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Genomics > GENOMICS Structural chromosomal abnormalities > Flashcards

GENOMICS Structural chromosomal abnormalities Flashcards

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?

A

4p16

25
Q

What microdeletion causes Williams syndrome?

A

7q11

26
Q

What microdeletion causes Smith-Magenis syndrome?

A

17p11

27
Q

What does unequal crossing over result in?

A

Explain how unequal crossing over can result in (micro)deletions and (micro)duplications

28
Q

What are prenatal sources of sample in detecting chromosomal abnormalities?

A

-Amniocentesis
-Choronic villus sampling
-Cell-free fetal DNA

29
Q

What are postnatal sources of sample in detecting chromosomal abnormalities?

A

-Blood
-Saliva

30
Q

What is the most common form of chromosome staining?

A

G-banding

31
Q

Why do we use bands in chromosome staining?

A

Because of chromatin
-2 different sorts: Euchromatin and heterochromatin

32
Q

What is Euchromatin rich in, how is it packed and what does this mean for gene activity?

A

-GC rich
-Loosely packed
-Gene active

33
Q

What is heterochromatin rich in, how is it packed and what does this mean for gene activity?

A

-AT rich
-Tightly packed
-Genes inactive

34
Q

What are the steps involved in the production of a karyotype?

A
  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
Q

What does G-banding look for?

A

Looks for aneuploidies, translocations & very large deletions

36
Q

What does FISH stand for?

A

Fluorescent in situ hybridisation

37
Q

What is hybridisation?

A

single stranded nucleic acid strand binds to a new single stranded nucleic acid
strand (DNA/DNA or DNA/RNA)

38
Q

What are the steps involved in FISH?

A

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
Q

What is a probe?

A

A single stranded DNA (or RNA) molecule

40
Q

How long is a probe?

A

A single stranded DNA (or RNA) molecule

41
Q

What is a probe labelled with?

A

Labelled with a fluorescent or luminescent molecule (less commonly a radioactive
isotope)

42
Q

What type of chromosomes does FISH use?

A

Uses metaphase chromosomes

43
Q

What is the complete process of array CGH?

A
  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
Q

What does array CGH look for?

A

Looks for microdeletions and microduplications

45
Q

What does QF-PCR stand for?

A

Quantitative fluorescence polymerase chain reaction

46
Q

What does QF-PCR detect?

A

Trisomies 13, 18 and 21

47
Q

What does QF-PCR use?

A

Uses microsatellites

48
Q

What are microsatellites?

A

Short repeated sequences with variable numbers of repeats

49
Q

What is the variability of microsatellites like between individuals?

A

 Number of repeats varies
between individuals
 Total length of microsatellite
sequence varies between
individuals

50
Q

What are short tandem repeats also known as?

A

Short tandem repeats are also known as microsatellites and simple sequence repeat(SSR)

51
Q

What are the steps involved in detecting microsatellites?

A

 Isolate DNA from individual
 Design primers specific to flanking sequences
 PCR amplification
 Gel electrophoresis

52
Q

What is PCR?

A

Exponential amplification of a DNA fragment of known sequence

53
Q

What are the steps involved in PCR?

A
  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
Q

What are the steps involved in QF=PCR when testing for downs?

A

 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
Q

What does Non-invasive pre-natal testing (NIPT) and NGS use?

A

Cell free fetal DNA

56
Q

What type of testing is NIPT and NGS?

A

Trisomy testing

57
Q

What type of sequencing is NIPT and NGS?

A

Next-generation sequencing

58
Q

What are the steps involved in NIPT and NGS?

A
  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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