CYTOGENETICS
Techniques Cytogenetic strategy
Anna Sowińska-Seidler, Phd
CYTOGENETICS
• Classical • Molecular - Karyotype analysis - Molecular probes - Banding techniques - FISH, aCGH
Elementary fibre
Chromatin fibre
Laemi loop
Chromatid
Metaphase chromosome Chromosome structure Chromosome types
Chromosome types in human:
Metacentric Submetacentric Akrocentric Human chromosome groups A 1-3 big metacentric chromosomes B 4-5 big submetacentric chromosomes C 6-12 and X medium submetacentric chromosomes D 13-15 big acrocentric chromosomes E 16-18 small submetacentric chromosomes F 19-20 small metacentric chromosomes G 21-22 and Y small acrocentric chromosomes
A B
C
D E
F G Aberrations autosomes sex chromosomes
Aberrations numerical structural Numerical abnormalities of chromosomes
Polyploidy Aneuploidy
Triploidy Tetraploidy Trisomy Monosomy 3n 4n 2n +1 2n - 1 Numerical chromosomal abnormalities
Polyploidy - Triploidy (69,XXX, XXY or XYY) 1-3% of all conceptions; amost never live born; do not survive Aneuploidy (autosomes) - Nullisomy (missing a pair of homologs) Pre-implantation lethal - Monosomy (one chromosome missing) Embryonic lethal - Trisomy (one extra chromosome) Usually lethal at embryonic or fetal stages, but trisomy 13 (Patau syndrome) and trisomy 18 (Edwards syndrome) could be live born and trisomy 21 (Down syndrome) Aneuploidy (sex chromosomes) - Additional sex chromosomes (47, XXX; 47, XXY; 47, XYY) present relatively minor problems, with normal lifespan - Lacking a sex chromosome 45, X = Turner syndrome, About 99% of cases abort spontaneously; survivors are of normal intelligence but infertile and show characteristic dismorphic features . 45, Y = not viable Triploidy 69,XXX 69,XXY 69,XYY Trisomy 47,XX+13, 47,XX+18, 47,XX+21 47,XY+13, 47,XY+18, 47,XY+21
12 47,XXY; 47,XXX; 47,XYY I 47,XXY= Klinefelter Syndrome
II 47,XXX = Triple X Syndrome
III 47,XYY = Jacob Syndrome Monosomy 45,X
14 Structural aberration
Balanced Unbalanced
Translocation Deletion
Inversion Duplication
Ring chromosome
Isochromosome
Marker chromosome 15 Translocations
Transfer of chromosome material between chromosomes
Types of translocation: Reciprocal Robertsonian (centric fusion) Insertional Balanced reciprocal translocation
Chromosomal material distal to breaks in two chromosomes is exchanged
Robertsonian translocation (centric fussion)
• involves two acrocentric chromosomes • two breaks at or near the centromere (short arms site) •cross fusion of the products •the decrease of the total number of chromosomes • it is balanced aberration because the loss of short arms do not cause the loss of active genes Inversion Inversion arise from two chromosomal breaks with inversion through 180° of the segment between breaks. Inversion is a balanced aberration
Paracentric inversion – both breaks are in a single arm, than the centromere is not included Pericentric inversion – breaks are on either side of the centromere and so the centromere is included Deletion Duplication A Loss of any part of chromosome Additional copy of a segment of a chromosome is present
Deletions and duplications are unbalanced aberrations – loss or gain of the genetic material
Ring chromosome
- unbalanced aberration
A ring chromosome arises from breaks in both arms of a chromosome: the terminal ends are lost and the two proximal sticky ends unite to form a ring
Isochromosome
Abnormal chromosome that has a deletion of one arm with the duplication of the other. It may arise from transverse division of the centromere Unbalanced aberration Addition
• Additional material of unknown origin attached to a chromosome region or band Marker chromosomes
• Additional small chromosomes of unknown origin, identified in 1/2500 pregnancies
• In 90% of cases they come from a short arms of acrocentric chromosomes (often involving chr 15)
When is chromosome analysis indicated? Problems noted during early growth/development
Stillbirths and neonatal deaths
Fertility problems
Pregnancy in women at age 35 or older
Family History
Dysmorphic features strongly suggestive for chromosomal anomalies Karyotype analysis
Various dividing cells can be used
• The most common: peripheral blood lymphocytes
• Bone marrow cells, skin fibroblasts
• Amniocytes or trophoblast cells – in prenatal diagnosis or in spontaneous abortions
• 2-5 ml (1 ml in newborns) of peripheral blood is taken
• Special heparin containing tubes are needed
• Blood should be stored at 4ºC or 37 ºC (depending on lab procedures)
• Blood samples can be send by post
PHA Colcemid Preparation
Blood Mitogen
Cells
Culture Centrifugation
Culture Cell medium Pellet
KCl- hypotonic Centrifugation
Pipeting Centrifugation
Cell Slide preparation Fixation pellet
Staining Cover Drying slide
Slide Analysis Giemsa solution
Karyotyping Microscope
Chromosome documentation
Karyogram preparation Metaphase, chromosome spread Methods
Cytogenetic Methods
Banding techniques
- G-banding with Giemsa stain - Q (fluorochrome: quinacrine) - C-banding (centromeres) - AgNor (satelites of acrocentric chromosomes) - R-banding (reverse to G-bandning)
Banding patterns allow individual chromosomes to be identified
Provide location of genes
Information about structural aberrations
34 G - banding
Chromosomes are subjected to controlled digestion with trypsin before staining with Giemsa, a DNA-binding chemical dye.
G-positive – dark bands contain less genes, AT-rich G-negative – pale G - bands bands contain more genes, GC-rich Q - banding Methods
Fluorescent dye (ex. Quinacrine, DAPI) binds to AT- rich DNA
Q - bands C - banding
Is thought to demonstrate constitutive heterochromatin, mainly at the centromeres.
C - bands Ag-NOR - banding
Is thought to demonstrate satellites of acrocentric chromosomes
Ag-NOR - banding R - banding
R-banding (Reverse) to G- banding pattern
R - bands Human ideogram Chromosome 4 (with accompanying ideogram) is shown at increasing levels of resolution: 400, 550 and 850 bands per haploid set General principles of karyotype description
1) Total number of chromosomes 2) Sex chromosome constitution 3) Abnormality designation (if occurs)
• Examples: 46,XY 46,XX – normal karyotype 47,XX,+21 - trisomy of 21 46,XX,del(15)(q11.2-q13)
Down syndrome 47,XY,+21 Patau syndrome 47,XX,+13 Edwards syndrome 47,XX,+18 Turner syndrome 45,X
X Klinefelter syndrome 47,XXY
21 22 20 19
Y X X
Chromosomal mosaicism
mos 47,XX,+21[25]/46,XX[25] Molecular cytogenetics
FISH – fluorescence in situ hybridization Slide with chromosomes Slide with chromosomes Molecular probe
Denaturation of chromosomal Double stranded DNA DNA
Probe denaturation, probe labelling
In situ hybridization
or
Indirect probe detection Direct probe detection
Microscopic analysis of the fluorescent signal on the slide FISH in medical genetics
• Diagnostics of submicroscopic chromosomal aberrations • Identification of the complex chromosomal aberrations • Identification of the additional genetic material in genome • Identification of marker chromosomes • Rapid prenatal diagnostics FISH
Probes used in FISH:
• Painting probes (wcp. – ang. whole chromosome paint/one arm painting probes)
• alfa-satelite (centromeric, telomeric)
• specific (unique) hybridizing to special locus or special sequence on chromosome FISH
Target cells used in FISH:
• fibroblasts • lymphocytes • Bone marrow cells • Amniotic fluid cells • Trophoblast cells • Paraffin embedded tissues FISH – most commonly used fluorohromes:
• FITC (Fluorescein isothiocyanate) • TRITC (rhodamine) • Texas Red • Aqua • DAPI • PJ (propidium iodide) • Cy3 • Cy5 Painting probes Chromoprobe multiprobe system
WCP 20 WCP 15 WCP 2
Interphase FISH
SKY – spectral karyotyping aCGH (Array based Comparative Genomic Hybridization)
Advantages: Whole genome screening High resolution Detects unbalanced aberrations Does not require metaphase chromosomes
Limitations: Cannot detect balanced aberration Interpetation
Case: Deletion of locus TAR in chromosome 1 (1q21.1) as the cause of TAR Syndrome (thrombocytopenia with absent radius) Resolution of cytogenetic techniques
46,XX,t(4;7)(p15.2;q11.2) GTG: 5 – 10 Mbp aCGH: 5 - 10 kbp
M. Connor, M. Ferguson-Smith, Podstawy genetyki medycznej, PZWL 1998 FISH: 40 - 250 kbp