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L3 Clinical Genomics > Module induction > Flashcards

Module induction Flashcards

1
Q

What is aneuploidy?

A

The gain or loss of one or a few chromosomes

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2
Q

What is the maximum resolution for G-banding?

A

3-5 megabases

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3
Q

Which condition is caused by trisomy 18?

A

Edwards Syndrome

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4
Q

Which phase of the cell cycle must cells be in for karyotype analysis?

A

Metaphase because the chromosomes are condensed and the nucleus has broken down so they are free in the cytoplasm

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5
Q

What is required for PND?

A

DNA from the foetus

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6
Q

How can DNA from the foetus be harvested for PND? (4)

A
  • Amniocentesis
  • Chorionic villus sampling
  • Foetal blood sample from umbilical cord
  • Cell Free Foetal DNA Sampling (cffDNA)
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7
Q

What is amniocentesis?

A

Taking a sample of amniotic fluid which contains epithelial cells from the foetus which fall off during development

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8
Q

What is chorionic villus sampling (CVS)?

A

Taking a sample of placental tissue

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9
Q

How are cells processed for PND after collection? (6)

A
  • Stimulate growth with additional hormones
  • Microtubule inhibitor used to prevent entry into anaphase
  • Swell the nuclei via osmosis to increase the space between the chromosomes
  • Cells are fixed using acetic acid and methanol
  • Adhere chromosomes to glass slide using fixative
  • Ageing period of chromosomes being exposed to sunlight for 48 hours
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10
Q

What is the purpose of fixing cells for analysis? (2)

A
  • Kills the cells and blocks cellular processes including chromosome condensation to maintain a minimum resolution of analysis
  • Kills possible contaminants (i.e. pathogens)
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11
Q

What is the purpose of the ageing period? (4)

A
  • Denature proteins
  • Remove residual fixative
  • Enhance adherence to the slide
  • Remove water from the chromosomes to improve banding quality
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12
Q

What is required to generate the banding structure for karyotyping? (2)

A
  • Partial digestion with trypsin
  • Stain with Leishman’s dye
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13
Q

What is euchromatin? (2)

A
  • Highly transcribed regions of the genome with an open conformation
  • Typically rich in GC sequences
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14
Q

What is heterochromatin? (2)

A
  • Highly condensed regions of the genome with little/no transcriptional activity
  • Typically rich in AT sequences
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15
Q

Which form of chromatin corresponds to the dark bands in G-banding chromosomes?

A

Heterochromatin (AT-rich)

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16
Q

Which form of chromatin corresponds to the pale bands in G-banding chromosomes?

A

Euchromatin (GC-rich)

17
Q

How is staining done using trypsin and Leishman’s dye? (2)

A
  • Trypsin degrades histones and causes chromatin collapse
  • Chromatin collapse excludes Leishman’s dye from its binding pocket so it is unable to access the chromatin
18
Q

What is the explanation of why heterochromatin (more highly condensed) stains darker than euchromatin? (3)

A
  • Trypsin digestion causes partial collapse of all chromatin structures
  • Regions that start off relatively open (i.e. euchromatin) are more accessible to trypsin digestion so suffer greater collapse
  • Euchromatin collapses more than heterochromatin so euchromatin corresponds to pale bands and heterochromatin corresponds to dark bands
19
Q

What is mosaicism?

A

When a person has two or more genetically different sets of cells in their body

20
Q

What kind of DNA is in the p arm of acrocentric chromosomes?

A

Repetitive DNA and ribosomal DNA genes (rDNA)

21
Q

How does FISH work?

A

Uses fluorescently labelled oligonucleotide probes which are complementary to regions of genomic interest to report on copy number and positional information

22
Q

What is stringency in FISH?

A

A measure of the experimental conditions that govern how likely 2 nucleic acid sequences are to anneal

23
Q

What are the major experimental parameters that can change the stringency conditions of a reaction? (2)

A
  • Temperature
  • Salt concentration
24
Q

How is FISH performed? (5)

A
  • Nuclei from patient samples are adhered to microscope slides
  • Chromosomal DNA is denatured to generate single stranded DNA (ssDNA) by increasing the temperature to 73 degrees (increasing stringency)
  • DNA is single stranded which allows the probes to bind to their complementary sequences
  • Temperature is cooled
  • Samples are washed in different stringency buffers to remove probe bound to off target sequences and reduce background signalling
25
Q

What are the conditions of high stringency? (3)

A
  • High temperature
  • Low salt concentration
  • DNA more likely to be in ssDNA form so probes can bind
26
Q

What is the importance of salt in stringency? (3)

A
  • Salts (e.g. NaCl) dissociate into positive and negative ions
  • Positive ions bind to the negatively charged DNA backbone to cancel the electrostatic repulsion between the strands
  • Therefore more salt lowers the stringency because reduces the repulsion between DNA strands keeping it in the double stranded form
27
Q

What information does metaphase FISH provide? (2)

A
  • Positional information
  • Low resolution copy number information
28
Q

What information does interphase FISH provide? (2)

A
  • Higher resolution copy number information
  • Presence of fusion of genetic elements
29
Q

What is a limitation of FISH?

A

It is possible for 2 signals to physically sit on top of each other by chance rather than be a true colocalisation

30
Q

What are the main classes of FISH probe used to characterise chromosome abnormalities? (4)

A
  • Gene specific probe
  • Centromeric probe
  • Telomeric probe
  • Chromosome-painting probe
31
Q

What are gene specific probes?

A

Reports copy number of disease critical regions e.g. Down syndrome

32
Q

What are centromeric probes? (2)

A
  • Probes complementary to alpha satellite sequences located in sub-centromeric regions of chromosomes
  • Often used to report on copy number of 13, 18, 21, X and Y for PND
33
Q

What are telomeric probes and whole chromosome paints used for? (2)

A
  • Characterising chromosomes which have been observed to be abnormal in G-banding
  • Look for gross structural rearrangements and if the abnormality was inherited from a parent
34
Q

What is an example of a gene specific probe?

A

TBX1 probe

35
Q

What is the relevance of TBX1? (2)

A
  • TBX1 gene is on 22q
  • Commonly deleted in DiGeorge Syndrome
36
Q

What is nuchal translucency? (2)

A
  • Area of fluid behind the foetal neck which can be seen in an ultrasound
  • Thickness is an important marker for genetic disease
37
Q

What is the normal range of nuchal translucency thickness?

A

1.5-3mm

38
Q

Which condition is caused by trisomy 13?

A

Patau Syndrome

39
Q

What symptoms are associated with Patau Syndrome? (3)

A
  • Holoprosencephaly
  • Microcephaly
  • Polydactyly

L3 Clinical Genomics (14 decks)

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