Since the discovery of chromosomes, the cytogenetic field has evolved rapidly. The techniques have unfolded several hidden mysteries of chromosomes. And later, it gave rise to two branches: molecular and clinical cytogenetics. The studies in clinical cytogenetics suggested that the structural and numerical aberrations of chromosomes (autosomal and sex) are the cause of several abnormalities in human beings. For example, Down’s syndrome, Turner’s syndrome, cancer, etc. The molecular cytogenetic techniques (for example FISH, multicolor karyotyping, CGH, etc.) proved to be an essential tool to study genetic disorders and find their possible treatments.

These techniques have also been widely used in the process of prenatal and postnatal diagnosis by researchers. Moreover, doctors also suggest pregnant women for prenatal cytogenetics analysis and prenatal ploidy analysis to detect any genetic abnormality in the fetus (if they have any family history of genetic diseases)[1]. The analysis is generally done by using the karyotyping and FISH technique.

The advanced cytogenetic techniques such as microarray aid in the high-resolution analysis and have the ability to map the copy number changes in the genome. These techniques have also proved very helpful in the diagnosis, therapy, and monitoring of the effect of the treatment on any cancer patient. We’ll discuss clinical cytogenetics and its relevance in the study of chromosomal aberrations.


Clinical Cytogenetics

Few categories[1] of chromosomal aberrations:

  1. Autosomal aneuploidy
  2. Structural chromosome rearrangements
  3. Sex chromosomal disorders
  4. Infertility
  5. Prenatal cytogenetics
  6. Chromosome instability.
  7. Spontaneous Abortion

In Clinical Cytogenetics – Pt.1 we discussed points 1-3 above and learned various chromosomal aberrations that included deletions, inversions, substitution, translocation, and aneuploidy of the chromosomes. We also talked about the mechanisms that lead to these aberrations and the diseases they cause in human beings.

So, for this article, we will continue looking into these categories, particularly categories 4-7, as follows;


4. Infertility

Infertility is the inability to conceive a child by a couple, despite having unprotected intercourse for at least one year. Both male and female factors can be responsible for infertility. The causes of infertility in both the sexes include:[1]


S.No.Causes of female infertilityCauses of male infertility
1.Fallopian tube blockage or adhesionVaricocele (swelling of veins in the testes)
2.Cervical and uterine abnormalityHormone imbalances
3.Endometriosis (endometrial tissue grows outside of the uterus)Ejaculation issue ( premature ejaculation, genetic disease, blockage of testicles, etc)
4.Early menopauseOligospermia (low sperm count)
5.Ovulation disordersChromosome defects and Cancer

Sometimes, amenorrhea is the cause of female infertility. It is of two types: (a) primary amenorrhea, which is the absence of menstruation in females; and (b) secondary amenorrhea, the occurrence of discontinuous menstruation. Cytogenetics studies have found primary amenorrhea as the major cause of infertility in women.

Examples of chromosomal abnormalities causing infertility in females
  1. 45, X (Turner syndrome): It is estimated that 1 in 2500 girls is born with 45, X; and 2-3 % of women undergo normal puberty and menstruation, but there are chances to suffer from secondary amenorrhea. It has also been found that women with 45, X chromosomes are more likely to give birth to a child without abnormality (though with lesser chances) than the women having 45, X mosaic chromosomes.[1]
  2. X Chromosome Deletions: Deletions in the region of the X-chromosome lead to ovarian failure or amenorrheic conditions. Deletions at the p11 region lead to ovarian failure in some women and in other women, menstruation irregularities have been observed, although with rare chances of fertility even if menstruation occurs. If the deletion occurs in the long arm of the X-chromosome, between Xq13 and Xq26, it is definite to cause ovarian failure. The phenotype of women with Xq13 includes no breast development, ovarian failure, primary amenorrhea, and high levels of FSH and LH. Deletions in the distant region of the X-chromosome show milder effects. These women may have normal menarche but fertility is rare.[1]
  3. Endometriosis: In this condition, the endometrial tissue forms outside the uterus (in the ovary, pelvis, or elsewhere in the body). Endometriosis is the cause of infertility in 6-10% of women of their reproductive age. This condition arises due to the loss of chromosomal regions such as  7p, 1p, and 22q. It can be studied by using molecular cytogenetic techniques such as dual-color FISH and comparative genomic hybridization (CGH).[1]
Examples of chromosomal abnormalities causing infertility in males
  1. The SRY Gene and Genetic Sex: Sex determining region Y (SRY) is present on the short arm of chromosome Y. Its function involves the differentiation of precursor cells into Sertoli cells. These cells secrete the anti-mullerian hormone which functions to repress the development of female genitalia. Moreover, it is also involved in the production of testosterone from Leydig cells, which is involved in the formation of internal male genitalia. Any defect in this region of the chromosome may cause infertility in men due to the absence or poor development of male genitalia.[1]
  2. Oligospermia: This is the condition of having low spermatozoa count in an ejaculation. This can be due to chromosomal abnormality of 47, XXY; 47, XYY; or structural abnormality in the Y chromosome. Oligospermia can also occur due to structural rearrangements of the autosomal chromosome (discussed in Clinical cytogenetics-Pt.1).
  3. Sex Chromosome Abnormalities: The various types of non-mosaic chromosomal abnormalities are: 47, XXY, and 47, XYY. Some other mosaic abnormalities include 47, XXY/46, XY, and 47, XYY/46, XY. The researchers found that the frequency of aneuploidy of the sex chromosome ranges from 0.3 to 15 % which leads to infertility in men.[1] This condition can be studied by semen analysis by using the FISH technique.
  4. Autosomal Abnormalities: Robertsonian translocation, reciprocal translocation, and inversion are some common types of autosomal abnormalities that lead to infertility in men. It has been studied that the incidence of Robertsonian and reciprocal translocation is 0.7% and 0.5%.  These findings are studied by using Karyotyping and FISH techniques.[1]


5. Prenatal cytogenetics

The key event in the history of clinical cytogenetics was when a scientist, James, developed a technique to determine the sex of the fetus from the amniotic fluid by the Papanicolaou method using Giemsa stains. Now, three procedures are available to collect amniotic fluid for the analysis and these are; Amniocentesis, Chorionic Villus Sampling, and Percutaneous Umbilical Cord Sampling (PUBS).

The collection of amniotic fluid by transabdominal and transcervical puncturing of the uterus is called amniocentesis. This technique was developed and has been practiced since the 1930s[1] and today it’s a common tool to detect prenatal and postnatal cytogenetic and molecular abnormalities.

In the Chorionic villus sampling technique, developing placental cells are taken from pregnant women through the abdomen or cervix. And, PUBS (also called Cordocentesis) involves the collection of blood through the abdomen from a vein of the umbilical cord of pregnant women. These procedures are very helpful to detect any genetic abnormality in the fetus and to provide genetic counseling. Table [1] below will provide a brief of all three techniques.

TechniquesTime period recommended for testing (weeks)Diagnostic/cytogenetic analysis

●      Karyotype

●      Biochemical studies

Chorionic Villus Sampling8-11

●      Karyotype

●      Cytogenetic analysis

●      Enzymatic studies

Percutaneous Umbilical Cord Sampling (PUBS)18-23

●      Karyotype and DNA analysis

●      Detection of disorders and infections.


(a) Amniocentesis   (b) Chorionic Villus Sampling   (c) Percutaneous Umbilical Cord Sampling (PUBS)


Figure: Image showing three procedures/techniques for prenatal cytogenetic analysis.

Source: ,



What are the conditions in which Prenatal Cytogenetic analysis should be performed?

There are some situations in which significant risks of chromosomal abnormalities have been studied by researchers. Some indications of the risks[1] are discussed below:

  • Maternal Age: It has been found in various studies that women undergoing pregnancy at the age of 35 or more (or pregnant with twins at the age of 31 or more), are at higher risk of fetal chromosomal abnormality. For example, Down’s syndrome, Klinefelter syndrome, Turner syndrome, and structural rearrangements.
  • Nuchal folds and cystic hygromas: These are fluid-filled sac-like abnormal structures observed in the fetus during the second or third trimester. There are 22-70% chances of chromosomal abnormality in the fetus if any of these abnormal structures are observed in the ultrasound image.
  • Cardiac anomaly: It has been estimated that the frequency of chromosomal abnormality in a child with a cardiac anomaly is 5–10% (indicated by postnatal data). The prenatal data showed that there are 32–48% chances of chromosomal abnormality in the fetus with the cardiac anomaly.
  • Renal Pyelectasis: In this condition, the renal pelvis is mildly dilated. Researchers found the association between renal pyelectasis (observed in the ultrasound image of the fetus) with the trisomy of chromosomes and other mosaic conditions such as 47, XYY/46, and XY.


6. Chromosome instability

The instability of the chromosome is categorized at two levels: nucleotide level and chromosome level. The instability at the nucleotide level includes deletions or substitutions of a few nucleotides that cause frameshift mutations. However, instability at the chromosome level includes structural rearrangements of chromosomes (deletions, duplications, inversions, and translocation) which occurs due to breaks in the chromosomes. Another cause of chromosome instability is the numerical changes (aneuploidy and polyploidy) in the chromosome. This occurs due to the dysregulation of genes involved in cell division.

Mutations in cellular processes such as impairment of DNA replication, DNA recombination, and DNA repair lead to some other instabilities that are: the formation of fragile sites, sister chromatid exchange, and chromosome breakage.[1]

We are already familiar with the structural and numerical instability of the chromosomes. So, here we will discuss fragile sites and associated diseases.


What are fragile sites?

Fragile sites are considered as the points/regions on the chromosome which form gaps or breaks when the cell is exposed to stress conditions. These sites are rare but they are inherited as codominant traits. Some of the commonly known fragile sites are 3p14.2 (FRA3B), 6q26 (FRA6E), and Xp22 (FRAXB).[1]

It has been found that fragile sites are induced by chemicals such as aphidicolin, 5-azacytidine, and bromodeoxyuridine (BrdU).


Figure: The image shows fragile sites on human chromosomes (shown by arrow)-induced by folate.

Source: The Principles of Clinical Cytogenetics (2013).[1]


Examples of syndromes due to chromosome breakage
  1. Fanconi anemia (FA): This is a rare disease that occurs due to a homozygous mutation of the FANCD1 gene. The phenotype of this disease includes congenital anomaly, bone marrow failure, malformation of organs such as the heart and kidney, and overlapping of skeleton and limbs. The frequency of occurrence of this disease is 1-5/million. The types of chromosomal abnormalities observed in the cells of the patients are chromatid breaks, acentric and dicentric fragments, endoreduplication chromosomes, and telomere shortening.[1]
  2. Ataxia Telangiectasia: It is an autosomal recessive disorder. Breakage in the ATM gene is responsible for causing this disease. The phenotype includes cerebellar degeneration, immunodeficiency (diminished level of IgG2 and IgA), radiosensitivity, and cancer. The frequency of occurrence of this disease is 1 in 89,000.[1]
  3. Xeroderma Pigmentosum:  This disease is inherited in an autosomal recessive manner and is caused due to impairment in DNA repair ( defective excision of pyrimidine dimers) or replication of damaged DNA. The phenotype includes sensitive skin to sunlight (even can develop skin cancer), severe sunburn with blistering, persistent erythema, neurologic degeneration, and sensorineural deafness.[1]
  4. Robert Syndrome (RS): This is the rarest disease that occurs due to mutation in the ESCO2 gene, which causes loss of acetyltransferase activity. The phenotype includes growth retardation, abnormal limbs, craniofacial defects, hypertelorism, and cleft lip and palate. In some patients, heterochromatin repulsion and premature centromere separation are observed in chromosomes 1, 9, and 16. Prenatal diagnosis and cytogenetic analysis are done by ultrasound examination and by using the C-banding technique.[1]


7. Spontaneous Abortion

The frequency of occurrence of abortion is 15-20% in the early gestation period or second and third trimester of pregnancy. Multiple studies suggested that cytogenetic abnormalities are significant factors contributing to spontaneous abortion. It has been also found that the chances of abortion or chromosomal abnormality increase with the maternal age(at the age of 35 or more). Some of the errors[1] leading to abortion are given below:

  1. Trisomies: The most frequent type of trisomies that have been observed are trisomy 21, 22, and 16 chromosomes. The frequency of occurrence of trisomy 21 is 1 in 700 live births. The studies have found an association between maternal age and down syndrome. So, it is generally recommended for pregnant women of age 35 or above for prenatal diagnosis.
  2. Sex Chromosome Aneuploidy: It is the most common chromosomal abnormality responsible for abortion. In the majority of cases 45, X (Turner syndrome) arrangement is found to be responsible for miscarriages. The frequency of occurrence of turner syndrome is 1 in 1,000 female live births. In some cases, trisomy of sex chromosomes, such as 47, XXX, 47, XXY, and 47, XYY, found to be responsible for infertility.
  3. Structural rearrangements: The most common type of structural rearrangements leading to abortions are Robertsonian translocation, reciprocal translocation, and inversions. These rearrangements lead to the production of unbalanced chromosomes due to the abnormal segregation of chromosomes during meiosis. It has been estimated that the frequency of abortions due to structural rearrangements is 1-2%.
  4. Errors in fertilization: Due to errors in fertilization, pregnant women may have a triploid or abnormal diploid condition. Both mother (digyny) and father (diandry) can contribute to an extra set of chromosomes in the fetus. The 69, XYY arrangement indicated diandry; and 69, XXX or 69, XXY arrangement is demonstrated either by diandry or digyny. The frequency of occurrence of triploidy ranges from 1-3%.



As seen, clinical cytogenetics is the study of the relation of chromosomal aberrations with genetic diseases. The study provides a deep insight into structural and numerical chromosomal abnormalities leading to variant genetic disorders. The most important aspect of clinical cytogenetics is that it helps in the analysis of fetal chromosomes for any genetic disorders and genetic counseling of parents. So, clinical cytogenetics provides a whole picture of chromosomal disorders and their causes, which proves to be a useful tool for disease diagnosis and treatment.



Gersen Steven L. and Keagle Martha B. (2013). The Principles of Clinical Cytogenetics (3rd ed.), Springer, New York.