Karyotype

Karyotype refers to the systematic examination of an individual’s chromosomes in terms of their number and structure. This analysis is a fundamental method for identifying genetic diseases, evaluating congenital anomalies and determining risks related to reproductive health.

The karyotype analysis procedure is performed by staining metaphase chromosomes obtained from cell culture and arranging them under a microscope. This process allows for a detailed identification of chromosomal breaks, translocations and numerical irregularities.

Prenatal karyotype assessment enables the examination of fetal chromosomal structures through amniocentesis or chorionic villus sampling. This method aims to detect chromosomal abnormalities such as Down syndrome at an early stage.

The clinical interpretation of karyotype results is based on evaluating the phenotypic effects of the identified chromosomal variations. At this stage, genetic counseling is critically important for explaining possible disease risks and determining appropriate follow-up strategies.

What Is a Karyotype?

A karyotype is the evaluation of the numerical and structural characteristics of an individual’s chromosomes by examining them under a microscope. It is used in the diagnosis of genetic diseases, fertility problems and certain types of cancer. With this test, chromosomal deficiencies, excesses or structural abnormalities can be detected. Karyotype analysis is usually performed on a blood sample and evaluated together with genetic counseling.

What Do the Terms Karyotype, Karyogram and Cytogenetics Mean?

Although these terms are used interchangeably in everyday language, each has a specific meaning in the laboratory:

• Karyotype: Refers to the complete set of chromosomes in an individual’s cells. It is a general view of that person’s genetic architecture; that is, the number, size and overall shape of the chromosomes.
• Karyotyping (Chromosome Analysis): This is the name of the laboratory process used to determine this chromosomal set. It involves studying living cells:
• Karyogram: This is the tangible output of the karyotyping process, in other words its visible photograph. In this image, chromosomes are digitally arranged, grouped in homologous pairs and ordered from largest to smallest (1 to 22) according to international standards. The sex chromosomes (X and Y) are placed at the end. This orderly image is used for the systematic detection of abnormalities.

All of these concepts are part of the field of cytogenetics, which studies the relationship between chromosome structure and patterns of inheritance.

What Does a Normal Human Karyotype Look Like?

A healthy human somatic cell is “diploid”, meaning it contains two complete sets of chromosomes, one inherited from the mother and one from the father. In humans this number is 46 (or 23 pairs).

These 46 chromosomes are divided into two categories.

• Autosomes: The 22 pairs of chromosomes that determine bodily characteristics (numbered from 1 to 22).
• Allosomes (Sex Chromosomes): The 23rd pair, which determines biological sex (X and Y).

The international standard reporting format (ISCN) for a chromosomally normal individual is as follows:

• Normal Female: 46,XX
• Normal Male: 46,XY

All clinical cytogenetic analyses are compared against this “normal” 46,XX or 46,XY standard. Any numerical or major structural deviation from this standard is considered a chromosomal abnormality.

How Is Karyotype Analysis (Chromosome Analysis) Performed in the Laboratory?

Obtaining a high-quality karyogram requires a precise laboratory process that transforms a simple blood sample into a detailed chromosomal portrait. The entire process is based on capturing chromosomes at a specific moment of cell division when they are most visible.

The main steps of this process are:

• Blood sample collection (into heparinized tubes)
• Cell culture (expansion of living cells)
• Arresting cell division (at metaphase, when chromosomes are most condensed)
• Harvesting and fixation (swelling and fixing the cells)
• Banding and staining (creating the “barcode” pattern of the chromosomes)
• Microscopic analysis
• Creating the karyogram (digitally arranging the chromosomes)

What Are the Limitations of the Karyotype Test?

The most important feature of karyotype analysis is that it requires living cells. The fact that the entire process depends on a successful cell culture leads to two main clinical disadvantages of this technique.

The first is the long time to results. Because the cells must proliferate in culture, the time from giving the blood sample to the final report is usually between 1 and 3 weeks.

The second is the risk of culture failure. If the collected sample (especially delicate tissues such as miscarriage material) has lost its viability or becomes contaminated during handling, the cells will not grow in culture and the test will be “non-informative”. This is a significant problem particularly in the analysis of products of conception (POC).

Which Chromosomal Abnormalities Can Be Detected with Karyotype Analysis?

Karyotype analysis can reveal deviations from the normal chromosomal pattern in two main categories:

Numerical Chromosomal Abnormalities

These are changes in the total number of chromosomes in a cell. They are usually caused by improper segregation of chromosomes during the formation of eggs or sperm.

• Trisomy (Presence of three copies of a chromosome, e.g. Trisomy 21 – Down syndrome)
• Monosomy (Absence of one chromosome, e.g. 45,X – Turner syndrome)
• Polyploidy (Presence of an extra complete set of chromosomes, e.g. triploidy)

Structural Chromosomal Abnormalities

These occur as a result of chromosomal breaks and the subsequent incorrect rejoining of broken ends. The genetic material is rearranged.

• Translocation (Exchange of segments between different chromosomes)
• Deletion (Loss of a segment from a chromosome)
• Duplication (Gain of an extra copy of a chromosomal segment)
• Inversion (A chromosomal segment turning 180 degrees)

Can Karyotype Analysis Detect Every Genetic Problem?

No. This is one of the most important points to understand. Karyotype analysis offers a panoramic, low-resolution view of the chromosomes, similar to a “satellite photo”. It can only detect very large changes (typically larger than 5 to 10 megabases).

This means that it is an excellent tool for detecting numerical abnormalities such as Down syndrome or large segmental changes (translocations), but it cannot identify smaller, submicroscopic abnormalities such as microdeletions or microduplications.

Therefore, a “normal” karyotype result rules out large-scale chromosomal problems, but does not eliminate the possibility of a smaller genetic issue or a disorder involving a single gene. This diagnostic gap is the reason higher-resolution molecular techniques such as chromosomal microarray (CMA) or NGS were developed.

Why Is Karyotype Testing So Important in Couples with Recurrent Pregnancy Loss (RPL)?

Experiencing the loss of two or more pregnancies in a row (RPL) is an extremely distressing process for couples. Among the many possible causes of this condition, chromosomal problems in the parents are one of the rare reasons that can be clearly identified and directly addressed.

The primary reason for performing karyotype analysis from blood samples in parents (both female and male) in RPL cases is to detect a balanced structural rearrangement (most commonly a “balanced translocation”).

An individual with this condition is called a “balanced carrier”. These people are usually completely healthy and have a normal appearance because their genetic material is complete; only the positions of some segments are changed. However, the problem begins when these individuals produce eggs or sperm. During meiosis, the rearranged chromosomes may not segregate properly. This leads to a high rate of “unbalanced” gametes (eggs or sperm) being produced. These gametes contain an extra copy of one chromosomal segment (duplication) and a deficiency of another segment (deletion):

When such a gamete participates in fertilization, the resulting embryo is genetically unbalanced and is usually not viable. This leads either to failure of the embryo to implant in the uterus (implantation failure) or to an early miscarriage (spontaneous abortion).

The rate of detecting a significant chromosomal abnormality (most commonly a balanced translocation) in couples with an RPL history is between 2 % and 6 %. This is much higher than the roughly 0.2 % rate seen in the general population. For this reason, karyotyping is a high-yield test and should definitely be performed in this patient group.

What Is the Role of Karyotype Analysis in Severe Male Infertility (Such as Azoospermia)?

There is a strong relationship between impaired sperm production (spermatogenesis) and a man’s chromosomal structure. In particular, in cases where there is no sperm in the ejaculate (azoospermia) or the sperm count is very low (severe oligozoospermia, usually below 5–10 million/mL), the risk of an underlying chromosomal abnormality increases significantly.

The most commonly observed findings in men with severe infertility are sex chromosome abnormalities, and Klinefelter syndrome (47,XXY) is the most frequent among them. In addition, structural rearrangements such as translocations are also found at increased rates in this group:

In patients with non-obstructive azoospermia (absence of sperm due to production failure) this rate can rise to 15–19 %.

Intracytoplasmic sperm injection (ICSI) technology has enabled many men with severe sperm deficiency to father children. However, ICSI bypasses natural barriers to fertilization. Therefore, if there is an underlying genetic defect in the man (e.g. a translocation), the risk of transmitting this defect to the child through ICSI increases. To assess this risk, to provide couples with appropriate genetic counseling and, in some cases, to establish important diagnoses concerning the man’s own health (such as Klinefelter syndrome), karyotype analysis is strongly recommended in this patient group.

Should Karyotype Testing Be Ordered in Recurrent IVF Failure (RIF)?

Recurrent implantation failure (RIF) is the failure to achieve pregnancy despite the transfer of apparently high-quality embryos. The rationale for karyotyping in RIF is similar to that in recurrent miscarriage: a balanced translocation in one of the parents may lead to the production of unbalanced embryos that fail to implant.

However, the contribution of parental karyotype to RIF is less significant than its role in pregnancy loss. The predominant causes of RIF are usually random numerical abnormalities in embryos (age-related aneuploidy in the mother) or problems with uterine receptivity, which are independent of parental chromosomal structure.

Studies have found that the prevalence of chromosomal abnormalities in couples with RIF is about 2.1 %. This is not significantly different from the approximately 2.0 % rate seen in the general population starting IVF treatment.

This shows that in most RIF cases, parental karyotype is not a decisive factor. Therefore, routine parental karyotyping is not strongly recommended for every couple with RIF. Instead, it is stated that the test “may be considered” and that the decision should be individualized based on the patient’s specific medical history, after discussing this low probability with the couple.

What Does It Mean If a ‘Translocation’ Is Found in the Parental Karyotype?

In a subset of couples being evaluated for infertility or recurrent miscarriage, identifying one parent as a “balanced translocation carrier” is a turning point. At this stage, karyotype analysis ceases to be merely a diagnostic test and becomes the foundational first step of a powerful therapeutic intervention: PGT-SR (Preimplantation Genetic Testing for Structural Rearrangements).

The parental karyotype report provides the master blueprint on which the PGT-SR process is built. The genetics laboratory needs the parental karyotype report (which chromosomes and which bands are involved) to design a customized test for the embryos. This diagnostic finding allows for a directly targeted IVF treatment plan that reduces the couple’s risk of miscarriage or transferring an unbalanced embryo.

How Does PGT-SR (Embryo Genetic Testing) Help in Translocation Carrier Status?

PGT-SR is a specialized IVF application designed to maximize the chance of a healthy pregnancy in couples where one partner is a balanced translocation carrier. The process combines IVF treatment with advanced genetic testing.

The general steps of the procedure are:

• Creating embryos via IVF (Eggs are collected and fertilized with sperm)
• Culturing embryos to the blastocyst stage (day 5 or 6)
• Embryo biopsy (removing 3–5 cells from the outer layer of the embryo without harming it)
• Genetic analysis (using technologies such as NGS to determine whether the cells are balanced or unbalanced with respect to the parental translocation)
• Freezing the embryos (while waiting for the results)
• Selecting a “balanced” embryo and transferring it to the uterus

The goal of PGT-SR is to identify genetically “unbalanced” embryos (i.e. those with missing or extra chromosomal segments) resulting from the parental rearrangement. These unbalanced embryos are not transferred. Only embryos with “balanced” (complete) genetic material are selected. This approach significantly reduces the couple’s risk of miscarriage and increases their chance of having a healthy baby.

Why Is Chromosome Analysis of Products of Conception (POC) Important?

Investigating the cause of pregnancy loss is of great emotional and medical importance. Genetic analysis of products of conception (POC) provides invaluable information to both couples and physicians.

• High Rate of Chromosomal Errors: It is known that random (sporadic) chromosomal abnormalities in the embryo are the single most common cause of 50 to 60 % of first-trimester miscarriages. Trisomy 16 is among the most frequent numerical excesses.
• Emotional Relief and Resolution of Uncertainty: Learning that the miscarriage was due to a random chromosomal error such as Trisomy 16 provides a clear medical explanation for the loss. This is “the best-case scenario of a bad outcome”. It greatly alleviates the guilt and the common question couples ask themselves, “Was it something I did?”. Knowing that the loss was a random biological event and that the risk of the same random error recurring is very low offers strong reassurance.

Guiding Future Treatment: The result of POC analysis is a critical turning point for future planning:

• If POC Is Abnormal (Aneuploid): This supports the diagnosis of recurrent embryonic aneuploidy. The likely source of the problem is the quality of the gametes (egg/sperm), and this may bring embryo testing methods such as PGT-A into consideration (especially in advanced maternal age).
• If POC Is Normal (Euploid): This strongly indicates that the loss did not result from a chromosomal problem in the embryo. This finding redirects the investigation to non-genetic causes of RPL (uterine anomalies, clotting disorders, endocrine disturbances, etc.) and prevents unnecessary genetic testing.

Why Is Conventional Karyotype Analysis Difficult in Products of Conception?

Although genetic analysis of products of conception (POC) is highly important, performing this analysis using conventional karyotyping involves serious technical challenges. All of these challenges arise from the dependence of karyotyping on living cell culture.

The main problems of conventional karyotyping in POC samples are:

• High rate of culture failure (Fetal cells in the sample have often lost viability)
• Bacterial or fungal contamination (The sample may not be sterile)
• Overgrowth of maternal cells (Maternal Cell Contamination – MCC)

Of these problems, the last one (MCC) is the most critical. By their nature, POC samples contain a mixture of fetal (embryonic) and maternal (maternal) tissue. During culture, the more resilient maternal cells may outgrow the more fragile fetal cells. This leads the laboratory to analyze the mother instead of the fetus.

This makes a “46,XX (Normal Female)” result completely ambiguous. Does this result represent a chromosomally normal female fetus, or is it the mother’s own cells masking an abnormal fetus such as Trisomy 16 or a male (46,XY)? With conventional karyotyping, it is impossible to distinguish this. Because of this high risk of failure and MCC, modern POC analysis now favors molecular methods such as CMA or NGS, which analyze DNA directly from tissue and do not require culture.

Which Genetic Test (Karyotype, CMA, NGS) Is Used Today and When?

In reproductive genetics, there is no such thing as the “best” test; rather, there is the “right test for the right clinical question”. While karyotype retains its place as a gold standard, it is now used together with higher-resolution molecular tests (CMA and NGS).

The use of the tests can be summarized as follows.

Situation: Recurrent Pregnancy Loss (RPL) OR Severe Male Infertility (Azoospermia, etc.)

• Test: G-banded Karyotype Analysis from Parental Blood

Purpose: To look for structural carrier states in the parents, such as a “balanced translocation”. Karyotype is the only test that can visualize balanced rearrangements.

Situation: Analysis of Products of Conception (POC)

• Test: Chromosomal Microarray (CMA) or NGS

Purpose: To identify the cause of the miscarriage (Trisomy 16, Monosomy X, etc.) with high success while eliminating the risk of maternal cell contamination.

Situation: Known Translocation Carrier Status in a Parent

• Test: PGT-SR (NGS-based) on Embryos

Purpose: To filter out unbalanced embryos resulting from the parental rearrangement in IVF and transfer only balanced embryos.

Situation: Advanced Maternal Age OR Recurrent IVF Failure (RIF)

• Test: PGT-A (NGS-based) on Embryos

Purpose: To screen for random (sporadic) numerical abnormalities (aneuploidies) arising in eggs/sperm, even when parental karyotypes are normal.

What Does a ‘Normal’ Karyotype Result Mean?

It is very important to provide couples with accurate counseling on how to interpret a “normal” parental karyotype result (46,XX and 46,XY).

Receiving a normal karyotype result is excellent news. It indicates that the couple (or individual) does not carry a large-scale, structural and hereditary chromosomal problem. It largely rules out “balanced translocation” and similar inherited chromosomal defects as the cause of recurrent miscarriages or infertility.

However, having a normal parental karyotype does not guarantee that their embryos will also be genetically normal.

The vast majority of embryonic aneuploidies (such as Trisomy 21 / Down syndrome) arise from sporadic errors during the formation of gametes (particularly eggs), independent of the parents’ chromosomal structure. This risk increases with advancing maternal age, even if the parental karyotypes are perfectly normal.

Frequently Asked Questions