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Cytogenetics
Typical ‘chromosome spread’
Chromosomes
obtained from
actively-dividing
mitotic cells
Jo Sanders
Dept of Haematology,
Christchurch Hospital, New Zealand
Cytogenetics
• Study of chromosomes and their abnormalities
• Chromosomes are genetic structures of cells containing
DNA
• Each chromosome has a characteristic length and
banding pattern
• All cells contain 23 pairs of chromosomes (46 in total),
and each chromosome contains thousands of genes
• Specimens: Peripheral Blood, Bone Marrow, Tumour, Solid tissue
• The chromosomes are spread out, fixed and stained
to allow examination down the microscope
• Abnormalities are identified by changes in banding
patterns along the chromosome.
• A karyotype is made which shows the chromosomes
of an individual arranged in pairs and sorted
according to size
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Chromosome Labeling
Chromosome is
identified with a
number ranging
1-22,or X and Y
Each arm
divided into
sub-regions
and identified
by a number
Each sub-region
divided into
bands identified
with a number
Example • The first chromosome, long arm, second region of the
chromosome, the fourth band of that sub-region
A Karyotype
• Light microscope used to
view chromosomes in
metaphase of mitosis
• Chromosomes arranged into
homologous pairs based on
size and banding patterns
• The normal human
karyotype is made of 46
chromosomes:
• 22 pairs of autosomes,
numbered from 1 to 22 by
order of decreasing length
• 1 pair of gonosomes, or sex
chromosomes: XX in the
female, XY in the male.
1
6
13
19
2
7
3
8
14
9
15
20
4
10
11 12
16
21
5
17
22
18
X Y
Importance of Karyotypes
• Karyotypes show the
chromosomal makeup of
an individual. Knowing
the number of
chromosomes is
essential for identifying
chromosomal variations
that cause genetic
disorders or idenifiying
malignancies ie. APML,
CML
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Chromosome nomenclature
• Patterns, and the nomenclature for defining
positional mapping have been standardised to
allow cytogeneticists to communicate and archive
information for medical purposes
• Numbering begins from the centromere and
continues outward to the end of each arm.
Conventionally, the arms are divided into a
number of regions by means of easily recognisable
"land-mark" bands, and bands numbered
sequentially within each. Sub-bands are catered
for by using a decimal system
Chromosome structure
short arm = p (petite)
Centomere
Chromatid
long arm = q
Telomere
Anomalies
• Chromosomes are genetic material and therefore
carry the organisation of cell life and inherited
traits
• Cell life will be disturbed if regular segregation
fails this can occur during embryogenesis
(constitutional anomalies) or in cancer (acquired
anomalies).
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Constitutional anomalies
• All the tissues ("the whole patient") hold the same
anomaly. The chromosome error was already
present in the embryo.
• "Constitutional anomalies" thus refer to the
chromosome inborn syndromes, such as trisomy
21, Turner syndromes, and others.
Acquired anomalies
• Only one organ is involved, the other tissues of the
body are normal.
• The patient has a cancer of the affected organ.
"Acquired anomalies" thus refer to malignancies.
Mosaic anomalies
• When only some cells carry the anomaly whilst
others are normal ( or carry another anomaly)
• Very common in leukaemias and other cancers
subject to continuous chromosome change
• In ALL there may be a normal clone, one clone
with a specific change, and a third with additional
changes (46, XY / 46, XY, t(4;11) / 46, XY,
t(4;11), I(7q))
ALL
(46, XY / 46, XY, t(4;11) / 46, XY, t(4;11), I(7q))
t(4;11), I(7q))
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Variations in Chromosomal
Number
• Euploidy – the normal number and sets of
chromosomes
• Polyploidy – the presence of three or more
complete sets of chromosomes
• Aneuploidy – the presence of additional or
missing individual chromosomes
Types of Polyploidy
• Triploidy – three sets of chromosomes 23 x 3 = 69
• Tetraploidy – four sets of chromosomes 23 x 4 = 92
Types of Aneuploidy
• Monosomy – one less chromosome (23 x 2) – 1 = 45
• Trisomy – one additional chromosome (23 x 2) + 1 = 47
Structural anomalies
• Structural changes occur within the chromosomes
but may not necessarily be accompanied by any
numerical change.
– if there is not loss or gain of genetic material the
change is balanced
– if there is deletion and/or duplication of
chromosome segment(s) the change is unbalanced
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AML
Philadelphia Chromosome (Ph)
• CML is an acquired cytogenetic abnormality that is
characterised by the presence of the Philadelphia
Chromosome (Ph)
• The Ph chromosome is a result of an exchange of
material (translocation) between the long arms of
chromosomes 9 and 22 eg t(9;22)
• This translocation brings together the BCR gene on
chromosome 22 and the ABL gene on chromosome 9
• The resulting hybrid gene BCR/ABL causes
uncontrolled cell growth
The t(9;22) translocation
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FISH for BCR/ABL
• Fluorescent in situ hybridization (FISH) is a
molecular cytogenetics technique that uses a
fluorescent-labeled DNA probe to determine the
presence or absence of a particular segment of DNA
— the BCR-ABL gene in the case of CML
• FISH can detect one leukemic cell in 500 normal cells
CML
Deletion
• Loss of a segment of chromosome
• Invariably, but not always, results
in the loss of important genetic
material – and is sometimes known as ‘partial
monosomy’
• Recorded as del, followed by a bracket with the
number of the chromosome, and a second bracket
indicating the breakpoint(s) and the deleted region
(eg del(5)(q14q34))
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Reciprocal translocation
• A mutual exchange between terminal segments
from the arms of 2 chromosomes
• Recorded as t, followed by a bracket with the
numerals of the 2 chromosomes, and a second
bracket indicating the presumptive breakpoints
eg AML t(15:17)
Inversion
• Inversion occurs when a segment of chromosome
breaks, and rejoins within the chromosome
effectively inverts it
• Recorded as inv, followed by a bracket with the
number of the chromosome, and a second bracket
indicating the breakpoints, where these can be
determined (eg inv(9) (p11q13))
Isochromosome
• Loss of a complete arm, “replaced” by the
duplication of the other arm (equivalent to a
monosomy for one arm and a trisomy for the
other).
• Recorded as i, followed by a bracket with the
number of the chromosome and the arm (eg i(17q)
or i(17)(q10): duplication of the q arm and loss of
the p arm)
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Insertion
• A segment of chromosome is deleted
and transferred to a new position in
another chromosome, or rarely within
the same chromosome.
• Recorded as ins, followed by a bracket with the
number of the chromosome which receives the
segment preceding the number of the chromosome
which donates the segment eg ins(2)(p13q31q34) and
ins(5;2)(p12;q31q34): the segment q31q34 from a chromosome
2 is inserted respectively in p13 of this chromosome 2, and in
p12 of a chromosome 5.
Duplication
• Direct: a segment of chromosome is repeated,
once or several times, the duplicated segment
keeping the same orientation with respect to the
centromere
• Inverted: the duplicated segment takes the
opposite direction
• Recorded as dup, followed by a bracket with the
nos of the chromosome, and a second bracket
indicating the breakpoint(s) and the duplicated
region
If in doubt ask
• Cytogenetics lab
• Haematologist / Oncologist
• CIMBTR
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