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GENOMICS Structural chromosomal abnormalities Flashcards

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1
Q

What is translocational structural abnormality?

A

Exchange of two segments between non-homologous chromosomes

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2
Q

What are the 2 types of translocation

A

-Reciprocal
-Robertsonian

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3
Q

What is reciprocal translocation?

A

In a reciprocal translocation, two different chromosomes have exchanged segments with each other.

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4
Q

What is robertsonian translocation?

A

In a Robertsonian translocation, an entire chromosome attaches to another at the centromere.

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5
Q

What is translocation due to inappropriate non homologous end joining?

A

Before:
-No net gain or loss of genetic material
-Involves any chromosome and any size fragment
After:
-Plus copy of normal 1 and normal 22
-Carrier of balanced translocation

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6
Q

Why is carriers of balanced translocation not always lucky? Give an example

A

Philadelphia chromosome
-Translocation involving chromosome 9 ABL and 22 BCR
-This encodes BCR-ABL protein which can lead to the development of chronic myelogenous leukemia

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7
Q

What is reciprocal translocation in meisois?

A

A reciprocal translocation usually involves breakage of two non-homologous chromosomes with exchange of the fragments.

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8
Q

What are the results of unbalanced reciprocal translocation?

A

-Many lead to miscarriage (hence why a woman with a high number of unexplained
miscarriages should be screened for a balanced translocation)
-Learning difficulties, physical disabilities
-Tend to be specific to each individual so exact risks and clinical features vary

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9
Q

What is robertsonian translocation?

A

Two acrocentric chromosomes join near centromere with the loss of p arms

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10
Q

What chromosomes does robertsonian translocation involve and why?

A

This type of translocation involves only chromosomes 13, 14, 15, 21 and 22, because the ends of their short arms have similar repetitive DNA sequences that predispose to their fusion.

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11
Q

How many chromosomes does an individual who is a balanced carrier of robertsonian translocation have?

A

Balanced carrier has 45 chromosomes

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12
Q

If there are 46 chromosomes present with robertsonian translocation then what does this mean?

A

If 46 chromosomes present including Robertsonian then must be unbalanced

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13
Q

What do the p arms of chromosomes encode?

A

p arms encode rRNA

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14
Q

What does a robertsonian translocation of 21;21 lead to?

A

21;21 translocation leads to 100% risk of Down syndrome in fetus

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15
Q

What does a terminal deletion result in?

A

A new telomere

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16
Q

What are examples of structural changes that represent interstitial deletion?

A

Examples:
-Prader-Will
-DiGeorge syndrome
-Cri du chat

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17
Q

What may a deletion structural chane to chromosomes be?

A

Deletion may be terminal or interstitial

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18
Q

What do deletions cause a region of?

A

Causes a region of monosomy

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19
Q

What can deletions cause insufficiency of in some genes?

A

Haploinsufficiency of some genes

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20
Q

What is phenotype specific for in deletion?

A

Phenotype is specific for size and place on deletion

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21
Q

What do gross deletions spread on?

A

Gross deletions seen on metaphase spread on G-banded karyotype

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22
Q

What techniques show microdeletions in chromosomes?

A

High resolution banding, FISH and now CGH showed ‘micro’ deletions

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23
Q

What microdeletion causes DiGeorge syndrome?

A

22q11

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24
Q

What microdeletion causes Wolf-Hirschhorn?

25
What microdeletion causes Williams syndrome?
7q11
26
What microdeletion causes Smith-Magenis syndrome?
17p11
27
What does unequal crossing over result in?
Explain how unequal crossing over can result in (micro)deletions and (micro)duplications
28
What are prenatal sources of sample in detecting chromosomal abnormalities?
-Amniocentesis -Choronic villus sampling -Cell-free fetal DNA
29
What are postnatal sources of sample in detecting chromosomal abnormalities?
-Blood -Saliva
30
What is the most common form of chromosome staining?
G-banding
31
Why do we use bands in chromosome staining?
Because of chromatin -2 different sorts: Euchromatin and heterochromatin
32
What is Euchromatin rich in, how is it packed and what does this mean for gene activity?
-GC rich -Loosely packed -Gene active
33
What is heterochromatin rich in, how is it packed and what does this mean for gene activity?
-AT rich -Tightly packed -Genes inactive
34
What are the steps involved in the production of a karyotype?
1. Extract 5mL of venous blood 2. Add phytohemagglutinin and culture medium 3. Culture at 37 degrees celcius for 3 days 4. Add colchicine and hypotonic saline 5. Cells fixed 6. Spread cells onto slide by dropping 7. Digest with trypsin and stain with Giemsa 8. analyse 'metaphase spread' 9. Have final karyotype
35
What does G-banding look for?
Looks for aneuploidies, translocations & very large deletions
36
What does FISH stand for?
Fluorescent in situ hybridisation
37
What is hybridisation?
single stranded nucleic acid strand binds to a new single stranded nucleic acid strand (DNA/DNA or DNA/RNA)
38
What are the steps involved in FISH?
Cultured cells, metaphase spread 1. Fluorescent probe 2. Denature probe and target DNA 3. Mix probe and target DNA 4. Probe binds to target
39
What is a probe?
A single stranded DNA (or RNA) molecule
40
How long is a probe?
A single stranded DNA (or RNA) molecule
41
What is a probe labelled with?
Labelled with a fluorescent or luminescent molecule (less commonly a radioactive isotope)
42
What type of chromosomes does FISH use?
Uses metaphase chromosomes
43
What is the complete process of array CGH?
1. Patient and control DNA are labelled with fluorescent dyes and applied to the microarray 2. Patient and control DNA compete to attach, or hybridise, to the microarray 3. the microarray scanner measures the fluorescent signals 4. Computer software analyses the data and generates a plot
44
What does array CGH look for?
Looks for microdeletions and microduplications
45
What does QF-PCR stand for?
Quantitative fluorescence polymerase chain reaction
46
What does QF-PCR detect?
Trisomies 13, 18 and 21
47
What does QF-PCR use?
Uses microsatellites
48
What are microsatellites?
Short repeated sequences with variable numbers of repeats
49
What is the variability of microsatellites like between individuals?
 Number of repeats varies between individuals  Total length of microsatellite sequence varies between individuals
50
What are short tandem repeats also known as?
Short tandem repeats are also known as microsatellites and simple sequence repeat(SSR)
51
What are the steps involved in detecting microsatellites?
 Isolate DNA from individual  Design primers specific to flanking sequences  PCR amplification  Gel electrophoresis
52
What is PCR?
Exponential amplification of a DNA fragment of known sequence
53
What are the steps involved in PCR?
1. Heat and Separate DNA strands at 94oC 2. Primers anneal with template (50-65oC) 3. DNA polymerase extends strand from primer, 72oC -2 identical copies of the region of interest are formed 4. After 2 cycles we have 4 copies of the region of interest
54
What are the steps involved in QF=PCR when testing for downs?
 Perform PCR using primers for microsatellite known to be on chromosome 21 (if testing for Down’s)  Should be two copies of microsatellite (one from mother, one from father, like any other autosomal locus, gene, whatever)  If homozygous, there will be a single peak of high signal  If heterozygous, there will be two peaks of similar, lower signal
55
What does Non-invasive pre-natal testing (NIPT) and NGS use?
Cell free fetal DNA
56
What type of testing is NIPT and NGS?
Trisomy testing
57
What type of sequencing is NIPT and NGS?
Next-generation sequencing
58
What are the steps involved in NIPT and NGS?
1. Cell free DNA in placenta is extracted from maternal plasma 2. Massively parallel sequencing of total DNA present in maternal plasma 3. Alignment of sequencing reads to human genome sequence an determination of relative chromosome representation 4. Detection of aneuploidy like trisomy 21

Genomics (6 decks)

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