Cytogenetic Analysis

Overview

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Cytogenetic is a branch of genetics that deals with the study of the structure and behaviour of chromosomes and their affiliation to human disease and disease processes. The cytogenetic analysis uses samples of blood, tissue, or bone marrow to detect changes in chromosomes (the physical structures that houses the genetic material, DNA), whether broken, missing, rearranged, or extra chromosomes. Changes in certain chromosomes is likely an indication of a genetic disease, medical conditions, or some types of cancer. Cytogenetic analysis has proven to be effective in the diagnosis of diseases and medical conditions, treatment planning, or treatment follow-up.

In the last three decades, the significance of clinical cytogenetic to the practice of obstetrics and gynaecology has rapidly increased due to the direct effect of clinical cytogenetic on the prevention, diagnosis, and management of many disorders that are caused by chromosomal abnormalities. 

Chromosomes aberrations cause a number of genetic disorders which may lead to developmental delay, mental retardation, infertility, and congenital malformations. 

There are three major methods of cytogenetic analysis:

• Routine karyotyping
• Fluorescent in situ hybridisation (FISH)
• Comparative genomic hybridisation (also known as CGH) and array comparative genomic hybridisation (also known as aCGH)

Routine Karyotyping

This was one of the very first methods invented for the analysis of chromosomes. This method makes use of light microscopy and standardised staining procedures on cells at the metaphase portion of the cell cycle, when chromosomes are lined along the equator of the cell, prior to separation and most condensed.

What makes this method of cytogenetic analysis more efficient and effective is the stains that were developed to bind with the DNA and produce characteristic banding patterns to help identify different chromosomes. The stain usually used is the Giemsa dye. The chromosomes are then arranged into a karyogram of 23 pairs, and any abnormality and large translocations (where parts of chromosomes are transplanted between each other) can then be identified.

Unfortunately, one of the downsides of this method is that it can only identify changes of over approximately 3 megabases in size. So any abnormality less than this size will not be picked up by routine karyotyping. Karyotyping can also be used to identify Turner syndrome and Down syndrome.

• Fluorescent in situ hybridisation (FISH)

This was first introduced in the late 1980s, and has swiftly become a well-known diagnostic cytogenetic analysis, both in congenital and acquired disease. Unlike the routine Karyotyping technique, the FISH has a higher resolution, especially when it is used on the interphase cells (the phase cells remain in when not dividing).

The FISH technique is designed to use a fluorescent probe with complementary base sequences to trace the presence or absence of specific portions of DNA on chromosomes. The target DNA and probe will be denatured with heat or chemicals to break the hydrogen bonds in the DNA and to allow for hybridisation to occur once the two samples are mixed. The fluorescent probes then create new hydrogen bonds with the complementary base pairs on the DNA, which can then be detected via microscopy.

The FISH method is, however, mostly used to detect specific chromosomal deletions or translocations that are associated with cancers or paediatric conditions. The FISH method can also be used for melanocytic lesions to distinguish atypical melanocytic naevi from melanoma. 

• Comparative genomic hybridisation (CGH)

This is the molecular cytogenetic analysis method. It detects variants of chromosomal copy number (that is, portions of the genome where sections of genes are doubled or tripled) without the need for cell culture. It was developed to identify such changes in tumours.

The CGH method uses 2 genomes, the analysis sample and a control sample. Both of which are fluorescently labelled for proper differentiation. The two samples are then denatured and mixed together, allowing hybridisation of metaphase chromosomes. The concentration of the fluorescent signal of the labelled test DNA in relation to the control sample DNA is then plotted along each chromosome. This shows whether there’s a loss or gain of genetic material and allows for the identification of any copy number variants.

The CGH method differs markedly from other methods of cytogenetic analysis in that it neither relies on a specific target nor requires previous knowledge of the region under examination. Rather, the CGH method can quickly scan a whole genome for chromosomal imbalances. This method has proven useful and effective in cases where the diagnosis is unknown. 

Its limitation, however, is that its resolution is poor and can only identify approximately 5–10 megabases.

Array comparative genomic hybridisation (aCGH)

This method is similar to CGH and utilises a similar technique. However, it has a much higher resolution as it uses microarrays. The aCGH method, however, uses small sections of DNA as targets for analysis. These sections are immobilised on a solid support, which anchors the DNA to a spot without altering its protein. The sample DNA and control sample is also fluorescently labelled to differentiate them. Afterwards, the samples are mixed and transferred to the microarray where they compete to bind to their probes. The concentration of the different fluorescent signals are then assessed, and gains or losses in the DNA are identified. 

A major disadvantage of this method, however, is that it unable to detect balanced chromosomal structural changes such as balanced translocations or inversions.

Reasons for cytogenetic analysis

Your doctor can request cytogenetic analysis for a number of reasons. These include

• Antenatal testing in high-risk pregnancy

Cytogenetic analysis can be requested of a pregnant woman to detect if the foetus is at risk of chromosomal abnormalities, such as trisomy 21 in Down syndrome.

• Diagnosis of congenital defects

Cytogenetic analysis is often requested for paediatrics to detect the underlying cause for developmental disorders or congenital defects. Being able to detect the underlying cause brings a huge relief and points toward appropriate management and prognosis.

• Haematological cancer

Cytogenetic analysis is also used in diagnosing haematological cancers such as chronic myeloid leukaemia, where a specific reciprocal translocation between chromosomes 9 and 22 results in the Philadelphia chromosome that is present in 95% of cases.

It has also proven its effectiveness to provide guidance on treatment.

Interpretation of results

This is done according to the International System for Human Cytogenetic Nomenclature (ISCN). This was established after several periodic, worldwide conferences of Cytogenetics.

When there’s a cytogenetic alteration, this indicates chromosomal abnormality. Leukaemia or other cancer type is considered to have abnormal results. 

However, lack of cytogenetic alteration is not a basis to conclude theirs is the absence of disease or a better prognosis. 

Your doctor will, however, study the results and give you a detailed interpretation. 

Benefits and disadvantages of cytogenetic analysis.

The adoption of cytogenetic analysis has proven to be very useful to carry out efficient diagnosis and help with the long-term management of relevant diseases. It also helps in genetic counselling for the patient and/or their parents about the associated risk in any future pregnancies. In certain cases, it guides the geneticist to know whether or not to test other family members.

Unfortunately, however, cytogenetic analysis is limited by its resolution. While all the different cytogenetic analysis technique can identify small gains and losses of genetic material, as well as larger translocations, they do not allow testing for a single nucleotide variant that might add to the patient’s condition. There is also the likelihood that cytogenetic analysis will, during the analysis, identify other chromosomal changes that are not necessarily related to the patient’s condition