1. Clinical Cytogenetics
In the Name of GOD
Clinical Cytogenetics
M.Dianatpour MLD, PhD

3. Definition
Cytogenetics is the study of chromosomes, their structure and their inheritance.
Clinical cytogenetics is the study of chromosomes, their structure and their inheritance, as applied to the practice of medical genetics.

4. Chromosome abnormalities
Microscopically visible changes in the number or structure of chromosomes, could account for a number of clinical conditions that are referred to as chromosome disorders.

5. Chromosome disorders
Chromosome disorders form a major category of genetic disease.
They account for a large proportion of all reproductive abnormalities, congenital malformations, and mental retardation and play an important role in the pathogenesis of malignant disease.

6. Chromosome disorders
Chromosome disorders are collectively more common than all the mendelian single-gene disorders together.
Cytogenetic disorders are present in nearly 1% of live births, in about 2% of pregnancies in women older than 35 years who undergo prenatal diagnosis, and in fully half of all spontaneous first-trimester abortions.

7. Karyotyping
Cells for karyotyping must be capable of growth and rapid division in cell culture medium.
The most accessible cells are WBC

8. karyotyping
Cell Culture
Harvesting
Banding
Analysis

9. Chromosome classification
Human chromosomes are often classified by the position of the centromere into three types:
metacentric central centromere
submetacentric off-center centromere
Acrocentric the centromere near oneend.
A potential fourth type of chromosome, telocentric, with the centromere at one end and only a singl arm, does not occur in the normal human karyotype but it is occasionally observed in chromosome rear rangements and is a common type in some other species.

10. Chromosome staining G banding Q banding (quinacrine mustard) R banding
High Resolution banding(prometaphase banding)
Fragile site

14. Indications for Chromosome Analysis
1- Problems of early growth and development.
Failure to thrive,
Developmental delay,
Dysmorphic faces,
Multiple malformations,
Short stature,
Ambiguous genitalia,
Mental retardation

15. Indications for Chromosome Analysis
2. Stillbirth and neonatal death.
The incidence of chromosome abnormalities is much higher among still- births (up to approximately 10%) than among live births (about 0.7%). It is also elevated among infants who die in the neonatal period (about 10%).
Chromosome analysis should be performed for all still- births and neonatal deaths.

16. Indications for Chromosome Analysis
3. Fertility problems. Chromosome studies are indicated for women presenting with amenorrhea and for couples with a history of infertility or recurrent miscarriage. A chromosome abnormality is seen in one or the other parent in a significant proportion (3%to 6%) of cases in which there is infertility or two or more miscarriages.

17. 4. Family history.
A known or suspected chromosome abnormality in a first-degree relative is an indication for chromosome analysis under some circumstances.

18. 5. Neoplasia
Virtually all cancers are associated with one or more chromosome abnormalities .

19. 6. Pregnancy in a woman of advanced age.
There is an increased risk of chromosome abnormality in fetuses conceived by women older than about 35 years. Fetal chromosome analysis should be offered as a routine part of prenatal care in such pregnancies.

20. Other cells for karyotyping
Fibroblast (cultured from skin biopsy)
Bone marrow
Fetal cells
Amniotic fluid
CVS (chorionic villus sampling)

21. Molecular karyotyping
FISH (Fluorescent insitu Hybridization)
CGH (Comparative Genome Hybridization)
Array CGH
QF-PCR (Quantitative Fluorescent PCR)
MLPA (Multiplex Ligation Probe Amplification)

22. FISH
DNA probes specific for individual chromosomes, chromosomal regions, or genes can be used to identify particular chromosomal rearrangements or to rapidly diagnose the existence of an abnormal chromosome number in clinical material

23. Gene-specific or locus-specific probes can be used to detect the presence, absence, or location of a particular gene, both in metaphase chromosomes and in interphase cells.
specific chromosomal loci including centromeres, telomeres, and regions of heterochromatin.
Whole chromosome painting

26. CGH

28. Array CGH

30. CHROMOSOME ABNORMALITIES

31. Chromosome abnormalities
Abnormalities of chromosomes may be either numerical or structural and
May involve one or more autosomes, sex chromosomes, or both simultaneously.

32. Neumerical (Heteroploidy)
Aneuploidy: < or > 2n, For example 47,45, 48,…
Polyploidy: Triploidt or tetraploidy

33. Triploid (3n) and tetraploid (4n), are occasionally observed in clinical material. Both triploidy and tetraploidy have been seen in fetuses, and although triploid infants can be liveborn, they do not survive long.

34. Triploidy is observed in 1% to 3% of recognized conceptions, and among those that survive to the end of the first trimester, most result from :
Fertilization by two sperm (dispermy)
Failure of one of the meiotic divisions, resulting in a diploid egg or sperm,

35. Tetraploids are always 92,XXXX or 92,XXYY;
Tetraploidy results from failure of completion of an early cleavage division of the zygote.

36. Aneuploidy
Aneuploidy is the most common and clinically significant type of human chromosome disorder, occurring in at least 5% of all clinically recognized pregnancies.

37. Most aneuploid patients have either trisomy or, less often, monosomy
Either trisomy or monosomy can have severe phenotypic consequences.
The most common type of trisomy in liveborn infants is trisomy 21 (karyotype 47,XX or XY,+21), Other trisomies observed in liveborns include trisomy 18 and trisomy 13.

38. It is notable that these autosomes(13, 18, and 21) are the three with the lowest number of genes located on them

39. Monosomy
Monosomy for an entire chromosome is almost always lethal; an important exception is monosomy for the X chromosome (Turner syndrome)

40. Although the causes of aneuploidy are not well understood, it is known that the most common chromosomal mechanism is meiotic nondisjunction.
The failure of a pair of chromosomes to disjoin properly during one of the two meiotic divisions, usually during meiosis I

42. Structural Chromosome Abnormalities
Structural rearrangements result from chromosom breakage, followed by reconstitution in an abnormal combination.
Rearrangements are less common than aneuploidy; overall, structural abnormalities are present in about 1 in 375 newborns.

43. Structural rearrangements:
Balanced, if the chromosome set has the normal complement of chromosomal material
unbalanced, if there is additional or missing material

44. Unbalanced Rearrangements
In unbalanced rearrangements, the phenotype is likely to be abnormal because of deletion, duplication, or (in some cases) both.
Duplication of part of a chromosome leads to partial trisomy;
deletion leads to partial monosomy.

45. Deletion

47. Deletions
Deletions involve loss of a chromosome segment, resulting in chromosome imbalance.
A deletion may occur at the end of a chromosom (terminal) or along a chromosome arm (interstitial)
Cytogenetically visible autosomal deletions have an incidence of approximately 1 in live births.
Smaller, submicroscopic deletions detected by microarray or FISH

48. Duplications
Duplications, like deletions, can originate by unequal crossing over or by abnormal segregation from meiosis in a carrier of a translocation or inversion.
Duplication appears to be less harmful than deletion.

49. isochromosome
Isochromosomes is a chromosome in which one arm is missing and the other duplicated in a mirror-image fashion. A person with 46 chromosomes carrying an isochromosome, therefore, has a single copy of the genetic material of one arm (partial monosomy) and three copies of the genetic material of the other arm (partial trisomy).

50. Balanced Rearrangements
Chromosomal rearrangements do not usually have a phenotypic effect if they are balanced because all the chromosomal material is present

51. Carriers of balanced translocations are likely to produce a high frequency of unbalanced gametes and therefore have an increased risk of having abnormal offspring range from 1% to as high as 20%.
There is also a possibility that one of the chromosome breaks will disrupt a gene, leading to mutation. This is a well-documented cause of X-linked diseases in female

52. Inversions
An inversion occurs when a single chromosome undergoes two breaks and is reconstituted with the segment between the breaks inverted. Inversions are of two types:
paracentric (not including the centromere), in which both breaks occur in one arm
pericentric (including the centromere), in which there is a break in each arm.
An inversion does not usually cause an abnormal
phenotype in carriers because it is a balanced rear- rangement. Its medical significance is for the progeny;

54. Translocations Translocation involves the exchange
of chromosome segments between two, usually nonhomologous, chromosomes. There are two main types:
Reciprocal
Robertsonian.

56. Mosaicism
When a person has a chromosome abnormality, the abnormality is usually present in all of his or her cells.
Sometimes, two or more different chromosome complements are present in an individual; this situation is called mosaicism. Mosaicism may be either

59. Genomic Imprinting
Differences in gene expression between the allele inherited from the mother and the allele inherited from the father are the result of genomic imprinting.
For some disorders, the expression of the disease phenotype depends on whether the mutant allele or abnormal chromosome has been inherited from the father or from the mother.

60. Imprinting is a normal process caused by alterations in
chromatin that occur in the germline of one parent, but not the other, at characteristic locations in the genome.
These alterations include the covalent modification of
DNA, such as methylation of cytosine to form 5-methyl-cytosine, or the modification or substitution in chromatin of specific histone types, which can influence gene expression within a chromosomal region.

62. Prader-Willi and Angelman Syndromes
Perhaps the best-studied examples of the role of genomic
imprinting in human disease are Prader-Willi syndrome and Angelman syndrome.
Prader- Willi syndrom a relatively common dysmorphic syndrome characterized by obesity, excessive and indiscriminate eating habits, small hands and feet, short stature, hypogonadism, and mental retardation
In approximately 70% of cases of the syndrome, there is a cytogenetic deletion involving the proximal long arm of chromosome 15 (15qll-q13), occurring only on the chromosome 15 inherited from the patient's father.

63. Angelman syndrome
Characterized by unusual facial appearance, short stature, severe mental retardation, spasticity, and seizures, there is a deletion of approximately the same chromosomal region but now on the chromosome 15 inherited from the mother.
Patients with Angelman syndrome, have genetic information in 15qll-q13 derived only from their fathers.
This unusual circumstance demonstrates strikingly that the parental origin of genetic material (in this case, on chromosome 15) can have a profound effect on the clinical expression of a defect.

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