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π’žπ“π’Ύπ“ƒπ’Ύπ’Έπ’Άπ“ π’’π‘’π“ƒπ‘’π“‰π’Ύπ’Έπ“ˆ > Overview of Genomic Technologies in Clinical Diagnostics > Flashcards

Overview of Genomic Technologies in Clinical Diagnostics Flashcards

1
Q

What is PCR used for?

A

➝ amplify a specific region of DNA

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2
Q

How does PCR work?

A

➝ Primers flank the region you want to amplify

➝ each cycle doubles the amount of DNA copies on your target sequence

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3
Q

What is fragment analysis?

A

➝ PCR followed by capillary electrophoresis

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4
Q

Why is fragment analysis done and what can it be used for?

A

➝ Sizing PCR product

➝ can be used to detect repeat expansions and other small size changes

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5
Q

What is an example of a disease with a repeat expansion in it?

A

➝ Huntington’s disease

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6
Q

What is Huntington’s disease caused by?

A

➝ CAG repeat expansion in the Huntington HTT gene

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7
Q

What is the difference between normal, intermediate and pathogenic Huntingtons?

A

➝ Normal < 27 copies
➝ Intermediate 27-35
➝ Pathogenic >35

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8
Q

What causes death in Huntingtons?

A

➝ The expanded protein is toxic and accumulates in neurons which causes cell death

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9
Q

How is Huntingtons diagnosed?

A

➝ Fragment analysis

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10
Q

How many bp can be sequenced in Sanger sequencing?

A

➝ 800bp per reaction

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11
Q

What are the two disadvantages of Sanger Sequencing?

A

➝ slow and low throughput

➝ costly

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12
Q

What can be identified in Sanger sequencing?

A

➝ SNPs or mutations

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13
Q

How does Sanger sequencing work?

A

➝ 4 DNA nucleotide chain terminators have a different dye so you can determine the nucleotide sequence by the color

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14
Q

What causes cutaneous vasculitis?

A

➝ R1042G mutation in gene C3 segregates with affected individuals

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15
Q

What is FISH?

A

➝ fluorescent in situ hybridiation

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16
Q

What 4 things can FISH detect?

A

➝ Large chromosomal abnormalities
➝ Extra chromosomes
➝ Large deleted segments
➝ Translocations

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17
Q

How does FISH work?

A

1) design a fluorescent probe to the chromosomal region of interest
2) denature the probe and target DNA
3) mix the probe and target DNA (hybridisation)
4) probe binds to target
5) target fluoresces

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18
Q

What is CGH used to detect?

A

➝ submicroscopic chromosomal abnormalities

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19
Q

How does CGH work?

A

➝ Patient DNA labelled green
➝ Control labelled red
➝ if there is equal hybridisation of patient and control DNA they β€˜cancel out’ and the signal is yellow

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20
Q

What does a red signal mean in CGH?

A

➝ loss of DNA

21
Q

What does a green signal mean in CGH?

A

➝ there is gain of DNA

22
Q

What is multiplex ligation dependent probe amplification (MLPA)?

A

➝ A variation of PCR that permits amplification of multiple targets

23
Q

What are the probes made of in MLPA?

A

➝ two oligonucleotides which recognise adjacent target sites on the DNA

24
Q

What is MLPA used for?

A

➝ to detect abnormal copy numbers at specific chromosomal locations

25
Q

What can MLPA detect?

A

➝ Sub-microscopic gene deletions/partial gene deletions

26
Q

How is a complete probe obtained in MLPA?

A

➝One probe oligonucleotide contains the sequence recognised by the forward primer
➝The other contains the sequence recognised by the reverse primer
➝Only when both probe oligonucleotides are hybridised to their respective targets can they be ligated into a complete probe

27
Q

What is the amount of product in MLPA proportional to?

A

➝ the amount that is bound to the patient DNA

28
Q

How do you use MLPA to determine relative ploidy at specific locations?

A

➝ probes may be designed to target various regions of the chromosome of the human cell
➝ the signal strength of the probes are compared with those obtained from a reference DNA sample known to have two copies of the chromosome

29
Q

What is an advantage of next generation sequencing?

A

➝ wide range of tests in a shorter time for less money

30
Q

What is the current use of next generation sequencing?

A

➝ enriching to sequence only the known disease genes relevant to the phenotype

31
Q

How many genes are there in the human genome?

A

➝ 21000

32
Q

What % does the exome make up of the genome?

A

➝ 1-2%

33
Q

What % of pathogenic mutations are protein coding?

A

➝ 80%

34
Q

What is target enrichment?

A

➝ capturing target regions of interest with baits

35
Q

What is the biggest challenge in genome sequencing?

A

➝ result interpretation

36
Q

What is array CGH used to detect?

A

➝ large sized chromosomal aberrations

37
Q

What are the three ethical considerations when sequencing someones genome?

A

➝ modified patient consent process
➝ data analysis pathways - inspect relevant genes
➝ strategy for reporting incidental findings

38
Q

What is the main role of a genetics lab?

A

➝ to help consultants reach a genetic diagnosis for individuals and families to help guide treatment and management

39
Q

What is clinical validity?

A

➝ how well the test predicts the phenotype

40
Q

What is clinical utility?

A

➝ how the test adds to the management of the patient

41
Q

What are the diagnostic reasons for doing a genetic test?

A

➝ inform clinical trials
➝ diagnosis
➝ management and treatment

42
Q

What are the 3 reasons for doing genetic testing other than diagnostic?

A

➝ family mutation - interpretation of pathogenicity
➝ predictive - life choices and management
➝ informed consent - genetic counselling

43
Q

What are the 3 outcomes of a genetic test?

A

➝ pathogenic mutations
➝ normal variation
➝ novel variant
➝ previously detected variance of uncertain significance

44
Q

How do you establish if a mutation is pathogenic?

A

➝ ACMG guidelines

45
Q

What do you look at to see if a mutation is common?

A

➝ look at sub populations

46
Q

What tools are used for missense and splicing mutations?

A

➝ in silico

47
Q

How do you establish if a mutation is pathogenic?

A

➝ mode of inheritance
➝ locus specific databases of published and unpublished data
➝ see what type of mutation it is :nonsense, frameshift, splice sites, mutations
➝ missense/intronic mutation

48
Q

What causes Charcot Marie Tooth disease type 2?

A

➝ Mitofusin 2 (MFN2)

49
Q

What does charcot marie tooth disease lead to?

A

➝ degeneration of long nerves in legs and arms leading to muscle wasting and sensory defects

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