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Cytogenetic Tests for Chromosomal Abnormalities

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What is Chromosomal Abnormality?

An error in chromosome number that arose during the development of an egg or a sperm cell can be termed as a chromosomonal abnormality. Unlike other cells, sperm and egg cells have only 23 unpaired chromosomes. When they unite, pregnancy begins and ultimately results in the formation of a fertilized egg with 46 chromosomes. But if an error occurs during cell division, it results in an embryo with a chromosomal abnormality. A common type of chromosomal abnormality is called a trisomy. This means that the individual has 3 copies, instead of two of a specific chromosome. Down syndrome is the best cited example for trisomic condition having 3 copies of chromosome 21.

What is Chromosome?

Chromosomes are tiny string-like structures in cells of the body that contain the genes. Humans have about 20,000 to 25,000 genes that determine traits like eye and hair color. They also direct the growth and development of every part of the body (3).

Each person normally has 23 pairs of chromosomes, or 46 in all. We inherit one chromosome per pair from our mother and one from our father.

Sometimes, however, a baby can be born with too many or too few chromosomes, or with one or more chromosomes that are missing a piece or are rearranged. These errors in the number or structure of chromosomes can cause a wide variety of birth defects ranging from mild to severe. Some chromosomal abnormalities result in miscarriage or stillbirth.

What causes Chromosomal abnormalities?

Chromosomal abnormalities usually result from an error that occurred when an egg or sperm cell was developing. It is not known why these errors occur. There are two main types of abnormalities:

1. Numerical abnormalities:

Sometimes the eggs and sperm cells divide incorrectly, resulting in an egg or sperm cell with too many or too few chromosomes.
When this cell with the wrong number of chromosomes joins with a normal egg or sperm cell, the resulting embryo has a chromosomal abnormality. A common type of chromosomal abnormality is called a trisomy. This means that an individual has three copies, instead of two, of a specific chromosome. Down syndrome is an example of a trisomy. Individuals with Down syndrome generally have three copies of chromosome 21.

In most cases, an embryo with the wrong number of chromosomes does not survive. In such cases, the pregnant woman has a miscarriage. This often happens very early in pregnancy, before a woman may realize she's pregnant. Up to 75 percent of first trimester miscarriages are caused by chromosomal abnormalities in the embryo.

2. Structural abnormailities:

When the chromosome's structure is altered. This can take several forms:

  • Deletions: A portion of the chromosome is missing or deleted. Known disorders include Wolf-Hirschhorn syndrome, which is caused by partial deletion of the short arm of chromosome 4; and Jacobsen syndrome, also called the terminal 11q deletion disorder.
  • Duplications: A portion of the chromosome is duplicated, resulting in extra genetic material. Known disorders include Charcot-Marie-Tooth disease type 1A which may be caused by duplication of the gene encoding peripheral myelin protein 22 (PMP22) on chromosome 17.
  • Translocations: When a portion of one chromosome is transferred to another chromosome. There are two main types of translocations. In a reciprocal translocation, segments from two different chromosomes have been exchanged. In a Robertsonian translocation, an entire chromosome has attached to another at the centromere; these only occur with chromosomes 13, 14, 15, 21 and 22.
  • Inversions: A portion of the chromosome has broken off, turned upside down and reattached, therefore the genetic material is inverted.
  • Rings: A portion of a chromosome has broken off and formed a circle or ring. This can happen with or without loss of genetic material.
  • Isochromosome: Formed by the mirror image copy of a chromosome segment including the centromere.
    Chromosome instability syndromes are a group of disorders characterized by chromosomal instability and breakage. They often lead to an increased tendency to develop certain types of malignancies.

3. Inheritance:

Errors in cell division also can occur soon after fertilization. This can result in mosaicism, a condition in which an individual has cells with different genetic makeups. For example, individuals with the mosaic form of Turner syndrome are missing an X chromosome in some, but not all, of their cells. Chromosome anomalies can be inherited from a parent or be "de novo". This is why chromosome studies are often performed on parents when a child is found to have an anomaly.

How are the Chromosomal abnormalities detected?

Chromosomal abnormalities can be diagnosed after birth using a blood test, or before birth using prenatal tests (amniocentesis or chorionic villus sampling). Cells obtained from these tests are grown in the laboratory, and then their chromosomes are examined under a microscope. The lab makes a picture (karyotype) of all the person's chromosomes, arranged in order from largest to smallest. The karyotype shows the number, size and shape of the chromosomes and helps experts identify any abnormalities. Also FISH cytogenetic studies are used for the identification of chromosomal abnormalities.

What is Kayotyping?

Karyotyping is one of the many techniques that help study the human genes for several genetic diseases. Karyotyping comes from the word karyotype. Karyotype is a complete profile of an individual's chromosomal set up. Any changes in the arrangement of a karyotype helps doctors study possible genetic disorders. In simpler terms, karyotyping is a close study of chromosomes.

What does Kayotyping show?

A karyotype shows the details of the chromosomes. Karyotyping identifies and helps determine the sex of an unborn child. When doctors study a human karyotype they look for some significant features. Here are a few important ones.

Check if the 46 chromosomes are present
Check the presence of the two identical chromosomes and 2 sex chromosomes
Check if there are any missing or rearranged chromosomes

How is Kayotyping performed?

There are usually no special requirements before performing the test. It is performed on a sample of blood, bone marrow, the amniotic fluid or the tissue from the placenta. Blood is drawn from the body if it requires blood sample. Amniocentesis is carried out to test amniotic fluid. A bone marrow test would require a bone marrow biopsy. The given sample is placed on a tray and allowed to grow in the confines of a laboratory. The cells from the growing sample are then stained. The stained sample is closely examined to study the chromosome arrangement.

How Kayotyping predicts disorders?

A normal human being has 46 chromosomes, 22 autosomes and two sex chromosomes. When there is a disharmony between this set up, a genetic disorder occurs. Too many chromosomes, missing chromosomes or mixed up bits of chromosomes show the presence of a problem. The state of the chromosomes helps predict any possible genetic disorder in an unborn child. Chromosomes carry information that is passed to the cell. Extra copies of the information, mixed information or missing information can inform about any abnormalities or defects.

What makes Kayotyping helpful?

Blood Karyotyping is a very helpful method of studying chromosomes and predicting genetic disorder. It counts the number of chromosomes and looks for any structural changes in chromosomes. It informs if the unborn baby will suffer from a genetic disorder or not. It is often used during pre-natal testing and diagnosing possible genetic diseases. It is extremely helpful for those who have suffered the loss of a child through a miscarriage. For couples coping with a miscarriage karyotyping can mean identifying and correcting problems to give birth to a healthy child.

What are the Karyotype Options?

• Abortus Material (Long term culture)
• Amniotic Fluid (Cell Culture)
• Ataxia Telengiectasia - Bleomycin assay
• Blood Chromosomes
• Bone Marrow chromosomes
• Chorionic Villi samples (Long term culture)
• Cord Blood Prenatal- Chromosomes
• Falconi’s Anemia (Mitomycin Assay)
• Fibroblast culture for other test
• Fragile X Syndrome - Thymidine block
• Prader Willi syndrome- microdeletion Chm 15
• Recurrent Abortions, Husband and Wife

What is FISH cytogenetic study?

Fluorescence in situ hybridisation (FISH) is a powerful tool for rapid detection of certain chromosome abnormalities that are otherwise undetectable or difficult to characterise by conventional cytogenetic methods. It represents a relatively new type of genetic testing called molecular cytogenetics, combining the ability to identify a specific gene or gene region (molecular) with direct visualisation of the cells and/or chromosomes under the microscope (cytogenetics).

Applications of FISH for constitutional abnormalities include detection of origin of marker chromsoomes, delineation of subtle rearrangements, assaying for deletions and duplications in cetain syndromes, and chromosomal rearrangements/deletions on the subtelomeric regions. Examples include: Williams-Beuren syndrome (7q11.2), DiGeorge/Velocardiofacial/CATCH 22 (22q11.2), Prader Willii and Angelman syndrome (15q11.2), Smith Magenis (17p11.2), Miller-Diecker/Lissencephaly (17p13), STS/Steroid sulfatase/Ichthyosis (Xp22.3), Kallman (Xp22.3), XIST for markers to determine presence of X inactivation gene in Turner Xq13, Y probes for sex reversal or other sex chromosome abnormalities (e.g. Turner with marker), and Charcot-Marie-Tooth disease.

What are the F.I.S.H Study options?

• Amniotic Fluid (5 probes 18, 21, 13, X, Y)
• Amniotic Fluid culture + F.I.S.H (5 probes)
• Chromosome 21/13 only or (X,Y,18)
• Chromosome 21
• Chromosome 16
• Chromosome X & Y

What is Microdeletion Syndrome?

A syndrome caused by a chromosomal deletion spanning several genes that is too small to be detected under the microscope using conventional cytogenetic methods. Depending on the size of the deletion, other techniques, such as FISH or other methods of DNA analysis can sometimes be employed to identify the deletion

What are the Microdeletion Syndrome options?

• Williams Syndrome
• Retinoblastoma
• Prader Willli's Syndrome
• Miller Decker/Lis gene
• Smith-Magenis
• Di George Syndrome-Tuple 1 probe
• Di George Syndrome-N25 probe

What is Cytogenetic test for Leukemia?

Cytogenetic test for leukemia looks at the chromosomes in individual cells. It uses a sample taken from a blood draw or a bone marrow or lymph node biopsy. The sample's chromosomes are microscopically examined for abnormalities that indicate damage to the cells' DNA.

What are the Cytogenetic test options for Leukemia?

• Bcr/Abl dual probe (CML)
• Translocation 8/ 21 probe (AML)
• Transloc. 15 / 17 probe (Ac. P.L)
• Breast cancer Her 2 gene amplification
• Small cell cancer of Lung - EGFR mutation
• Translocation 8/14 (Burkitts, others)

What are the DNA options?

• Achondroplasia
• Albinism-OCA 1 Tyrosinase gene sequencing/ Albinism-OCA 2 gene-Common deletion
• Alkaptonuria-linkage studies/ Prenatal Diagnosis-linkage
• Alpha 1 Anti Typsin (Z, S & M Mutation)
• Alpha thalassemia-deletions
• Aneuploidy screening (21, 18, 13, X, Y, chm)
• Angelman Syndrome (methylation test)
• Apert Syndrome
• Apo E Genotyping
• Ataxia Telangiectasia-carrier screening by linkage
• Ataxia Telangiectasia-PND by linkage
• Canavan Disease- Asparto asylase (ASPA) gene sequencing
• Charcot Marie Tooth disease 1/ HNPP (Del/Dupl. PMP gene)
• CMV-Cytomegalovirus-PCR
• Congenital Adrenal Hyperplasia-Common deletion
• Congenital Adrenal Hyperplasia- 5 mutations
• Congenital Adrenal Hyperplasia-deletions by dosage test
• Congenital Adrenal Hyperplasia-Prenatal diagnosis-linkage
• Congenital Adrenal Hyperplasia-Cyp 21 gene sequencing
• Craniosynostosis ( non specific) C749-FGFR 3
• Crigler Najjar Syn.- UGT1A1 gene sequencing
• Cruozon disease: FGFR 2 mutation (Ser 354 Cys)
• Cystic Fibrosis- Diagnosis (Delta 508 mutation)
• Cystic Fibrosis- 254 Mutations + Poly T
• Cystic Megalencephaly- MLC1 gene sequencing
• Cystic Megalencephaly- Prenatal Diagnosis CVS
• Deafness Connexin 26 gene-sequencing
• DMD deletion testing - 18 exons
• DMD 79 exons- deletion/duplication test
• DMD-Dosage studies in females
• DMD - Prenatal diagnosis + maternal cell contamination
• Dystonia (DYT 1 gene- common deletion)
• Ectodermal dysplasia X- linked –PND by linkage +MCC
• Ectodermal dysplasia X- linked, gene sequencing
• Epidermolysis bullosa dystrophia (PND- by linkage)
• Factor V Leiden
• Familial hypercholesterolemia (linkage, Prenatal)
• FGFR 3 gene sequencing (Ach, Hypochond, Thanatophoric dw)
• Folate Polymorphism 3' 5 MTHFR ( 677C>T, 1298 A>C)
• Fragile X Screen- PCR based
• Fragile XA- methylation test
• Friedreich Ataxia
• G-6-PD one mutation
• Galatosemia gene sequencing (GALT)
• Gaucher's disease (4 common mutations)
• Gilbert's disease (UGT1A1 Promoter polymorphism)
• Glycogen storage 1a gene sequencing
• Hallorverden-Spantz disease (PND by linkage)
• Hypochondroplasia (Sequencing)
• Hemochromatosis (2 mutations in HFE gene)
• Hemophilia A/B, Carrier test
• Hemophilia A/B, (Prenatal diagnosis)
• Herpes Virus infection (PCR)
• Hunter Syndrome - deletions
• Huntington disease
• Hypochondroplasia-common mutation C1620A in FGFR3
• Jak 2 mutation
• Krabbes disease- common deletion
• Leb Hered Optic Atrophy- 3 mutations
• Lowe Syndrome - linkage studies/ family
• Lowe Syndrome - Prenatal diagnosis-linkage
• Maternal Cell Contamination
• Marfan Syndrome-linkage studies
• Marfan Syndrome - Prenatal diagnosis-linkage studies/ family
• MCAD mutation (Medium chain acyl-coA dehyd)
• McArdle disease (R49 X mutation, Sequencing)
• Merosin deficiency-linkage/ PND
• Metaphyseal Dysplasia-COL 10A gene sequencing
• Mitochondrial/ LEIGHS or NARP-3 mutations
• Mitochondrial 1/ MELAS + MERRF-5 mutations
• Mitochondrial package (110, 111)
• Mitochondrial genome- deletion/duplication
• Mytotonic dystrophy- type 1-19q 13.3
• Mytotonic dystrophy- type 2- 3q 21
• NCL -infantile (2 mutation)
• NCL -infantile (2 mutation)
• NCL –Juvenile (Batten Dis) deletion
• Neuroblastomatosis (linkage, PND)
• Parkinson disease (Gly 19 ser mutation, by sequencing)
• Parvo virus-PCR
• Pelizaeus Merzbacher deletion/duplication
• Polycystic Kidney dis (Aut. Rec. ARPKD) PND by linkage
• Porphyria- Acute intermittent Common Mutation
• Porphyria- Sequencing of Porphobilinogen gene
• Prader Willi Syndrome-methylation test
• Prothrombin gene polymorphism (G20210A)
• Restrictive Dermopathy (Specific mutation by sequencing)
• Retinoblastoma- deletion/duplication
• Retinoblastoma (Prenatal diagnosis by linkage)
• Retinoblastoma gene sequencing
• Rett Syndrome MECP2 deletion/ duplication
• Rett Syndrome MECP2 -Sequencing
• Rh typing - (Rh+ or Rh-)
• Rh typing on fetal DNA in maternal blood
• Rubella (PCR)
• Russel Silver Syndrome (UP Disomy)
• Spinal Muscular atrophy, diagnosis
• Spinal Muscular atrophy-PND
• SMA Carrier Screening for deletion
• Spinal Muscular atrophy- SMN 1 gene sequencing
• Spino- Cerebellar ataxia -One type
• Spino- Cerebellar ataxia -Two type
• Spino- Cerebellar ataxia -package (1,2,3,6,7,8,12, 17 DRPLA)
• Spinal bulbar muscular atrophy (SBMA) CAG repeats
• Spondyloepiphyseal dysplasia X-linked gene sequencing
• Sry+Amxy gene study (Y chromosome)
• Subtelomeic deletions & duplications
• Thalassemia-beta (Confirmation of known mutation)
• Thalassemia-beta mutation study ( 5 common mutation)
• Thalassemia-beta globin gene sequencing
• Thalassemia-Prenatal diagnosis
• Thalassemia-Prenatal diagnosis-Repeat at GRH
• Thanotrophic dwarfism (common mutation)
• Thanotrophic dwarfism sequencing
• Thrombophilia Profile- 3 genes- MTHFR, Factor v Leiden,Prothrombin • Toxoplasmosis (PCR)
• Waardenburg Syndrome Pax 3 gene sequencing
• Waardenburg Shah syn- EDN3 gene-3 80A>G
• Wilson linkage presymptomatic
• Wilson diseases-PND by linkage
• Wilson diseases-ATP7B gene sequencing
• UGT1A1 * 28 Genotyping
• X-linked ichthyosis (Deletion in STS gene)
• XMN Polymorphism Gr gene (thalassemia child)
• Y-Chromosome deletions (10)

• AB
• AB+DR - Additional person (beyond 2 persons)
• AB+DR - One person
• AB+DR - Two persons
• B27
• DQ Alpha - Recurrent abortions
• DQ Beta - Recurrent abortions
• DQ Alpha & beta - Recurrent abortions
• DR2-Narcolepsy, M.S. Goodpasture syndrome
• DQ2/DQ8 Celiac disease High risk genotype
• DR3- , Addison disease, Derm Nerpc HLA-B5, Behcet's disease
• HLA- Y STR Polymorphism (for two)




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