Infertility Management

Indications for Cytogenetic Analysis:

  • Couples with repeated spontaneous miscarriages
  • Couples with primary infertility
  • Males with oligozoospermia and azoospermia
  • Males with hypogonadism, breast development and lack of facial hair
  • Women with primary amenorrhoea, short stature, and streak gonads.

Sample: 2 ml Blood in sodium heparin vaccutainer (Green top tube), transported at room temperature. No fasting is required.


Indication for Cytogenetics Analysis

Routine analysis of sperm chromosomes is not feasible in clinical practice. However, interphase FISH on spermatozoa offers an accurate and reliable method of analysis even in the presence of a low sperm count.

The percentage of sperm with hypo/hyperhaploidy (less chromosomes / more chromosomes) is calculated to counsel the couple.

Sample : Fresh / Frozen-thawed semen sample.

Outstation samples are also accepted.

Note: All samples should be accompanied with a copy of the semen analysis report at the time of sample collection which should include the name of the patient, age, count, motility and morphology of the sperm.

Y chromosome micro-deletions like DAZ (deletion in azoospermia) and RBM (RNA binding motif gene) cause spermatogenic defects. In the Yq arm (long arm of the Y chromosome), intervals V and VI comprise an Azoospermia Factor (AZF) which contains the DAZ and RBM genes. Several genes have been identified within this region and have been proposed candidates for infertility. We can check for 29 different micro-deletions including 5 partial deletions in the AZF region by multiplex PCR.

If Y chromosome microdeletions are seen only in the AZFc region, there is a good chance that TESA will be successful. However, if microdeletions are seen in the AZFa and AZFb regions, the chances of success after TESA are extremely low.


Multiplex PCR for Y microdeletion detection


The Sperm DNA Fragmentation Index (DFI) test is used to determine whether the male partner of an infertile couple has a high, fair, or poor fertility potential by studying fragmentation of his Sperm DNA.

Apoptosis is a mode of programmed cell death based on a genetic mechanism that induces a series of cellular, morphological and biochemical alterations, resulting in fragmentation of the genomic DNA. The sensitive TUNEL method is based on the detection of single and double stranded DNA breaks occurring at early stages in apoptosis.

After an enzymatic reaction, the fluorescein label incorporated at the damaged sites of DNA is visualized by fluorescence microscopy. The apoptotic sperm appear greener, while the normal non-apoptotic sperm take up more of the DAPI stain and appear blue. Partially apoptotic sperm will appear partially blue and green. This test allows the detection of apoptosis at the single cell level and may serve as an indicator for use of antioxidants prior to IVF.

The DFI is a ratio expressed as a percentage of sperm which has fragmented DNA due to apoptosis divided by the total number of sperm analyzed.

The sperm apoptosis test provides a reliable analysis of sperm DNA integrity that may help to identify men who are at a risk of failing to initiate a healthy ongoing pregnancy. It may help in the clinical diagnosis, management and treatment of male infertility and could be of prognostic value in assessing the outcome of various methods of Assisted Conception.

Apoptosis may not completely eliminate the cell’s competence for fertilization. Hence, an apoptotic spermatozoon, possessing high levels of DNA fragmentation, can fertilize the oocyte using ICSI. Such a pregnancy with DNA damage in the sperm may lead to miscarriage.


Follicular fluid is a novel source of gonadal cells for detection of low-grade mosaicism in the ovaries. Study of gonadal cells present in the follicular fluid of women undergoing IVF can determine the chances of a successful pregnancy. If there is evidence of gonadal mosaicism, the chances of a live birth could be low. Mosaicism for the X chromosome can be detected rapidly by FISH on follicular fluid cells and can be one more indication for Preimplantation Genetic Testing (PGT) in the same and subsequent cycles.


Mosaicism is the presence of chromosomally normal and abnormal cells in the same individual. The percentage of mosaicism is known to vary in different tissues. We can easily study buccal, urine and blood cells by FISH. When more than 5% aneuploidy for the X chromosome is detected in the follicular fluid cells derived from the ovary, we check for aneuploidy in these other tissues as well.

MTHFR Mutation testing:

Methylenetetrahydrofolate Reductase (MTHFR) Deficiency is the most common genetic cause of elevated levels of homocysteine in plasma (Hyperhomocysteinemia).

Clinical Significance and Utility:

Hyperhomocysteinemia is a risk factor for arterial disease and venous thrombosis. Homocysteine levels are affected by nutritional and genetic factors.

  • Two mutations (C677T and A1298C) in the MTHFR gene have been associated with increased levels of circulating homocysteine. Homozygosity for the C677T mutation or compound heterozygosity for C677T and A1298C is associated with reduced MTHFR activity. Decreased MTHFR activity leads to hyperhomocysteinemia and lowers plasma folate levels. Homozygosity for 677C>T may increase risk for venous thrombosis and pregnancy complications (pre-eclampsia, placental abruption, intrauterine growth restriction).
  • In case of homozygosity for the C677T mutation or compound heterozygosity for C677T and A1298C mutations and homocysteine results, physicians can develop dietary and medical recommendations – increased intake of methylfolate alone or in combination with vitamins B6 and  B12 are recommended.

Prothrombin Mutation testing:

Prothrombin or Factor II is a protein in the blood that is required for the formation of fibrin in blood clotting process.

Clinical significance and utility:

  • Low levels of prothrombin causes frequent bleeding whereas high levels cause unwanted blood clots.
  • A history of recurrent pregnancy loss or stillbirth, may be indicative of an underlying thrombophilia (the blood has an increased tendency to clot).
  • Mutation G20210A in the prothrombin gene leads to increased levels of prothrombin which ultimately leads to increased risk of blood clotting. Individual with this mutation have an increased risk of developing Deep Vein thrombosis (DVT).

Indications for Testing:

Indications for testing as part of the screening for thrombophilia include: venous thromboembolism (especially if in an unusual site), deep vein thrombosis during pregnancy, venous thromboembolism while on oral contraceptives, fetal death after 10 weeks gestation, fetal growth restriction and/or preclampsia, and/or family history of stroke, pulmonary embolus, deep vein thrombosis in first degree relatives under the age 50.


What is Genetics?

Genetics is the study of heredity and genetic variation. It deals with hereditary diseases and birth defects.

What are the different types of Genetic Diagnostic Tests?

Genetic Diagnostic Tests can be broadly classified into:

  • Cytogenetic Tests – Karyotyping & FISH for chromosome analysis.
  • Molecular Genetic Tests – PCR, sequencing, microarray and Next Generation Sequencing for DNA analysis.
  • Biochemical Genetic Tests – To detect inborn errors of metabolism.

What are chromosomes?

Chromosomes are X shaped thread like structures made up of DNA, and carry the hereditary material of an individual. Different genes are located at specific points on chromosomes, which are visible under the microscope when the nucleus of a cell is dividing.

How many chromosomes are present in the cells of a human being?

Human beings have 46 chromosomes. These are present in pairs. This is termed as a diploid set of chromosomes. The sex chromosomes are XX in females and XY in males. The other chromosomes, besides the sex chromosomes are called autosomes. The ova and sperm however contain only 23 unpaired chromosomes each (a haploid set) so that when fertilization takes place, the cells of the embryo will again have 46 chromosomes.

What are the main types of chromosome abnormalities?

Chromosome abnormalities are mainly of two types.

  • Numerical – e.g. Trisomy, Monosomy, Triploidy, Tetraploidy, Mosaicism
  • Structural – e.g. Translocation, Deletion, Inversion, Duplication

What is trisomy?

Trisomy is the most common type of numerical chromosome abnormality. There is one extra chromosome in any pair e.g. Trisomy 21. These individuals suffer from Down syndrome. Thus the total number of chromosomes in each cell will be 47 instead of 46.

What is Down Syndrome?

Down Syndrome is a genetic disorder where the individual is usually mentally challenged. Such individuals have typical facial features like upslanting eyes, depressed nasal bridge, and an open mouth with a rough protruding tongue. They often have a single palmar crease or Simian crease on their palm. Trisomy 21, is the most common cause of Down syndrome.

What are the other causes of Down syndrome?

Down syndrome is occasionally caused by a translocation when 2 chromosomes have fused, so the total number of chromosomes remains 46 instead of 47. This can be inherited from a parent who is a carrier, having 45 chromosomes instead of 46 because of this fusion. In such cases, there is a risk that subsequent children may also be affected. Prenatal Diagnosis is important in these cases to determine if the fetus has Down syndrome. In the rare instance of a parent carrying a 21/21 translocation, all the children will have Down syndrome, so assisted reproduction with donor sperm or oocytes can be offered accordingly. This illustrates the importance of Karyotyping.

What is karyotyping?

Karyotyping is the process of chromosome analysis using banding techniques. The chromosomes seen under the microscope are arranged in pairs and scrutinized for any visible chromosome abnormalities. The method involves tissue culture to obtain dividing cells. Hence collection of appropriate samples under aseptic conditions is important.

What are the indications for Karyotyping?

  • Turner Syndrome (45,X and variants)
  • Klinefelter Syndrome (47,XXY and variants)
  • Down Syndrome (Trisomy 21, translocation and mosaicism)
  • Couples with infertility of unknown cause
  • Couples with recurrent spontaneous miscarriages
  • Children with ambiguous genitalia
  • Female children with inguinal hernia
  • Children with mental subnormality and dysmorphic features
  • Suspected cases of Fanconi anaemia, Ataxia Telangiectasia, Bloom syndrome
  • Bone marrow analysis in leukemias (blood cancer).
  • Prenatal Diagnosis of fetal chromosome disorders in high-risk pregnancies.

What is aneuploidy?

Aneuploidy is the presence of one extra chromosome (trisomy) or absence of one chromosome (monosomy) in each cell. This leads to different abnormalities such as:

  • Trisomy 21- Down syndrome or Mongolism
  • Trisomy 13 – Patau syndrome
  • Trisomy 18 – Edward syndrome.
  • Sex chromosome abnormalities- XXX, XXY, XO, XYY.

In products of conception (tissue from spontaneous abortions) trisomy 16 and trisomy 22 are quite common.

Common aneuploidies can be rapidly detected by a cytogenetic technique called Fluorescence in situ hybridization (FISH).

What is FISH?

FISH (Fluorescence in situ hybridization) is a rapid molecular cytogenetic technique. FISH is mainly used to detect common aneuploidies like trisomy or monosomy of chromosomes 21, 18 or 13, sex chromosome abnormalities like Turner (XO) or Klinefelter (XXY) syndrome and mosaicism where there is a mixture of normal and abnormal cells. This test is important in a variety of cases ranging from prenatal diagnosis to cancer. The test results are available in 1-2 days as tissue culture is not required. There is no risk of a culture failure due to contamination or inadequate sample size.

What are the benefits of FISH?

The FISH test has many benefits. It reduces parental anxiety especially in prenatal diagnosis when the Triple test shows a high-risk pregnancy, as the FISH report is available much earlier than the karyotype reports. A large number of interphase nuclei can be studied to detect low-grade mosaicism. The test can also be carried out on a wide range of samples like chorionic villi, amniotic fluid, cord/adult blood, placental biopsy, products of conception, buccal cells and sperm. FISH has wide applications in detecting the type of  cancer and in the prognosis of the disease.

What is mosaicism?

Mosaicism is the presence of chromosomally normal and abnormal cells in a person. In such cases, the clinical manifestation varies according to the percentage of normal and abnormal cells. Low-grade mosaicism, where the percentage of one of the cell-lines is very small, can be easily detected by FISH.

What are microdeletions?

Microdeletions are deletions of very small segments of chromosomes. They are often missed by karyotyping, but can be easily detected by FISH.  Prader-Willi /Angelman Syndromes may be caused by a microdeletion on chromosome 15.

How is FISH analysis done?

Commercially available DNA probes labeled with different fluorescent dyes are hybridized to the nuclei of cells, and analyzed under a fluorescence microscope. If the probe for chromosome 21 is labeled with an orange fluorescent dye, for example, we will see 2 orange signals under a fluorescence microscope in normal cells, and 3 orange signals in cells of an individual with Down syndrome (Trisomy 21). The diagnosis is thus made by counting the number of signals of different colours in each cell. The cells are counterstained with a blue dye DAPI, to differentiate the cells.

What are the limitations of FISH?

All chromosome abnormalities cannot be ruled out by FISH. Hence it cannot replace conventional karyotyping. FISH is useful to detect probe-specific abnormalities only.

Which are the common leukemias where FISH is useful?

FISH is commonly used in the rapid diagnosis, prognosis and management of chronic myeloid leukemia (CML) and acute promyelocytic leukemia (AML-M3), especially since specific treatment is available in each case. FISH is also used in many other hematological malignancies such as ALL, AML, MDS, Multiple Myeloma, CLL, Lymphomas and in solid tumors.

What is prenatal diagnosis?

Prenatal diagnosis is the detection of certain cytogenetic, molecular or biochemical genetic abnormalities in the unborn child.

When is prenatal diagnosis recommended?

Prenatal diagnosis is recommended in the following cases:

  • Advanced maternal age
  • Screening tests show high risk of abnormality
  • Abnormalities on ultrasonography
  • A parent with a balanced translocation
  • History of a previous abnormal child
  • X-linked genetic disorders
  • Couples with Thalassemia trait
  • Couples with family history of known monogenic disorders such as Beta Thalassemia
  • Cases in which NIPT (Non-Invasive Prenatal Testing) show a high risk for Trisomy 13, 18, 21.

Prenatal diagnosis can be carried out at what stage of pregnancy?

Prenatal diagnosis can be carried out in the 1st, 2nd or 3rd trimester depending on the stage at which an abnormality is detected or suspected. Different tissues are sampled according to the gestational age, e.g.

  • Chorionic villus (which forms the placenta) at 10-12 weeks
  • Amniotic fluid (which surrounds the fetus) at 16-18 weeks
  • Cord blood (from the umbilical cord) at greater than 19 weeks.

What are the requirements for pre-conception or prenatal diagnosis?

As per the PCPNDT (Prohibition of sex selection) Act 2003, the sample collection and analysis has to be carried out in registered clinics/ laboratories/centers as applicable after the mother has signed an informed consent form. The sex of the fetus is not revealed.

What is PCR?

PCR (Polymerase Chain Reaction) is a molecular diagnostic technique used to generate (amplify) large amounts of specific sequences of genes from DNA, for genetic analysis. It can be used to diagnose single gene disorders like beta-Thalassemia and Cystic Fibrosis, Sickle Cell Anaemia, Duchenne Muscular Dystrophy,  Metabolic Disorder in the new born such as Phenyl Ketonuria and Familial Hereditary Cancer Syndromes.

What are Y-Chromosome Microdeletions?

There are small regions on the Y chromosomes which are responsible for mature sperm formation. If a part or parts of the region is lost, it is noted as a deletion. These regions on the Y chromosome are too small to be detected through the microscope. These deletions can be detected by multiplex PCR technique. They are usually seen in males with azoospermia (No sperm found in the semen sample). Depending on which region is deleted, men with these deletions can father a child with Assisted Reproduction Techniques, but the couple has to be counselled that the male partner may transmit infertility to the male offspring.

What is PGT?

PGT is Preimplantation Genetic Testing. It is an additional step during the ICSI procedure, where trophectoderm cells from an embryo can be tested to rule out certain genetic conditions such as chromosomal aneuploidy, thus allowing only normal embryos to be transferred.

Can all genetic disorders be diagnosed or ruled out by these tests?

No. There are thousands of genetic disorders. Though recent technologies such as Next Generation Sequencing (NGS) and Chromosome Microarray (CMA) can pick up a large number of abnormalities, there are many others that need specific tests and some that may not be picked up on testing. You can visit our IVF center in Mumbai for consultation

What is Genetic Counseling?

During Genetic Counseling, the inheritance pattern of a particular genetic disorder in a family is studied. The chances of recurrence of the same abnormality in the family are explained. If genetic tests for diagnosis of that disorder are available, arrangements are made to send the required samples for testing. Prenatal diagnosis in a subsequent pregnancy in family members ‘at risk’ can be carried out. As most genetic disorders cannot be cured, genetic counseling helps to prevent the recurrence of the same disorder in the extended family.