1. Chromosomes Dr Pupak Derakhshandeh, PhD
Ass Prof Medical Science of Tehran University

2. What are chromosomes?
Chromosomes are the structures that hold our genes
Genes are the individual instructions that tell our bodies how to develop and function
They govern our physical and medical characteristics, such as hair color, blood type and susceptability to disease.
Each chromosome has a p and q arm; p is the shorter arm and q is the longer arm.
The arms are separated by a pinched region known as the centromere

4. How many chromosomes do humans have?
The typical number of chromosomes in a human cell is 46 - two pairs of 22 + XX/XY
Holding an estimated 30,000 to 35,000 genes.
One set of 23 chromosomes is inherited from the biological mother (from the egg), and the other set is inherited from the biological father (from the sperm).

5. study of the chromosomes
with a microscope , then Stainning
The chromosomes look like strings with light and dark "bands"
A picture, or chromosome map, of all 46 chromosomes is called a karyotype
The karyotype : identify chromosome abnormalities: that are evident in either the structure or the number of chromosomes.

6. Study of the chromosomes
The first 22 pairs of chromosomes are called "autosomes"
Final pair is called the "sex chromosomes."
The sex chromosomes an individual has determines that person's gender; females have two X chromosomes (XX), and males have an X and a Y chromosome (XY)

8. Karyotype 46), Xy)

10. How Chromosome Abnormalities Happen?
Meiosis
Mitosis
Maternal Age
Environment

11. Meiosis

12. Meiosis

14. Chromosome abnormalities
Abnormality of chromosome number or structure:
Numerical Abnormalities
Structural Abnormalities

15. Numerical Abnormalities
When an individual is missing either a chromosome from a pair (monosomy) or has more than two chromosomes of a pair (trisomy).
An example: Down Syndrome, also known as Trisomy 21 (an individual with Down Syndrome has three copies of chromosome 21, rather than two).
Turner Syndrome is an example of monosomy the individual is born with only one sex chromosome, an X.
Kleinfelter Syndrome is an example of trisomy the individual is born with three sex chromosome, XXY.

16. Trisomy 18, 47 Ch.

17. Trisomy 18, 47 Ch. incidence of about 1 in 3,000
There is a 3:1 preponderance of females to males
Thirty percent of affected newborns die within the first month
50% by two months
and 90% by one year.
severe mental retardation
microcephaly
overlapping fingers, and rocker bottom feet
Neurologically they are hypertonic
Other common malformations include congenital heart, kidney, .... abnormalities.

18. Trisomy 18, 47 Ch.

20. Trisomy 13 (XX/XY, 47 Ch) has an incidence of 1 in 5,000
Forty-four percent of affected newborns succumb in the first month of life
and 69% by six months
Only 18% of the babies born with trisomy 13 survive the first year
microcephaly
microophthalmia (small eyes)
cleft lip or cleft palate
polydactyly (extra fingers)
congenital heart defects
urogenital defects
brain malformations
severe mental retardation.

21. Turner Syndrome ( 45, X)
45, X

22. Turner Syndrome (45, X)

23. Turner syndrome Only females One X chromosome
Or has two X chromosomes but one is damaged
Short stature
Delayed growth of the skeleton
Sometimes heart abnormalities
Usually infertile due to ovarian failure
Diagnosis is by blood test (karyotype)
1 out of every 2,500 female live births worldwide
Short neck with a webbed appearance

24. Kleinefelter
XXY

25. Kleinefelter/47XXY

26. Klinefelter syndrome (47, XXY)
In boys and men
47 chromosomes with XXY sex chromosomes
XXY is one of the most common chromosomal abnormalities
1 in 500 male births
the most common genetic cause of male infertility
Often : undiagnosed : variation in clinical presentation
Small testes , insufficient production of testosterone , and infertility

27. Klinefelter syndrome (47, XXY)
Breast enlargement, lack of facial and body hair, a rounded body type , to be overweight , and be taller than their fathers and brothers
Learning and/or behavioral problems
Testosterone replacement corrects the symptoms of androgen deficiency

28. Fragile X Syndrome
1 in 3,600 males and 1 in 4,000 to 6,000 females with the full mutation worldwide
It is estimated that 1 in 250 females and 1 in 700 males are carriers of the premutation.
It is second only to Down Syndrome as a cause of mental retardation
Fragile X syndrome appears in children of all ethnic, racial and socio-economic backgrounds

29. Fragile X Syndrome
most common inherited form of familial mental retardation
(CGG)n trinucleotide expansion in the FMR1 gene leading to the typical Martin-Bell phenotype
Clinical features vary depending on age and seX
Expansion of a (CCG)n repeat in the FMR2 gene corresponds to the FRAXE fragile site which lies distal to FRAXA and is also associated with mental retardation, but it is less frequent and lacks a consistent phenotype

30. Fragile X Syndrome

31. Fragile X Syndrome

32. Down Syndrome (Trisomy 21( Trisomy 13 & 18

33. Down Syndrome (Trisomy 21(

34. Down Syndrome (Trisomy 21(

35. Down syndrom) Trisomy 21, 46)
critical region:
A region on the long (q) arm of chromosome 21
Down syndrome causes mental retardation, a characteristic facial appearance, and multiple malformations
Associated with a major risk for heart malformations a small but still significant risk of acute leukemia .
3 copies of chromosome number 21

36. incidence of 1 in 660 and is by far the most common chromosomal abnormality
Slight flattening of the face
A low bridge of the nose (lower than the usually flat nasal bridge of the normal newborn)
An epicanthal fold (a fold of skin over top of the inner corner of the eye, which can also be seen less frequently in normal babies)
A ring of tiny harmless white spots around the iris
mental retardation

37. Down Syndrome

38. Down Syndrome: Prenatal Risk
The risk of trisomy 21 is directly related to maternal age
Patients who will be 35 years or older on their due date should be offered chorionic villus sampling or second-trimester amniocentesis

39. The use of ultrasound to estimate gestational age improves the sensitivity and specificity of maternal serum screening. (Am Fam Physician 2000;62:825-32,837-8.)

40. Etiology and Clinical Manifestations
Trisomy 21 is present in 95 percent of persons with Down syndrome.
Mosaicism, a mixture of normal diploid and trisomy 21 cells, occurs in 2 percent.

41. Etiology and Clinical Manifestations
The remaining 3 percent have a Robertsonian translocation in which all or part of an extra chromosome 21 is fused with another chromosome.

42. Robertsonian translocation
The reciprocal transfer of the long arms of two of the acrocentric chromosomes: 13, 14, 15, 21 or 22
On rare occasions, other non-acrocentric chromosomes undergo Robertsonian translocation

43. Robertsonian translocation
a reciprocal transfer of the whole long or short arms close to the centromere
A relatively common Robertsonian translocation is between chromosome 14 and chromosome 21
In meiosis, a trivalent is formed.

44. Frequency of Dysmorphic Signs in Neonates with Trisomy 21
Dysmorphic sign Frequency (%)
Flat facial profile
Poor Moro reflex
Hypotonia
Hyperflexibility of large joints
Loose skin on back of neck
Slanted palpebral fissures 80

45. Frequency of Dysmorphic Signs in Neonates with Trisomy 21
Dysmorphic sign Frequency (%)
Dysmorphic pelvis on radiograph 70
Small round ears
Hypoplasia of small finger 60

46. Persons with Down syndrome usually have mild to moderate mental retardation
School-aged children with Down syndrome often have difficulty with language, communication
Adults with Down syndrome have a high prevalence of early Alzheimer's disease

47. Adult Down Syndrome

48. Incidence of Some Associated Medical Complications in Persons with Down Syndrome Disorder Incidence (%)
Mental retardation >95
Growth retardation >95
Early Alzheimer's disease %
by age 60
Congenital heart defects
(atrioventricular canal defect,
ventricular septal defect, atrial septal
defect

49. Disorder Incidence (%)
Hearing loss to 75
Ophthalmic disorders (congenital cataracts,
glaucoma(
Epilepsy to 10
Gastrointestinal malformations (duodenal atresia,
Hirschsprung disease) 5
Hypothyroidism
Leukemia

50. Disorder Incidence (%)
Increased susceptibility to
infection (pneumonia, otitis media, sinusitis, pharyngitis( 1-6
Infertility >99% in men
anovulation in % of women

51. Estimated risk of Down syndrome according to maternal age. . .
                                                                                                                             
FIGURE 1. Estimated risk of Down syndrome according to maternal age. Data from reference 8.
                                                                                                                             
FIGURE 1. Estimated risk of Down syndrome according to maternal age. Data from reference 8.
                                                                                                                             
FIGURE 1. Estimated risk of Down syndrome according to maternal age. Data from reference 8.
Estimated risk of Down syndrome according to maternal age
Maternal Serum Screening
Maternal Serum Screening
Maternal Serum Screening

52. The risk of having a child with Down syndrome
1/1,300 for a 25-year-old woman;
at age 35, the risk increases to 1/365
At age 45, the risk of a having a child with Down syndrome increases to 1/30

53. Maternal Serum Screening
If all pregnant women 35 years or older chose to have amniocentesis
about 30 percent of trisomy 21 pregnancies would be detected
Women younger than 35 years give birth to about 70 percent of infants with Down syndrome

54. The risk of having a child with Down syndrome
Maternal serum screening (multiple-marker screening) can allow the detection of trisomy 21 pregnancies in women in this younger age group.

55. Maternal Serum Screening "triple test" or "triple screen" "Multiples of the Median (MoM)"
Alpha-fetoprotein (AFP)
unconjugated estriol
human chorionic gonadotropin (hCG)

56. "Multiples of the Median (MoM)"
AFP is produced in the yolk sac and fetal liver.
Unconjugated estriol and hCG are produced by the placenta.
The maternal serum levels of each of these proteins and of steroid hormones vary with the gestational age of the pregnancy.

57. "Multiples of the Median (MoM)"
With trisomy 21, second-trimester maternal serum levels of AFP and unconjugated estriol are about 25 percent lower than normal levels
maternal serum hCG is approximately two times higher than the normal hCG level

58. Maternal Serum Screening "triple test" or "triple screen"
The triple test can detect approximately 60 percent of the pregnancies affected by trisomy 21, with a false-positive rate of about 5 percent.

59. Recurrence Risk and Family History
If a patient has had a trisomy 21 pregnancy in the past, the risk of recurrence in a subsequent pregnancy increases to approximately 1-3
percent above the baseline risk determined by maternal age

60. Diagnosis of a chromosome-21 translocation in the fetus or newborn is an indication for karyotype analysis of both parents
If both parents have normal karyotypes, the recurrence risk is 1 to 3 percent

61. Ultrasonographic Findings Associated with Fetal Down Syndrome
Chorionic villus sampling
10 to 12 weeks 0.5 to 1.5 %
Early amniocentesis
12 to 15 weeks 1.0 to 2.0 %
Second-trimester amniocentesis
15 to 20 weeks 0.5 to 1.0 %

62. a woman having amniocentesis

63. Counseling Aspects
Women who will be 35 years or older on their due date should be offered chorionic villus sampling or second-trimester amniocentesis.
Women younger than 35 years should be offered maternal serum screening at 15 to 18 weeks' gestation.

64. Ultrasound
During the first trimester of the majority of pregnancies, it is possible to measure the size of the fluid area at the back of the fetus’s neck, known as the nuchal translucency or NT The increasing size of the NT indicates a greater risk of the fetus having Down’s syndrome.

65. Ultrasound

66. Fluorescent In Situ Hybridisation techniques

67. female fetus with trisomy-21
chromosomes 18 (aqua), X (green), and Y (red).
chromosomes 13 (green), and 21 (red)

68. Quantitative fluorescent polymerase chain reaction
2:1 ratio (Down's Syndrome)
1:1 ratio (normal fetus)

69. Chromosome abnormalities
Abnormality of chromosome number or structure:
Numerical Abnormalities
Structural Abnormalities

70. Structural Abnormalities
Deletions: A portion of the chromosome is missing or deleted (>5 Mb).
Paraderwilli Syndrome (Ch 15)
Angleman Syndrome (Ch 15)
Imprinting effect

71. Deletion refers to the loss of a segment of a chromosome
DELETIONS
Deletion refers to the loss of a segment of a chromosome
This can be terminal (close to the end of the chromosome on the long arm or the short arm)
or it can be interstitial (within)
ig.DGS II

72. DELETIONS

73. Structural Abnormalities
Duplications: A portion of the chromosome is duplicated, resulting in extra genetic material.
Oncogenes (c-onc, c-fos, c-myc)

74. DUPLICATIONS
refers to an extra chromosomal segment within the same homologous chromosome or an extra chromosomal segment on another nonhomologous chromosome.
Again, the clinical findings are highly variable depending upon the chromosomal segments involved.
Gene expantion:
in Huntington Disease/ Fragile X, ….

75. DUPLICATIONS

76. Structural Abnormalities
Translocations: When a portion of one chromosome is transferred to another chromosome.

77. 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.

78. TRANSLOCATIONS

79. Balanced reciprocal translocation

81. Robertsonian translocation
The reciprocal transfer of the long arms of two of the acrocentric chromosomes: 13, 14, 15, 21 or 22
On rare occasions, other non-acrocentric chromosomes undergo Robertsonian translocation
a reciprocal transfer of the whole long or short arms close to the centromere
A relatively common Robertsonian translocation is between chromosome 14 and chromosome 21
In meiosis, a trivalent is formed.

82. Robertsonian translocation

85. Structural Abnormalities
Inversions: A portion of the chromosome has broken off, turned upside down and reattached, therefore the genetic material is inverted.
eg Ch9 inv in Iran

86. involve only one chromosome
Inversions
involve only one chromosome
the intervening segment is rejoined in an inverted or opposite manner.
Since there is no loss nor gain of chromosomal material, inversion carriers are normal
Paracentric: does not include the centromere
pericentric:inverted segment contains the centromere
In meiosis, the normal chromosome and the inverted chromosome will form a loop to allow pairing of specific DNA sequences
that occur within the inversion loop result in gametes with both deletions and duplications
inversion carriers have a relatively low risk of having abnormal offspring.

87. Inversions

89. 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.

90. Ring

91. Oncology Chronic Myelogenous Leukemia (CML)
a clonal expansion of transformed hematopoietic progenitor cells:
Myeloid
Monocytic
Erythroid
Megakaryocytic
lymphoid lineages

92. Hematology Bone marrow

93. Chronic myelogenous leukemia (CML)
15% to 20% of leukemias in adults incidence of 1 to 2 cases per 100,000 population

94. Chronic myelogenous leukemia
occurs more frequently in males than in females (ratio of 1.3 to 1)
Incidence: increases with age
the median age at presentation is between 45 and 55 years
Up to 30% of patients with CML are 60 years or older
which is an important consideration for the selection of therapeutic strategies
stem-cell transplantation
treatment with interferon-alfa (Intron A, Roferon-A)

96. The Philadelphia Chromosome
a reciprocal translocation between the long arms of chromosome 9 and chromosome 22
the large segment of the c-abl gene from chromosome 9q34
to the part of the bcr gene on chromosome 22q11 in a head-to-tail fashion
creating a hybrid bcr-abl gene that is transcribed into a chimeric bcr-abl mRNA

99. Role of the bcr-abl Fusion Gene in CML Pathogenesis
Ch 9: c-abl gene :a proto-oncogene
Encodes: a nonreceptor tyrosine kinase
with a molecular mass of 145 kd (p145c-abl)
It is localized in both cytoplasm and nucleus
It consists of 11 exons
230 kilobases (kb)

100. Role of the bcr-abl Fusion Gene in CML Pathogenesis
c-abl gene : Exon 1 has two alternative forms
1a and 1b
In most cases, the breakpoint :
within the segment between exons 1a and 1b
creating a bcr-abl fusion mRNA of 8.5 kb
The fusion mRNAs are translated into a 210-kd chimeric protein called p210bcr-abl

101. Detection of bcr-abl Cytogenetic analysis
Ph chromosome in 90% of patients with CML
Such analysis is tedious and time-consuming
allows the examination of only 20 to 25 metaphases per bone marrow sample
misses the 5% of patients who are Ph-negative but bcr-abl-positive

102. Molecular tools
important for detecting the molecular abnormalities associated with Ph
for monitoring the course of disease during treatment
These include polymerase chain reaction (PCR)

103. RT-PCR Quantitative reverse transcriptase–polymerase chain reaction
following patients with CML after stem-cell transplantation
Its use for monitoring patients receiving interferon-alpha

104. FISH Fluorescence in situ hybridization
allows for the analysis of metaphase
and nondividing interphase cells
Results of FISH studies are easily quantifiable

105. fluorescence in situ hybridization (FISH)

106. fluorescence in situ hybridization (FISH)

107. FISH
Bcr
Abl
Abl-Bcr

108. Abl-Bcr