Microarray chromosome analysis (XMA) is a high-tech method for assessing the karyotype for the presence of certain mutations associated with an increase in the number of DNA copies (duplication), or with the loss of part of the genetic material (deletion). Such anomalies often become the cause of hereditary diseases, so HMA is an important diagnostic tool in modern medicine. Typically, this technology is used to verify the genotype of the fetus, as well as newborns and children.
General characteristics of the method
Microarray chromosome analysis is also called molecular karyotyping. The method is based on DNA hybridization technology with genetic markers (previously known specific nucleotide sequences) embedded in a carrier (matrix). The study allows you to analyze many sections of chromosomes and identify the presence of structural rearrangements (aberrations) associated with a lack or excess of genetic material.
The method is not intended to determine point mutations in genes, but it has a higher resolution compared to traditional karyotyping. With the help of HMA, submicroscopic rearrangements that play an important role in the pathogenesis of various diseases, including congenital malformations and impaired mental development, can be detected.
The meaning of molecular karyotyping
The main purpose of HMA is to identify small additional (micro duplication) or missing (micro deletion) fragments of genetic information regarding a standard sample. Such deviations are called copy number variations (CNVs).
The prefix "micro" means that this technology is aimed at detecting very small changes. However, HMA is also suitable for detecting large chromosomal abnormalities, such as various aneuploidies (Down syndrome, Patau, etc.). However, the study is not able to determine changes within a particular gene.
In addition to microdeletions and microduplications, the analysis reveals the genetic identity of large parts of chromosomes, which may indicate:
- blood relationship of the child's parents;
- receiving both copies of chromosomes from only one parent.
With XMA, translocations can also be detected, but only if they are not balanced.
Microarray chromosome analysis is not a method for decoding a genotype or a method for detecting any genes. This study is aimed only at comparing the amount of genetic material in the patient's chromosomes with the control. After the discovery of CNV, the laboratory determines which genes were contained there and, based on this, interprets the result. Variants of the number of copies play an important role in the pathogenesis of various diseases, but their presence does not always lead to any violations.
Purpose of the study
Chromosomal microarray analysis is performed to check if the child has CNV, which may be the cause of:
- autism
- global developmental delay;
- mental retardation;
- various birth defects;
- seizures
- unusual physical features (dysmorphisms);
- congenital malformations.
The study also determines the presence or absence of numerical chromosomal abnormalities (Down Syndrome, etc.).
There are 2 main reasons for conducting an HMA test:
- prophylactic - checking the child’s genome for microdeletions or micro duplications;
- diagnostic - carried out to establish the genetic causes of various disorders that may be associated with CNV.
Sometimes, in order to clarify the results of the study, the parents' genome is checked.
According to the international standard and the recommendations of several medical communities, HMA is a first-level test for people with congenital malformations, autism or developmental disorders of unclear origin.
Numerous reviews of the chromosomal microarray analysis confirm its important diagnostic value. The method allows you to find the genetic causes of problems in a child when common and fairly obvious chromosomal abnormalities (such as Down syndrome) are absent. Sometimes, HMA, on the contrary, helps to eliminate the presence of chromosomal abnormalities in children with developmental problems. Such results are considered favorable, since acquired defects can be corrected, while genetic disorders cannot be corrected.
Method technology
XMA allows you to simultaneously analyze a large number of different DNA fragments, each of which corresponds to a specific genetic marker deposited on the matrix. The latter is an object stack covered with thousands of such probes.
For the test, 2 types of DNA are used:
- the patient;
- standard (corresponds to the normal human genome).
Genetic material is applied to the matrix where a hybridization reaction takes place between the probes and their corresponding sample fragments. That is, sequences from identical chromosome regions are combined with each other.
A special device separately evaluates the degree of hybridization of each probe with control and with a prototype. In the normal case, it should be the same. If a fragment of the patient contains an excess of genetic material, the device gives a green signal, and if the deficiency is red.
Thus, all parts of the genome to which the matrix contains markers are evaluated. The signals of the device are captured by the scanner and processed by a computer.
HMA types
There are 3 varieties of chromosomal microarray analysis:
- targeted
- standard;
- advanced.
Their main difference is the resolution, which is regulated by the number of DNA markers used. This parameter is also called matrix density. In the target analysis, it is the lowest (350 thousand markers). This is the most affordable and cheapest type of test, which reveals the most common microdeletions and micro duplications. It is used to confirm known specific syndromes associated with CNV.
For standard HMA, 750 thousand markers are used that check all clinically relevant parts of the human genome. This test allows you to detect not only common CNV, but also chromosomal abnormalities that cause undifferentiated syndromes. An expanded chromosome microarray analysis performs the same function, but much more informatively. It represents the most in-depth study of the genome using a matrix containing 2.67 million DNA markers.
HMA effectiveness
HMA is a modern and very effective way to detect chromosomal abnormalities. Previously, a standard cytogenetic method was used to detect them, which consisted of a visual examination of the patient's chromosomes. In comparison, the resolution of molecular karyotyping is 1000 times higher and allows you to find the smallest changes that previously could not be detected. This increased the diagnostic yield by 10. In addition, HMA does not require preliminary cultivation of cells and allows you to analyze many sections of chromosomes at the same time.
The usefulness of molecular karyotyping for a particular patient depends on:
- the selected analysis type (advanced, targeted or standard);
- correct assessment of the result;
- equipment and a set of DNA chips (markers embedded in the matrix) that a particular laboratory uses.
The name of one of the highest quality medical and genetic centers where chromosome microarray analysis can be carried out is “Genomed”. Reviews about this institution describe it as a high-level medical organization with modern technological equipment that allows for a wide range of different genetic tests, including quite rare ones. For HMA in Genomede (Moscow, Podolskoye Shosse, 8) sets of DNA markers from a leading manufacturing company are used.