1. Clinical Cytogenetics: The Chromosomal Basis of Human Disease
Chapter 6
Clinical Cytogenetics:
The Chromosomal Basis of Human Disease

2. Karyotypic analysis collecting and culturing tissues
metaphase arresting by spindle poisons (eg. colchicine)
placing the cell sediment and rupturing the cell membranes with a hypotonic saline solution
staining and photographing

3. Examples of Karyotypic analysis
A banded karyogram of a normal male. The banded metaphase chromosomes are arranged from largest to smallest.

4. Chromosome Classification
Metacentric, submetacentric, and acrocentric chromosomes. Note the stalks and satellites present on the short arms of the acrocentric chromosomes.

5. A banding pattern of a G-banded karyotype
300 bands are represented in this ideogram. The short and long arms of the chromosomes are designated, and the segments are numbered according to the standard nomenclature adopted at the Paris conference in In this illustration, both sister chromatids are shown for each chromosome.

6. Standard Nomenclature for Chromosome Karyotypes

7. Chromosome banding techniques
Q-banding (Quinacrine banding)
G-banding (Giemsa-banding): 300 bands
R-banding (Reverse banding)
C-banding: constitutive heterochromatin
NOR (nucleolar organizing region) staining: satellites and stalks of acrocentric chromosomes
high resolution banding
during prophase or prometaphase
up to 800 bands

8. Q-banding/G-bainding

9. G-banding/R-banding t(8;21)(q22;q22)
G- banding (left); R- banding (right)

10. C-banding/High resolution banding

11. Fluorescent in situ hybridization (FISH)

12. Examples of FISH analysis
A metaphase cell positive for the bcr/abl rearrangement using FISH. The chromosomes can be seen in blue. The chromosome that is labeled with green and red spots (up left) is the one where the wrong rearrangement is present
Interphase cells positive for a chromosomal t(9;22) rearrangement

13. Examples of FISH analysis
The thinner arrows point to a centromere-hybridizing probe for chromosome 17, and the thicker arrowpoints to a probe that hybridizes to 17p. The latter probe reveals only one spot in this individual, who has a deletion of 17p, producing the Smith-Magenis syndrome.(Courtesy of Dr. Arthur Brothman, University of Utah Health Sciences Center.) B, Face of an infant girl with Smith-Magenis syndrome. Note the broad forehead and relatively flat face. (Courtesy of Dr. Marilyn C. Jones, Children's Hospital, San Diego.)

14. Spectral Karyotyping (SKY)
SKY analysis of a variant CML case

15. Spectral Karyotyping (SKY)
The power of spectral karyotyping is demonstrated by the identification of a rearrangement between chromosomes 2 and 22. Note that a portion of chromosome 2 (purple) has exchanged places with a portion of chromosome 22 (yellow). (Courtesy of Dr. Art Brothman, University of Utah Health Sciences Center.)

16. The comparative genomic hybridization (CGH) technique
 A, Red-labeled test DNA (from a tumor sample) and green-labeled reference DNA (from normal cells) are both denatured and hybridized to normal chromosomes. The ratio of green to red signal on the hybridized chromosomes indicates the location of duplications (red signal) or deletions (green signal) in the tumor chromosomes. B, Array CGH: Test and normal DNA are hybridized to probes embedded in a microarray. Duplications are indicated by hybridization of more red-labeled DNA to a probe containing a DNA sequence that is complementary to the duplicated region. Conversely, hybridization of only green-labeled DNA (reference DNA) indicates a deletion of the corresponding region. C, In a patient with DiGeorge sequence, a CGH test was performed in which the patient's DNA was labeled green and the control DNA was labeled red. The figure demonstrates a lack of green signal and excess red signal, signifying a deletion of chromosome 22q11.

17. Abnormalities of Chromosome number
Polyploidy
triploidy (69 chromosomes): lethal
tetraploidy (92 chromosomes): lethal

18. Abnormalities of Chromosome number
Autosomal Aneuploid
Sex Chromosome Aneuploidy

19. Nondisjunction of Sister Chromatids

20. Down syndrome Cause Symptoms
trisomy of chromosome 21 by nondisjuction or translocation (maternal age effect)
DYRK gene (a kinase), APP gene (amyloid β precursor protein)
Symptoms
1/800 live births
abnormal features
Malformation: atresia of esophagus, duodenum or anus, structural heart defects, hearing loss, hypothyroidism, eye abnormalities
respiratory infection, leukemia
mental retardation
sterile

21. Edwards syndrome Cause Symptoms
trisomy 18 (47, XX, +18) by nondisjunction or translocation
1/6,000 live births
spontaneous abortion (over 95%)
Symptoms
abnormal characteristic features
congenital heart defects (VSD), Omphalocele, diaphregmatic hernia, spina bifida

22. Patau syndrome Cause Symptons
Trisomy 13 (47, XY, +13) by nondisjunction or translocation
1/10,000 live births
spontaneous abortion (over 95%)
maternal age effect
Symptons
abnormal characteristic feature (serious)
oral-facial clefts, microphthalmia, postaxial polydactyly
defects in CNS, heart, and kidney
cutis aplasia

23. Maternal Age Effect Hypotheses
older women less likely to spontaneously abort
older women increase in nondisjucional occation
other internal and external factors

24. Turner Syndrome (45, X) characteristic phenotypes
short stature
sexual infantilism, ovarian dysgenesis, infertile
malformation: congenital heart defects, structural kidney defects
mentally normal
1/2,500-1/5,000 female births
chromosome abnormality
50% 45, X
30-40% mosaics (45, X/46, XX;  45, X/46, XY)
10-20% deletion of the short arm
Related genes
SHOX gene (a transcription factor) involved in short stature
a genomic imprinting effect

25. Klinefelter Syndrome (47, XXY)
characteristic phenotypes
1/1,000 male births
tall
small and firm testes, atrophy of seminiferous tubules → sterile
gynecomastia
subaverage intelligence
Cause
50% maternal (maternal age effect), 15% mosaicism
50% spontaneous abortion
Treatment
testosterone treatment → improvement
48, XXXY/ 49, XXXXY: more severe phenotype

26. Trisomy X (47, XXX) 1/1,000 female births characteristic phenotypes
rare physical abnormality
sometimes sterility, mild mental retardation
Cause
nondisjunction in the mother
48, XXXX/ 49, XXXXX: more severe phenotype
Yahoo/ raregeneticdisorders

27. XYY syndrome 1/1,000 male births taller, minor behavioral disorders
subaverage IQ
maternal age effect

28. Chromosomal Abnormality and Pregnancy Loss
frequency of chromosomal abnormality
1/3 of pregnancies: lost after implantation
lost before implantation: unknown
10-15% conception: chromosomally abnormal
95% chromosomally abnormal conception: miscarriage
structural abnormality of chromosomes
oocytes: 20-25% aneuploidy, 1% structural abnormalities
sperm cells: 3-4% aneuploidy, 5% structural abnormalities
FISH analysis
0.15% disomy for each autosome
0.26% disomy for sex chromosome

29. Prevalence of Chromosomal Abnormalities among Newborns

30. Scientific Basis of Genetic Diseases
Mutation : base change
Deletion : loss of a chromosome segment
Duplication : extra copies of a chromosome segment
Translocation : movement of a segment of one chromosome to another chromosome
Inversion : a reversal in the order of a chromosome segment

31. Chromosome Lining-up
Spermatogenesis and oogenesis in animal cells.

32. Translocations nonhomologous interchanges of chromosomes
Reciprocal Translocation
mutual exchanges of chromosomes
eg. 46,XX,t(3p;6p)
offsprings of carriers: normal or carrier (partial trisomy)

33. Translocations Robertsonian Translocation
The short arms of two nonhomologous chromosomes are lost and    the long arms fuse. →  a single chromosome
chromosome 13-15, 21, 22
eg. 45,XY,der(14;21)(q10;q10)
offsprings
alternate segregation → normal or balanced tranlocation
adjacent segregation → translocation, Down syndrome,  monosomy 21, trisomy 14, monosomy 14

34. Robertsonian Translocation

35. Deletion by a chromosome break and loss of chromosomes
termial deletion/interstitial deletion
Cri-du-chat syndrome
46,XY, del(5p): deletion of the short arm
1/50,000
mental retardation, small head
Wolf-Hirschhorn syndrome
46,XX, del(4p)

36. Microdeletion syndrome
identified by a series of RFLP and FISH techniques
Prader-Willi syndrome
  paternal chromosome deletion of 15q11-q13 (70%)
WAGR syndrome (Wilms tumor, Aniridia, Genitourinary abnormalities, mental Retardation)
a microdeletion of 11p13
contiguous gene syndrome
Williams syndrome
mental retardation, supravalvular aortic stenosis (SVAS), etc
a microdeletion of 7q11.2, deletion of elastin gene → SVAS
LIMK1 (a brain-expressed kinase)  
multiple repeats  → unequal crossing-over  → microdeletions or duplications

37. Microdeletion Syndromes
Deletion 1p36

38. Unequal Crossing-over of Chromosomes

39. Uniparental Isodisomy
Prader-Willi syndrome, Angelman syndrome, CF, Beckwith-Wiedemann syndrome
two copies of a chromosome from one parent
Causes
trisomy at conception → disomy (by chromosome lost)
two copies + no copy at conception → disomy (by nondisjunction)

40. Ring chromosomes deletion at both tips → a ring chromosome
46,X, r(X) → resulting in monosomy

41. Inversion
by the reinsertion in inverted order (balanced rearrangement)
normal phenotypes of inversion carriers (1/1,000) → abnormality in offspring  
pericentric/paracentric inversion
→ resulting in deletion or duplication
eg. 5% of offsprings of 46,XX, inv(8) → recombinant 8 syndrome

42. Inversion
A pericentric inversion in chromosome 8 causes the formation of a loop during the alignment of homologous chromosomes in meiosis. Crossing over in this loop can produce duplications or deletions of chromosome material in the resulting gamete. The offspring in the lower right received one of the recombinant 8 chromosomes from this parent.

43. Isochromosomes by division of chromosomes along the axis perpendicular
lethal
Examples
isochromosome Xq, 46,X,i(Xq) → feature of Turner syndrome
isochromosome 18q: Edwards syndrome

44. Philadelphia syndrome
chronic myelogenous leukemia (CML)
Translocation
der(9): most of chromosome 22 onto 9q
der(22): small distal 9q onto chromosome 22
altering the gene product of ABL (a protooncogene) → increasing tyrosine kinase activity → malignancy in hematopoietic cells

45. Burkitt lymphoma a childhood jaw tumor
by reciprocal translocation between chromosome 8 and 14
MYC from 8q24 to 14q32
expression of abnormal MYC (uncontroled activation of MYC)    → malignancies
Burkitt's lymphoma, standard
H&E stain

46. Specific Cytogenetic Changes in Leukemias and Solid Tumors

47. Chromosome Instability Syndromes
atacia-telangiectasia : by mutations of ATM gene located on chromosome 11q22-23
Bloom syndrome : by mutations in the BLM gene, a member of the DNA helicase family (15q26.1)
Fanconi anemia : >13 genes in various autosomal chromosomes (FANCA – FANCN)
Xeroderma pigmentosum (Type A – G, V)
a higher cancer risk
results of faulty DNA replications or repair