L16 - chromosome abnormalities Flashcards
1
Q
How many subunits do histones have?
A
8 - octamer
2
Q
Describe the structure of chromatin
A
Hanging loops of DNA on a protein scaffold
3
Q
From which type of chromatin are genes expressed?
A
active chromatin
4
Q
Which types of epigenetic modifications change chromatin from its inactive to active form?
A
DNA demethylation
Histone acetlyation etc…
5
Q
Which types of epigenetic modifications change chromatin from its active to inactive form?
A
DNA methylation
Histone deacetylation etc…
6
Q
In epigenetic modification changes are not made to which part of DNA structure?
A
The DNA sequence is not changed
7
Q
Chromosomes from which part of the cell cycle are used for chromosome analysis?
A
Metaphase chromosomes
8
Q
How are metaphase chromosomes gathered for chromosome analysis?
A
Living cell in vitro are cultured, chromosomes are gathered at metaphase by using spindle inhibitors.
9
Q
What is the name of the process whereby chromosomes are systematically sorted?
A
Karyotyping
10
Q
Different sample types of chromosomes yield chromosomes of different lengths. What different specimen types of chromosomes are used?
A
Bone marrow Blood (T-lymphocytes) Amniotic fluid CVS (chorionic villus sample) Solid tissue
11
Q
What does karyotyping involve?
A
Metaphase chromosomes are:
- Stained
- Paired up and grouped together
- Described using standard nomenclature (ISCN 2013)
12
Q
What type of chromosome contains no eukaryotic genes of consequence on its p arm?
A
acrocentric chromosomes
13
Q
Which type of chromosome has p and q arms of similar length?
A
metacentric chromosomes
14
Q
Chromosomes are grouped from A to G by which properties?
A
Size and shape
15
Q
Which chromosome was incorrectly number and is actually larger than its previous numbered chromosome?
A
chromosome 22 (is bigger than 21)
16
Q
G-banding is a staining method which uses trypsin to digest proteins which are then stained with Romanowski dye to produce light and dark bands. Why do the dark G (+ve) bands stain darker than the light G (-ve) bands?
A
Dark G(+ve) bands are AT rich (gene poor) Light G(-ve) bands are GC rich (gene rich)
17
Q
How many pairs of chromosomes do humans have?
A
23 pairs
18
Q
How many pairs of autosomes do humans have?
A
22 pairs
19
Q
How many pairs of sex chromosomes do humans have?
A
1 pair
20
Q
Describe a normal male karyotype using the correct nomenclature
A
46,XY, Normal male karyotype
21
Q
What are chromosome ideograms?
A
Standard diagrams which show the standard banding patterns for each chromosome.
Dark and light bands are numbered according to international convention: ISCN 2014 - therefore international results and research are comparable
22
Q
What is automated karyotyping?
A
Slides scanned automatically
Images taken
Digital karyotypes from images
Analyse chr’s paired up on screen
23
Q
How are chromosomes described in a chromosome report?
A
Using ISCN 2013 standard format: 1. Chromosome number 2. Sex complement 3. Structural changes Separated by commas and NO SPACES!
24
Q
Why do cytogenetic analysis?
A
- Accurate diagnosis/ prognosis of clinical poblems
- Better clinical management
- Assess future reproductive risks
- Prenatal diagnosis
25
What are the types of constitutional abnormalities (abnormality present from birth) that cause people to be referred for cytogenetic analysis?
1. Prenatal diagnosis
2. Birth defects
3. Abnormal sexual development
4. Infertility
5. Recurrent fetal loss
26
What are the type of acquired abnormalities that cause people to be referred for cytogenetic analysis?
1. Leukaemias
2. Solid tumours
3. Specific translocations/ abnormalities can give prognostic information (advise on best treatment)
27
What is sampled in chorionic villus sampling?
Chorionic villus (placental tissue)
28
What is sample in amniocentesis?
Amniotic fluid containing fetal tissues from the amniotic sac
29
When can CVS be done?
11-12 weeks gestation
30
When can amniocentesis be done?
15 weeks onwards
31
What is the risk of miscarriage with CVS?
1.2% miscarriage risk
32
What is the risk of miscarriage with amniocentesis?
0.8% miscarriage risk
33
What does trisomy 21 cause?
Down syndrome
34
What is meant be aneuploidy?
Loss and gain of whole chromosomes
35
Why does aneuploidy arise?
Due to errors at cell division of meiosis
36
What are the three viable trisomies at birth?
Down Syndrome
Patau syndrome
Edwards syndrome
37
What trisomy causes Edwards syndrome?
Trisomy 18
38
What trisomy causes Patau syndrome?
Trisomy 13
39
Which is the only full monosomy syndrome to be viable?
Turner syndrome 45,X
40
Why is Turner syndrome the only viable monosomy?
X chromosome inactivation
41
What is polyploidy?
The gain of a whole haploid set of chromosomes e.g. 69,XXX
42
What is the most common form of polyploidy?
Polyspermy: fertilisation of an egg by more than one sperm
43
What type of polypoidy is accountable for 2-3% of all pregnancies and approximately 15% of all miscarriages (term deliveries die shortly after birth)?
triploidy
| Diploid triploid mosaicism is seen in livebirths
44
What can cause aneuploidy?
1. Non-disjunction at one of the meiotic cell divisions
| 2. Can occur during cell division -> mosaicism
45
What is meant by mosaicism?
Two cell populations present in an individual
46
What is anaphase lag?
When chromosomes are "left-behind" at cell division. The lagging chromosomes may be lost entirely in mitosis or meiosis
47
What are the causes of anaphase lag?
Defects in spindle function or attachment to chromosomes
48
What is the incidence of Down syndrome?
1 in 650-1000
49
What are individuals with Downs syndrome at higher risk of?
Leukaemia
| Early alzheimers
50
What are the signs and symptoms of Down Syndrome?
Hypotonia - decreased muscle tone
Characteristic facial features
Intellectual disability
Heart defects
51
What is the incidence of Edwards syndrome?
1 in 6000
52
What are the signs and symptoms of Edwards syndrome?
```
Small lower jaw
Prominent occiput (back of head)
Low-set ears
Rocker bottom feet
Overlapping fingers
```
53
Which sex is Edwards syndrome more common in?
Female predominance
54
What causes Edwards syndrome?
Maternal meiosis II error
55
What is the modal lifespan of a baby with Edwards syndrome?
5-15 days
56
When is Edwards syndrome normally diagnosed?
Prenatally- presents with abnormal scan
57
What are the signs and symptoms of Patau syndrome?
Multiple congenital abnormalities
Polydactyly
Holoprosencephaly (forebrain fails to split into 2 hemispheres) - present from single eye-> cleft lip
58
What is the incidence of Patau syndrome?
1 in 12000
59
What is the lifespan of a baby with Patau syndrome?
Majority die in neonatal period
60
What are the signs and symptoms of Turner syndrome?
```
Puffy feet
Redundant skin at back of neck (neck webbing)
Short stature
Heart defects
Mild learning difficulties
Infertility
```
61
Which sex is Turner syndrome most common in?
45,X - therefore only occurs in females
62
What causes phenotypic differences in the presentation of Turner syndrome?
The parental origin of X - majority of cases lack paternal X
63
What is X chromosome inactivation?
Only one X chromosome is ever active in a human cell. This occurs because females have 2 and males have 1, therefore it ensures that they have the same chromosome complement
64
Why is a single X chromosome a problem in Turner syndrome, since X chromosome inactivation occurs to make only a single chromosome active in a human cell anyway?
It affects pairing up of chromosomes at mitosis and meiosis. Although males have a single X chromosome the X and Y chromosomes have short regions in common called the pseudo-autosomal regions which can pair up.
65
Which gene is present in the pseudoautosomal region that is associated with the short stature seen in Turner syndrome?
SHOX gene
66
What is mosaicism?
Presence of 2 or more cell lines in an individual
67
What causes mosaicism?
Usually caused by MITOTIC non-dysjunction
68
Why is the degree of mosaicism in an individual so variable?
Degree of mosaicism depends on when the error occurred:
1. First post zygotic division -> looks like a meiotic event
2. Subsequent divisions -> 3 cell lines (monosomy cell line usually lost - unless X chromosome)
69
What is the meaning of uniparental disomy (UPD)?
Presence of homologous chromosomes from one parent
70
Why does UPD matter?
If the chromosomes is imprinted. Imprinted chromosomes show differential expression of specific genes depending on the parental origin of the chromosome,
71
Why does UPD for the same chromosome cause two different disease: Prader-Willi and Angelman syndrome?
Imprinted genes show differential expression depending on the parental origin of the chromosome.
Prader-Willi syndrome is caused by paternally inherited chromosomes.
Angelman syndrome is caused by maternally inherited chromosomes.
72
List the four "common" mechanisms to generate UPD
1. Trisomy rescue
2. Monosomy rescue
3. Gamete complementation
4. Mitotic error
Each require two separate abnormal events
73
Which is the most common mechanism to generate UPD?
Trisomy rescue
74
What happens in trisomy rescue?
2 abnormal events:
1. Meiotic error -> trisomy
2. Mitotic error-> disomy (1 in 3 chance leads to UPD)
75
How do you test for UPD?
Molecular genetic test using informative repetitive DNA markers on imprinted genes/ regions of interest, to see whether inheritance is bi-parental or not
76
List the cytogenic structural abnormalities you can get
```
Translocations - Robertsonian and Reciprocal
Inversions - paracentric and pericentric
Deletions - including microdeletions
Duplications
Insertions (into different chromosomes)
Rings
Marker chromosomes - small chromosome with centromere
Isochromosomes
```
77
What is a reciprocal translocation?
A two-break rearrangement that is usually unique to a family. Carriers produce balanced and unbalanced gametes
78
How do you assess umbalanced segregant outcomes?
1. Establish likely segregation - viable offspring an option?
2. Have the imbalances been reported before?
3. Quote risks if established
79
What is a Robertsonian translocation?
Two acrocentric chromosomes fused together
80
In phenotypically normal, balanced carriers of Robertsonian translocations - how many chromosomes do you see?
45 - only time you see a normal individual with 45 chromosomes
81
How does a Robertsonian translocation pair up during meiosis?
Forms a trivalent - not very stable
82
What are Robertsonian carriers at risk of during meisosis?
Anueploidy
83
Can homologous carriers of Robertsonian translocations have a normal pregnancy?
No - gametes always have a monosomy or trisomy
84
What does der(14;21) mean?
A robertsonian translocation between chromosome 14 and 21.
85
How do deletions arise?
Uneven pairing and recombination during meiosis
86
What is the difference between a terminal and an interstitial deletion?
Terminal deletion - affects ends
| Interstitial deletion - within arm
87
What is the effect of deletions on the phenotype?
Likely (but not always) accounts for phenotype
88
What is a microdeletion?
A deletion smaller than 100Kb
89
How can you detect a microdeletion?
Can't always see on G banding as its too small, need to use FISH technique to diagnose and confirm the specific region associated with the phenotype
90
What is FISH?
fluorescent in situ hybridisation
91
What is FISH used for?
To answer SPECIFIC questions. You need to know what you are looking for and therefore which probes to use for specific chromosomes or loci.
92
How is FISH done?
1. Denature chromosome and fluorescently labelled DNA probe to single strand
2. Reanneal - hybridisation
3. Wash to remove unbound probe
4. Visualise using a fluorescent microscope
93
What are locus/ gene specific FISH probes used for?
Microdeletion/ duplication syndromes that are too small to see on G banded chromosomes
94
What are centromere probes used for?
Identifying chromosome of origin, marker chromosomes and copy number analysis
95
What are whole chromosome paints used for?
To identify a chromosome in a rearrangement
96
What are the benefits of using FISH probes for common aneuploidies (13,18,21,X and Y) compared to full karyotypes?
Full karyotypes take up to 14 days as cells need to be cultured, whereas FISH probes can be used on uncultured cells and take 24-48hrs. They also have 99+ % accordance with full karyotype.
97
What different types of probes can be used in Leukaemia FISH and how do they work?
1. Fusion probes - detect translocations of genes involved
2. Breakapart probes - detect gene rearrangement
3. Locus specific probes - detect amplifications e.g. oncogenes, her2, c-myc
98
What are the benefits of microarray methodology?
Examines the whole genome at high resolution
99
What can microarrays detect and not detect?
They can detect copy number changes but can't detect balanced rearrangements or specific mutations which don't results in a copy number change
100
How are microarrays done?
1. Take an equal amount of patient DNA and reference DNA - each with attached green or red fluorescent marker - and mix.
2. Add to array slide spotted with oligonucleotides (60mers)
3. Hybridise for 48 hours
4. Wash slide
5. Scan
6. Input scan images to analysis software - detects ratio of green:red fluorescence and analyses relative copy numbers
101
Who is referred for aCGH?
1. Learning difficulties/developmental delay/multiple congenital abnormalites (15-20% abnormality rate)
2. Normal karyotype
3. Balanced de novo karyotype - is it really balanced?
4. Unbalanced karyotypes to assess gene content
102
What can array platforms detect?
copy number changes
| loss of heterozygosity (using SNP)
103
What are the advantages of aCGH?
1. Examines the entire genome at high resolution
2. Targeted against known genetic conditions and sub telomere regions
3. 1 array is equivalent to many thousands of FISH investigations and can be automated
4. Detailed information on genes in del/dup region
5. Better phenotype/ genotype correlation
104
What are the disadvantages of aCGH?
1. Arrays are more expensive than karyotyping
2. Will not detect balanced rearrangements - therefore not suitable for all referrals
3. Copy number variation - genuine abnormality?
4. Mosaicism may be missed
105
What will be future developments for prenatal testing?
1. Microarrays used instead of karyotyping for woman with an abnormal scan
2. Non-invasive prenatal testing (NIPT) - free fetal DNA in maternal plasma tested, enough there to capture from 9 weeks gestation
3. Digital PCR and next generation sequencing technology
