymorphisms to be detected directly at the DNA level and which we will talk about below.
1. RFLP Markers
RFLP (Restriction Fragment Length Polymorphism) genetic markers They are obtained after the extraction and fragmentation of DNA, by cutting an endonuclease by restriction enzymes
The restriction fragments obtained are then analyzed using gel electrophoresis. They are a fundamental tool for carrying out genomic mapping and in the analysis of polygenic diseases.
2. AFLP Markers
These markers are biallelic and dominant Variations at many loci (multilocus naming) can be screened simultaneously to detect single nucleotide variations from unknown genomic regions, where a given mutation may frequently be present in undetermined functional genes.
3. Microsatellites
Microsatellites are the most popular genetic markers in genetic characterization studies Its high mutation rate and co-dominant nature make it possible to estimate genetic diversity within and between different breeds, and genetic mixing between breeds, even if they are closely related.
4. Mitochondrial DNA markers
These markers provide a quick way to detect hybridization between species or subspecies
Polymorphisms in certain sequences or in the control region of mitochondrial DNA have contributed, to a large extent, to the identification of the progenitors of domestic species, the establishment of geographical patterns of genetic diversity and the understanding of domestication behaviors.
5. RAPD Markers
These markers are based on the polymerase chain reaction or PCR technique. The fragments obtained by RAPD are amplified in different random regions.
Its usefulness lies in the fact that it is an easy-to-use technique and allows many polymorphisms to be distinguished quickly and simultaneously. It has been used in the analysis of genetic diversity and the improvement and differentiation of clonal lines.
Genome sequencing techniques
Many of the diseases that exist have a genetic basis. The cause is usually determined by the appearance of one or more mutations that cause the disease or, at least, increase the risk of developing it.
One of the most common techniques to detect these mutations and that has been used until recently is the genetic association study which involve the sequencing of the DNA of one or a group of genes that are suspected of being involved in a certain disease.
Genetic association studies study the DNA sequences in the genes of carriers and healthy people, in order to find the gene(s) responsible. These studies have attempted to include members of the same family to increase the probability of detecting mutations. However, these types of studies only allow us to identify mutations linked to a single gene, with the limitations that this entails.
In recent years, new sequencing techniques have been discovered that have allowed us to overcome these limitations, known as next generation sequencing (NGS) techniques. These allow the genome to be sequenced investing less time (and less money). Thanks to this, so-called genome-wide association studies or GWAS (for their acronym in English, Genome-Wide Association Studies) are currently being carried out.
Genomic sequencing using GWAS allows all mutations present in the genome to be explored, exponentially increasing the probability of finding the genes responsible for a certain disease. This has led to the creation of international consortia with researchers from around the world sharing chromosomal maps with the risk variants of a multitude of diseases.
However, GWAS are not free from limitations, such as their inability to fully explain the genetic and familial risk of common diseases, the difficulties in evaluating rare genetic variants or the small effect size obtained in most studies. Undoubtedly problematic aspects that will have to be improved in the coming years.
