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MBD/MI (Wothaya) > Overview Of Genome Technologies In Genetic Diagnostics > Flashcards

Overview Of Genome Technologies In Genetic Diagnostics Flashcards

1
Q

Why do you need to do PCR for diagnostics?

A

Amplify enough DNA molecules so we have sufficient material for downstream applications

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2
Q

What is fragment analysis used for?

A

Detect repeat expansions or other small size changes

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3
Q

What is fragment analysis?

A

PCR followed by capillary electrophoresis

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4
Q

What is an example of a repeat expansion disease?

A

Huntingtons

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5
Q

What is the mutation in huntingtons?

A

CAC repeat expansion in the huntingtin HTT gene

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6
Q

Why is the huntingtons mutation bad?

A

The resulting protein is toxic and accumulates in neurons causing cell death

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7
Q

How is huntingtons diagnosed?

A

Fragment analysis

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8
Q

What mutation causes cutaneous vasculitis?

A

R1042G mutation in gene C3

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9
Q

What does FISH stand for?

A

Fluorescent in situ hybridisation

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10
Q

What is FISH used for?

A

Detect large chromosomal abnormalities

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11
Q

What is the method for FISH?

A

Design fluorescent probe to chromosomal region of interest
Denature probe and target
Mix probe and target DNA

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12
Q

What does CGH stand for in array-CGH?

A

Comparative genome hybridisation

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13
Q

What colour is the patient DNA labelled in array-CGH?

A

Green

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14
Q

What colour is the control DNA labelled in array-CGH?

A

Red

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15
Q

In array-CGH, what does an increase in green signal indicate?

A

A gene in the patient not present in control

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16
Q

What does MLPA stand for?

A

Multiplex ligand dependent probe amplification

17
Q

What is MLPA?

A

Variation of PCR that permits amplification of multiple targets

18
Q

What does a MPLA probe consist of and what do they do?

A

Two oligonucleotides that recognise adjacent target sites on the DNA

19
Q

What is MLPA used for?

A

To detect abnormal copy numbers at specific chromosomal locations

20
Q

What do the two probes in MLPA detect?

A

One contains the sequence recognised by the forward primer

One contains the sequence recognised by the reverse primer

21
Q

What has to happen before amplification can take place in MLPA?

A

Both probes hybridised and ligated into a complete probe

22
Q

What happens after amplification in MLPA?

A

Fragment analysis of the product

23
Q

What is next generation sequencing used for?

A

Enriching to sequence the only known disease genes relevant to the phenotype

24
Q

What is the next generation sequencing method?

A

Target enrichment
Capture regions of interest with baits
Carry out hybridisation and column purification

25
Q

What are the ethical considerations needed for exome and genome sequencing?

A

Inspect relevant genes first when analysing
Long patient consent process
Need some form of strategy for reporting incidental findings

26
Q

What does the 100,000 genome project sequence?

A

Rare diseases- index cases and families

Cancer- germline and tumour samples

27
Q

What does the 100,000 genome project do?

A

Brings direct benefit of whole genome sequencing and genetics to patients

28
Q

What are tier 1 variants in the 100,000 genome project?

A

Known pathogenic,

protein truncating

29
Q

What are tier 2 variants in the 100,000 genome project?

A 
Protein altering (missense)
Intronic (splice site)
30
Q

What are tier 3 variants in the 100,000 genome project?

A

Loss- of-function variants in genes not on the disease gene panel

31
Q

Where is most of the genetic testing in the UK done?

A

NHS diagnostic laboratory

32
Q

What is the main role of the NHS diagnostic laboratory?

A

Help consultants reach a genetic diagnosis for patients to help guide their treatment and clinical management

33
Q

What is clinical validity?

A

How well a test predicts the phenotype

34
Q

What is clinical utility?

A

How well a test adds to the management of the patient

35
Q

What are the options for the outcome of a diagnostic test?

A

Pathogenic mutation
Normal variation
Novel variant

36
Q

How do you establish if a mutation is pathogenic?

A

Mode of inheritance
Genetic databases of published and unpublished data
Different types of mutagens
Missense/intronic mutation

MBD/MI (Wothaya) (57 decks)

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