Chromosome Abnormalities Flashcards
(260 cards)
1
Q
How is DNA packaged?
A
DNA wrapped around an octomer of histones
2
Q
What does a octomer of histones consist of?
A
2 molecules each of H2A, H2B, H3 and H4
3
Q
How many bp is in each octomer?
A
166
4
Q
What is the purpose of histone H1?
A
It stabilises
5
Q
How is higher order DNA structure established?
A
By hanging loops of DNA onto a protein scaffold to form chromatin
6
Q
When are gene expressed?
A
When they form active chromatin
7
Q
How can chromatin switch between active and inactive?
A
Epigenetic modification
8
Q
How is chromatin converted from active to inactive?
A
By DNA methylation and histone deacetylation
9
Q
How is chromatin converted form inactive to active?
A
DNA demethylation, histone acetylation
10
Q
Where are changes made in activation and inactivation of chromatin?
A
To DNA and histones, not actual DNA sequence
11
Q
What is being studies in chromosome analysis?
A
Metaphase chromosones
12
Q
What does the study of metaphase chromosomes require?
A
Living cells for in vitro growth
13
Q
What must be done to study metaphase chromosomes?
A
The cells must be cultured, accumulated at metaphase and harvested
14
Q
Why does analysis of metaphase chromosomes take a long time?
A
Because it must be done stepwise
15
Q
What are the steps in the analysis of metaphase chromosomes?
A
- Add spindle inhibitor
- Make hypotonic
- Add fixative
- Slides prepared and stained
- Visualised on light microscope
16
Q
Give an example of a spindle inhibitor
A
Colcemid
17
Q
What can be added to make the cell culture hypotonic?
A
Potassium chloride in varying concentrations
18
Q
What fixative can be used in metaphase chromosome analysis?
A
3:1 methanol:acetic acid
19
Q
What can the slides in metaphase chromosome analysis be stained with?
A
Giemsa stain
20
Q
How are the slides from metaphase chromosome analysis interpreted?
A
Count, go through systematically to check all pairs, and check banding pattern is the same for each pair
21
Q
What specimen types can be used for chromosome analysis?
A
- Bone marrow
- Blood (T-lymphocytes)
- Amniotic fluid
- CVS
- Solid tissue
22
Q
How are bone marrow and blood for chromosome analysis grown?
A
In suspension
23
Q
How long is bone marrow cultured for?
A
0-1 day
24
Q
What long is blood cultured for?
A
2-3 days
25
Where is amniotic fluid, CVS and solid tissue grown for use in chromosome analysis?
On substrate
26
How long is amniotic fluid, CVS and solid tissue cultured for?
7-21 days
27
What do different sample types yield?
Chromsomes of differing lengths
28
How does the process of chromosome analysis differ depending on the sample type?
It doesn’t
29
What is true of chromosome analysis of all sample types?
Defined quality scores required to meet
30
How can chromosomes be analyses?
Karyotyping
31
What is karyotyping?
Systematic sorting of chromosomes
32
How is karyotyping carried out?
Metaphase chromosomes stained, paired up and grouped together
33
How are chromosome abnormalities described?
Using standard nomenclature ISCN
34
What are chromosomes composed of?
2 arms
35
What are the 2 arms of the chromosome called?
#NAME?
36
What are the possible configurations of the chromosome arms?
- Metacentric- centromere in the centre, so p and q arms same length
- Submetacentric- centromere slightly more to one side, so p arm shorter than q arm
- Acrocentric- the centromere is the right at the end, so only the q arm is present
37
What does the p arm not contain in acrocentric chromosomes?
Euchromatic material, and therefore no genes of importance
38
What are chromosomes grouped based on?
Size and shape
39
What are the groups of chromosomes?
A → G
40
What groups are acocentric chromosomes?
D and G
41
What do groups D and G have on their p arms?
Satellites
42
Which of the chromosomes are not in size order?
22 is bigger than 21
43
What group is the X chromosome considered to be in?
C
44
What group is the Y chromosome considered to be in?
G
45
What methods of staining chromosomes are there?
- Solid staining
- G-banding
- C-banding
- Q-banding
- Replication
46
How is G-banding carried out?
#NAME?
47
What is produced from G-banding?
Dark and light bands
48
Why are the metaphases exposed to trypsin?
It digests proteins differentially
49
Give 2 examples of Romanawksi type dyes?
#NAME?
50
Which of the bands are gene rich in G banding?
The light G-ve bands
51
What are the dark G+ve bands in gene banding rich in?
AT
52
What are the light G-ve bands in gene banding rich in?
GC
53
What is shown in chromosome ideograms?
Standard banding pattern for each chromosome
54
How are the dark and light bands produced in chromosome ideograms numbered?
According to international convention ISCN
55
What does C-banding do?
Stains heterochromatin at centromeres, and 1, 9, 16 and Y q
56
When would the C-banding staining method be used?
If wanted to determine if change in chromosome is abnormality, or normal variations
57
What happens to normal chromosomes?
The chromosome lengths vary
58
What does Q-banding determine?
Y q variation
59
When would the replication staining method be used?
When testing for an active or inactive X in females
60
How can karyotyping be carried out faster?
Using automated or semi-automated systems
61
What happens in automated karyotyping?
The slides are scanned, images are taken, and digital karyotyping from images is carried out by cutting out the chromosomes and pairing them up on screen
62
What is the advantage of comparing chromosomes paired up on the screen?
Easier to compare chromosomes when lined up side by side
63
What is the problem with automated karyotyping?
It’s expensive and time consuming to create equipment
64
What is used to describe the karyotype in a chromosome report?
Standard ISCN format
65
How are chromosomes described using the standard ISCN format?
Chromosome number, sex complement and structural changes are given, separated by a comma
66
What is a chromosome report for a normal female?
46,XX
67
What is the chromosome report for a normal male?
46,XY
68
What is the chromosome report for a female with an extra chromosome 21?
47,XY,+21
69
What is the chromosome report for a male with a chromosome 7 inversion?
46,XY,inv(7)(p.11.2q11.3)
70
What happens in an inversion?
Segment between two break points is inverted
71
When are spaces found in the karyotype?
Never
72
What is the purpose of cytogenic analysis?
- Accurate diagnosis/prognosis of clinical problems
- Better clinical management
- Assess future reproductive risk
- Prenatal diagnosis
73
How can cytogenic analysis be involved in the accurate diagnosis/prognosis of clinical problems?
- Can identify the syndrome associated with an abnormality
- Accounts for the phenotype
- Accounts for pregnancy loss
74
Give an example of where cytogenic analysis can lead to better clinical management?
In the case of Klinefelter syndrome, where if detected before puberty, the person can lead a relatively normal life
75
What is Klinefelter syndrome?
When people carry 2 X chromosomes, as well as Y chromosome
76
When is the assessment of future of reproductive risk important?
When people already have an affected child
77
What future reproductive risk can be assessed using cytogenic analysis?
The risk of a live born abnormal child
78
What happens to the risk of having a Downs syndrome child after a previous Downs pregnancy?
It increases by 1%
79
Why is prenatal diagnosis important?
It provides information to clinicians and parents, who can then choose to terminate, or clinicians can plan for when the child is born
80
Why may a pregnant woman be referred?
- If the foetus displays constitutional abnormalities
- Infertility
- Recurrent fetal loss
81
What are constitutional abnormalities?
Abnormalities present from birth
82
Give 2 constitutional abnormalities
- Birth defects
| - Abnormal sexual development
83
What acquired abnormalities may be reason for referral for cytogenic analysis?
- Leukaemia's
| - Solid tumours
84
What kind of leukaemia's are there?
- Acute
- Chronic
- Myelodysplasia/myeloprolifierative disorders
85
What can specific translocation/abnormalities found in cancers give?
Prognostic information
86
How is Down syndrome screened for?
Maternal serum screening
87
How is maternal serum used to determine risk of Down syndrome?
Biochemical markers found in serum, as well as gestation and age are inserted into an algorithm, which can be used to determine chance
88
What happens if the chance of Down syndrome is found to be higher than 1 in 150 in a screening test?
An invasive test is offered
89
When is routine screening of foetuses performed?
First trimester
90
What happens in first trimester screening?
Test for biochemical markers and nuchal translucency on an ultrasound scan
91
What is happening as foetal scanning improves?
More abnormalities are found using ultrasound
92
Give 4 disorders that can be picked up on an abnormal ultrasound scan
- Cystic hygroma
- Cleft lip/plate
- Heart abnormality
- Limb abnormalities
93
What is a cystic hygroma?
A swelling at the back of the neck
94
What can be detected on prenatal DNA studies?
#NAME?
95
What chromosome abnormalities can be detected prenatally?
FH chromosome abnormaility
96
How are DNA studies carried out prenatally?
DNA is directly extracted from chorionic villus
97
Give 5 examples of birth defects
- Dysmorphism
- Congenital malformations
- Mental retardation
- Developmental delay
- Specific syndromes
98
What can result from developmental delay?
#NAME?
99
Give 3 specific syndromes that are birth defects
- Downs syndrome
- Williams syndrome
- DiGeorge syndrome
100
What is aneuploidy?
The loss or gain of whole chromosomes
101
What does aneuploidy result from?
Due to errors at cell division in meiosis
102
What are the two main types of aneuploidys?
- Trisomies
| - Monosomies
103
Give 3 examples of trisomies
- Down syndrome
- Patau syndrome
- Edwards syndrome
104
What is the only viable monosomy?
Turners syndrome
105
What happens in Turners syndrome?
X-inactivation
106
What is polyploidy?
Gain of a whole haploid set of chromosomes
107
What is the most common of polyploidy?
Polyspermy
108
What is polyspermy?
The fertilisation of an egg by more than one sperm
109
How many pregnancies does triplody occur in?
2-3% of pregnancies
110
What % of miscarriages are caused by triploidy?
~15%
111
What happens to triploidy deliveries?
They die shortly after birt h
112
How many pregnancies does tetraploidy occur in?
1-2%
113
Where are tetraploid cells often found?
At prenatal diagnosis
114
What is the tetraploidy finding at prenatal diagnosis often caused by?
A cultural artefact caused by the failure of cell membranes to divide
115
What is seen in live births where babies die shortly after?
Diploid/triploid mosaicism
116
What does aneuploidy originate from?
Non-disjunction at one of the meiotic cell divisions
117
What does non-disjunction at one of the meiotic cell divisions form?
Gametes with a missing chromosome, and an extra chromosome
118
What affects the viability of gametes with missing or added chromosomes?
Which chromosome is involved
119
When can non-disjunction occur, other than in meiosis?
During mitotic cell division
120
What is the result of non-disjunction in mitotic cell division?
Mosaicism
121
What is mosaicism?
Two cell populations within an individual
122
What is meiosis?
The method by which we go to 46 diploid to 23 haploid
123
How can non-disjunction in meiosis occur?
#NAME?
124
What normally happens when both chromosomes go into one cell in the first meiotic division?
Non-viable cell will be lost
125
What is the result when the cell is not lost when both chromosomes go into one cell in the first meiotic division?
2 gametes with 2 chromatids, and 2 with none
126
What is the result of both chromatids going into one cell at the second meiotic division?
Leaves one gamete with 2 chromatids, and one game with no chromatids
127
What can fertilisation of a gamete that has no or two chromatids with a normal gamete lead to?
Trisomy or monosomy
128
When may a pregnancy be viable despite the gametes being produced from meiosis where non-disjunction has occurred?
When the chromosome is 13, 18 or 21- the X must be involved
129
What happens in anaphase lag?
Chromosomes can be ‘left behind’ at cell division
130
What may cause anaphase lag?
Because of defects in spindle function or attachment to chromosomes
131
What can result from anaphase lag?
The lagging chromosome may be lost entirely in mitosis or meiosis
132
What is trisomy 21?
Down syndrome
133
What is the frequency of Downs syndrome?
1 in 650-1000
134
What is Down syndrome characterised by?
- Hypotonia
- Characteristic facial features
- Intellectual disability
- Heart defects
- Increased prevalence of leukaemia
- Increased prevalence of early Alzheimers
135
What is trisomy 18?
Edwards syndrome
136
What is the incidence of Edwards syndrome?
1 in 6000, with female predominance
137
What causes Edwards Syndrome?
Maternal meiosis 11 error
138
What is the medial lifespan of a Edwards Syndrome sufferer?
5-15 days
139
How are nearly all diagnoses of Edwards Syndrome made?
Prenatally
140
What are the symptoms of Edwards Syndrome?
- Small lower jaw
- Prominent occiput
- Low-set ears
- Rocker bottom ears
- Overlapping fingers
141
What is trisomy 13?
Patau syndrome
142
What is Patau syndrome?
Multiple congenital abnormalities, including polydactyl, and holoprosencephaly
143
What is the incidence of Patau Syndrome?
1 in 12,000
144
What is the chance of survival with Patau syndrome?
Majority die in neonatal period
145
What causes the majority of cases of Turner syndrome?
Absent paternal X
146
What do phenotypic differences in Turners syndrome depend on?
The parental origin of X
147
What are the symptoms of Turners syndrome?
- Short-stature
- Heart defects
- Mild learning defects
- Neck webbing
- Puffy feet
- Infertility
148
What is active in human cells?
Only one chromosome
149
What is the purpose of X inactivation?
Ensures that individuals have the same X chromosome complement that is active, as females have 2 X chromosomes, whereas males only have 1
150
What do X and Y chromosomes have in common?
Short regions at the tips of the long and short arms
151
What is at the short regions at the end of the P and Q arms of X and Y chromosomes?
Two pseudo-autosomal regions (PAR1 and PAR2)
152
What do PAR1 and PAR2 do?
Essential for pairing during mitosis
153
What will Turners syndrome patients be regarding the PARs?
They will be monosomic for the genes
154
What gene is found within PAR?
SHOX
155
What is the SHOX gene associated with?
Short stature
156
What is mosaicism?
Presence of 2 or more cell lines in an individual
157
What usually causes mosaicism?
Mitotic non-disjunction
158
Where is mosaicism found?
Either throughout the body, or tissue limited
159
What does the degree of mosaicism depend on?
When the error occured
160
What happens if the mitotic disjunction occurs in the first post zygotic division?
There is no mosaicism, and the disjunction looks like a meiotic event
161
How can mitotic non-disjunction lead to a non-mosaic karyotype?
In the first post-zygotic division, one cell gets 47,+N, and one gets 45,-N. The monosomy cell line is usually lost unless it involved X, as it is not viable, and the 47,+N then divides to produce 2 47,+21 gametes
162
What happens if the mitotic disjunction occurs in subsequent divisions?
There are 3 cell lines, of which the monosomy cell line is usually lost
The first 46,N cell divides into 2 46,N cells. If there is non-disjunction in one of those cell lines, the gametes are 27+N and 45,-N. The monosomy cell line is usually lost unless it involves the X chromosome
163
What is uniparental disomy (UPD)?
Presence of homologous chromosomes from one parent
164
What is isodisomy?
2 identical chromosomes from one parent
165
What is heterodisomy?
2 homolougous chromosomes from one parent
166
What is segmental UPD?
When only one part of the chromosome is involved
167
What is acquired UDP?
Solid tumours and leukemias
168
What do imprinted chromosomes show?
Differential expression of specific genes, depending on the parental origin of the chromosome
169
What is the effect of UDP is the chromosome involved is not imprinted?
It has no phenotypic efect
170
What chromosomes can UDP syndromes occur in?
6, 7, 11, 14, 15 and 16
171
Give 3 examples of UDP syndromes
- Prader-Willi (15)
- Russel-Silver (7)
- Beckwith-Wiedeman (11)
172
What are the 4 ‘common’ mechanisms to generate UDP?
- Trisomy rescue
- Monosomy rescue
- Gamete complementation
- Mitotic error
173
What do each UDP generation mechanisms require?
Two separate abnormal events
174
What is the most common mechanism of generating UDP?
Trisomy rescue
175
What happens in trisomy rescue?
If a disomic gamete from a meiotic error combines with a monosomic gamete, will get a trisomic conceptus. If then, during post-zygotic mitosis, a mitotic error occurs, there is a 1 in 3 chance of loosing the single chromosome from the monosomic gamete, leaving the 2 from the same gamete
176
What does trisomy rescue usually produce?
Heterodisomy
177
How can UDP be tested for?
Using molecular genetic testing, using information from repetitive DNA markers on imprinted genes/regions of interest
178
What does molecular genetic testing for UDP show?
Wether inheritance is bi-parental or not
179
What can be determined if a UDP test is confirmed?
It identifies the parental origin and allows the syndrome to be defined
180
What are the possible cytogenetic structural abnormalities?
- Translocations
- Inversions
- Deletions
- Duplications
- Insertions
- Rings
- Marker chromosomes
- Isochromosomes
181
What are the two types of translocations?
- Reciprocal
| - Robertsonian
182
What are the two types of inversions?
- Paracentric
| - Pericentric
183
What does the type of inversion that occurs depend on?
Wether the break point is within the same chromosome arm, or in both chromosome arms
184
What is generally true of marker chromosomes?
Generally quite small, and have a centromere that are not easily identifiable from banding pattern
185
What are isochromosomes?
Ones that are identical at both ends- mirror images
186
What are reciprocal translocations?
Two break rearrangements- there is a break in one chromosome, and a break in another, giving two segments of a chromosome that basically swap over
187
What are reciprocal translocation usually unique to?
A family
188
What is the exception to reciprocal translations being unique to families?
t(11;22)
189
What do carriers of reciprocal translations produce?
Balances and unbalanced gametes
190
What tends to happen if an individual carries a reciprocal translocation?
They are phenotypically normal
191
Why are reciprocal translocation carriers phenotypically normal?
All the chromosomal material is there, just in a different place
192
What is wether unbalanced offspring have abnormal phenotypes dependent?
Which regions are in trisomy, and which in monosomy
193
How can translocation imbalance be assessed?
Segregation analysis using a pachytene diagram
194
What are the 3 segregation types in reciprocal translocations?
- Alternate
- Adjacent 1- non homologous centromeres
- Adjacent 2- homologous centromere
195
What is the most common form of segregation that gives imbalance?
Adjacent 1- non homologous centromeres
196
What can be produced from adjacent 2?
3:1 disjunction and 4:0 disjunction, both of which are unbalanced
197
What does translocation form?
Quadrivalent
198
What is produced when segregation is alternate?
Either two normal chromosomes, or two derivative chromosomes
199
What needs to be done to assess unbalanced segregant outcomes?
- Establish likely segregation
- Check to see if imbalances have been reported before
- Quote risks if established
200
What causes Robertsonian translocations?
Two acrocentric chromosomes fusing together
201
Which are the acrocentric chromosomes?
13, 14, 15, 21 and 22
202
What kind of Robertsonian translocations can be produced?
Mono or dicentric
203
What is the most common Robertsonian translocation?
13;14
204
What is the chromosome count in balanced carriers of Robertsonian translocations?
45
205
Why is the chromosome count 45 in balanced carriers of Robertsonian translocations?
Because two chromosomes are fused together
206
What is formed at meiosis in Robertsonian translocations?
Trivalent
207
Are trivalents stable?
No
208
What is the risk with Robertsonian translocations?
Aneuploidy risk
209
Who is at higher risk from Robertsonian translocations?
Females
210
What are homologous carriers of Robertsonian translocations unable to do?
Have normal pregnancies
211
Why can homologous carriers of Robertsonian translocations have normal pregnancies?
Because they can only pass over the Robertsonian chromosome
212
What do deletions arise through?
Uneven pairing and recombination during meiosis
213
What are the two types of deletions in chromosomes?
#NAME?
214
Where does a terminal deletion affect?
The ends of the chromosome
215
Where does an interstitial deletion affect?
Within the arms of the chromosome
216
What is required to diagnose or confirm a microdeletion?
FISH technique
217
Why is the FISH technique required to diagnose or confirm microdeletions?
Because they can’t always be seen on G bandings, because the resolution of a G banded karyotype is around 5-10M (depending on what sample type you’re looking at), and some microdeletions are only around 100Kb in size
218
What must be done when reporting abnormal results of chromosome analyses?
- Give correct ISCN
- Describe abnormality in words and what it means
- Balanced or unbalanced
- Is there monosomy/trisomy for a region
- Relate to clinical problems
- Request parental/family samples if required
- Refer to clinical genetics
- Provide appropriate literature if available
219
What kind of technique is FISH?
Molecular cytogenetic
220
What does FISH allow?
The answering of specific questions
221
What is a requirement for FISH?
Need to know what we’re looking for
222
What is used in FISH?
Probes for specific chromosome or loci
223
How is FISH carried out?
- A DNA probe is flourescently labelled
- Target material is added to DNA probes, and heat to denature probe and chromosomes to single strand
- Hybridisation by reannealing at 37º c .
- Washing to remove unbound probe
- Visualisation under fluorescence microscope
224
What are the 4 types of probes used in FISH?
- Locus/gene specific probes
- Centromere probes
- Telomere probes
- Whole chromosome paints
225
What are locus/gene specific probes used for?
Detecting microdeletion/duplications syndromes that are too small to see on G-banded chromosomes
226
What size are centromere probes?
Large
227
What is the advantage of centromere probes being large?
Easy to see
228
What are centromere probes used for?
- To identify the chromosome of origin
- Visualise metaphase and interphase
- Copy number analysis
- Identifying derivative chromosomes and markers
229
What are whole chromosome paints used for?
To identify a chromosome in rearrangement
230
What is prenatal aneuploidy screening (PND) analysing?
Interphase
231
What can be used for PND?
Cultured cells or uncultured cells
232
How long are cells cultured in PND?
Up to 14 days
233
What does PND culturing cause?
Anxiety
234
What is used in uncultured cells in prenatal aneuploidy screening?
FISH probes for 13, 18, 21, X and Y
235
What are FISH probes for 13, 18, 21, X and Y used in prenatal aneuploidy screening?
Because these are common aneuploidies
236
How quickly can a result for prenatal aneuploidy screening be obtained?
- For those testing using FISH probes, 24-48 hours
| - A full karyotype in 14 days
237
What is the concordance rate of prenatal aneuploidy screening using the FISH probes compared with the full karyotype?
99+%
238
What does microarray examine?
The whole genome at high resolution
239
What can be looked for using microarray?
Copy number changes
240
What can’t be detected using microarray?
Balanced rearrangements or mutation
241
What does microarray compare?
Patient DNA to normal control DNA
242
What are the advantages of microarray technology?
High resolution
Lots of different genetic conditions can be looked at at once
Automated
Get detailed information about the genes
243
What are the disadvantages of microarray?
Cost compared to karyotype
Will not detect balanced rearrangements , copy number variation and what is abnormal
Mosaicism may be missed
244
What can cause problems with microarray technology?
Variation of uncertain significance
245
Why does variation of uncertain significance create a problem?
Because there could be a novel pathogenic call (not seen before), a novel call with no genes in that region or a novel call that doesn’t fit with the patient phenotype
246
What does non-invasive prenatal resting use?
Cell free foetal DNA found in the maternal plasma from 9 weeks gestation
247
What is the problem with non-invasive prenatal testing?
Technically challenging
| DNA quality deteriorates quickly
248
How is the problem of the quality of DNA deteriorating quickly in prenatal genetic testing overcome?
Using special tubes to stabilise sample
249
What techniques are used for non-invasive prenatal testing?
Digital PCR
| Next generation sequencing
250
What does NIPT reduce?
The need for invasive testing
251
What may invasive testing be needed?
Confirmation of abnormal NIPT
252
What aspect of NIPT has been approved?
NIPT testing for single gene disorders
253
What does next generation sequencing allow?
Fragmenting of genomic DNA
254
What is the advantage of fragmenting of genomic DNA?
So it can all be sequenced at the same time
255
What does next generation sequencing create?
A lot of data which needs to be protected and stored carefully
256
What is next generation sequencing suitable for?
Multiplexing with biological barcodes
257
What is used to conform NGS findings?
Sanger sequencing
258
What is the advantage of NGS sequencing?
It reduces the cost of testing individual genes by offering panels of gene testing
259
What is whole exome sequencing?
The targeted sequencing of al exons
260
What must be done in whole exome sequencing?
Identify de novo mutations in trio analysis
