Block D Lecture 3: Genetic Testing

Question 1

What is a clinical geneticist?

Answer 1

A physician which has undergone specific training in genetics after recieving general professional training in medicine or paediatrics, or another related discipline.

(Slide 7)

Question 2

What does specific training for a clinical geneticist involve?

Answer 2

The specialist training covers a broad range of sub-specialities such as the genetics of adult and paediatric (children or infant) disorders, cancer, dysmorpolohy and neuro-psychiatry which training also including basic theoretical genetics couselling theory and practice, lab experiance and research.

(Slide 7)

Question 3

What is a genetic counsellor / genetic counselling?

Answer 3

A health care professional who helps patients and families understand their risk of genetic conditions, and how to manage them

(Slide 9)

Question 4

What is the main aim of genetic counselling?

Answer 4

To help people gain sufficient understanding of their situation so that they can make informed decisions about what they wish to do

(Slide 10)

Question 5

What are 3 examples of “sub-aims” of genetic counselling which are used to help achieve the main aim?

Answer 5

Answers include:

Help people to:

Understand information about the genetic condition

Appreciate the inheritance pattern and risk of recurrence

Understand the treatment options avalible

Make decisions appropiate to their personal or family situation

Make the best possible adjustment to the disorder / risk

(Slide 10)

Question 6

What are 3 possible reasons someone might want to carry out a clinical genetics test?

Answer 6

To provide information (on what the condition is, treatment options, explain inheritence or discuss reoccurance)

To help guide patient choices (whether to have more children or have genetic tests before or during pregnancy)

To offer support to any other family or to offer genetic tests to anyone else who may be at risk

(Slides 12, 13 and 14)

Question 7

What is prenatal genetic testing and what is it used for?

Answer 7

A test done before the foetus is born. It can be used to determine the carrier status of the parents and to determine the genetic status of the foetus.

(Slide 15)

Question 8

What is neonatal genetic testing and what can it be used for?

Answer 8

A test done after the foetus is born. It can be used for early diagnosis and treatment

(Slide 15)

Question 9

What can be done for the patient if their genetic diagnosis is predictive and treatable?

Answer 9

Patient can choose to receive early treatment, and future surveilance to prevent occurance / reoccurance

(Slide 16)

Question 10

What potential personal decisions will the patient / family have to make if they are diagnosed with a predicatble but non-treatable genetic condition?

Answer 10

Family has to decide whether they want to find out their carrier status

Possible prenatal selection

Preparation

(Slide 16)

Question 11

What is prenatal selection?

Answer 11

The process of assessing a fetus’s viability and predicting the severity of a genetic condition

(Slide 16)

Question 12

What happens regarding genetic testing on a disease with a later onset and no cure?

Answer 12

Children ARE NOT TESTED under ANY circumstances due to social stigma with family, education, relationships etc and as it deprives individual of the right to choose vs right to not know.

Once the child turns 18 they can make their own informed decision

(Slide 17)

Question 13

What are 3 other ethical issues not related to age concerning genetic testing of a disease?

Answer 13

Non-paternity issues ( when genetic testing reveals presumed parent is not the father)

Potential implications for untested relatives

Insurance / employer discrimination

(Slide 17)

Question 14

What does prognosis mean?

Answer 14

The likely cause of a medical condition

(Slide 21)

Question 15

What is an issue concerning prognosis in genetic testing?

Answer 15

One gene can cause multiple different disorders

(Slide 21)

Question 16

What is a issue concerning selection in genetic testing?

Answer 16

Some disorders can be caused by one of many genes

(Slide 22)

Question 17

What are molecular diagnostic tests and what should their properties be?

Answer 17

They are used to confirm a disease and associate it with a specific alteration in DNA.

The test should be relatively simple, robust and able to reflect the incidence of mutations in the general population

(Slide 24)

Question 18

What are 2 different types of genetic methods avalible for mutation detection?

Answer 18

Methods where the mutations are unknown

Methods where the mutation is already known

(Slide 26)

Question 19

What are 2 different methods which can be used if the mutations you’re looking for are unknown (aka “mutation scanning”)?

Answer 19

PCR followed by high-resolution melting temperature analysis of candidate genes

Genome sequencing

(Slide 26)

Question 20

What are 2 methods which can be used if the mutations you’re trying to confirm in the patient are already known?

Answer 20

Answers include:

Amplification refractory mutation system (ARMS)

Multiplex Ligation-dependent probe amplification (MLPA)

Oligonucleotide Ligation Assay (OLA)

(Slide 26)

Question 21

When is mutation scanning used?

Answer 21

When many different mutations have been discovered throughout a gene, but the causative gene is unknown.

(Slide 27)

Question 22

What is a downside of sequence analysis?

Answer 22

It might be excessively time-consuming due to the size of the gene

(Slide 27)

Question 23

What might mutation scanning not tell you?

Answer 23

Whether or not the mutation actually affects gene function

(Slide 27)

Question 24

Why is whole genome sequencing becoming more feasible?

Answer 24

As it is becoming very cheap.

(Slide 29)

Question 25

What is the Amplification Refractory Mutation System (ARMS)?

Answer 25

A technique which uses 2 PCR reactions with 3 primers, 1 primer in common and 2 other primers which are specific for the mutant or wildtype allele.

The 2 seperate PCR amplification reactions are carried out for each individual with several sets of primers to detect the 12 most common types of mutations, and control primer sets are also used.

(Slides 32 and 33)

Question 26

What is the Multiplex Ligation-Dependent Probe Amplification (MLPA) used to detect?

Answer 26

Genomic deletions / insertions (of one or more entire exons)

Changes in copy number such as an abnormal number of chromosomes or gene duplications

DNA methylation (genomic imprinting)

(Slide 34)

Question 27

What is genomic imprinting?

Answer 27

Where only 1 copy of a gene (from a specific parent) is expressed

(Slide 35)

Question 28

What are the steps of MLPA?

Answer 28

1. Two synthetic DNA probes are designed to bind adjacent to the target DNA sequence of interest, with each probe consisting of a target DNA region complementary to the target DNA and a universal primer sequence for PCR amplification.
2. DNA is denatured and hybridised.
3. If both probes successfully hybridize to the target sequence, a thermostable DNA ligase enzyme joins them together. This ensures only correctly bound probes are amplified later.
4. All probe ligation produces are amplified by PCR using only 1 primer pair, with this resulting in the amplification product of each probe having a unique length.
5. Amplification products are seperated by electrophoresis. Relative amounts of probe amplification products, as compared to a control DNA sample, reflect the relative copy number of target sequences. E.g spike between wildtype and mutation indicates insertion, and a large dip indicates deletion

(Slide 35)

Question 29

How does the Oligonucleotide Ligation Assay (OLA), differ from MLPA?

Answer 29

It’s similar, but it detects known base change mutations instead

(Slide 37)

Question 30

What is a symptom of cystic fibrosis in sweat which has been discribed since the middle ages?

Answer 30

That it has a salty taste
(Slide 39)

Question 31

Why can’t patients with cystic fibrosis meet up?

Answer 31

As they have different lung microbiomes and there is a risk of cross-infection with harmful bacteria that can thrive in the lungs of people with cystic fibrosis

(Slide 42)

Question 32

Cystic fibrosis patients experience brochiectasis. What is this?

Answer 32

Abnormal and irreversible widening of the bronchial tubes (airways in the lungs which leads to a reduced ability to clear mucous from the lungs, chronic inflammation, infections and progressive lung damage

(Slide 43)