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Genomics > Genomics and disease > Flashcards

Genomics and disease Flashcards

1
Q

In which fields does genomics particularly want to be involved in?

A

Rare diseases

Cancer

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2
Q

What percentage of rare diseases are genetic?

A

80%

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3
Q

What is the difference between the use of lab based and point of care tests?

A

Less urgent cases like cancer diagnosis = lab based

Testing for warfarin sensitivity in a stroke patient = point of care testing

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4
Q

What is the 100 000 genome project?

A

Aims at genotyping 70 000 rare disease patients and their families

To look for genes associated with these patients

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5
Q

Potential benefits of 100 000 genome project

A

Improve current treatments

Discover new treatments

Diagnose future patients

Help understand the underlying mechanisms of disease

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6
Q

What are the ethical concerns of genomic sequencing?

A

Clone a person from DNA

Finding out about being adopted

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7
Q

What project is taking place in the North East Regional Genetics Unit?

A

100 genetic point mutation tests are being done looking at parts of the genome

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8
Q

How is looking at specific sequences better than the whole genomic sequence?

A

Looking at the whole genomic sequence is

  • expensive
  • not accessible to everyone
  • complex to interpret
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9
Q

Why is X-linked genetic testing important?

A

A lot of diseases occur on the X chromosome

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10
Q

Conditions occuring on the X chromosome

A

Haemophilia

Duchenne Muscular Dystrophy

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11
Q

How are X linked conditions currently being diagnosed?

A

Single gene testing

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12
Q

What is warfarin?

A

Anticoagulant that thins the blood

Treatment for stroke

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13
Q

What is the characteristic of warfarin sensitive patients?

A

Patients that have low tolerance to the drug

This means they are less able to break down warfarin, and so the dose used must be lower than usual

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14
Q

Which patients are prescribed warfarin?

A

Heart valve disease

Irregular heart beat

History of heart attack/stroke

Prior blood clot in the deep veins of the arms and legs

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15
Q

Which genes are involved with warfarin sensitivity?

A

Polymorphisms of :

CYP2C9

VKORC1

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16
Q

What percentage of variation to warfarin metabolism do CYP2C9 and VKORC1 polymorphisms represent?

A

30%

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17
Q

How can polymorphisms in warfarin metabolism be detected?

A

Lab based test

Point of care test

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18
Q

Why is there a need for POCT in detecting warfarin sensitivity?

A

Highly urgent nature of patients who take warfarin

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19
Q

Example of a POCT used to test for warfarin sensitivity

A

QuantumDX

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20
Q

What is the turnaround time for QuantumDX?

A

20 minutes

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21
Q

What are other potential applications for POCT?

A

UTI

MRSA

Viral outbreaks

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22
Q

What does NIPT stand for?

A

Non invasive prenatal diagnostic testing

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23
Q

What is the aim of NIPT?

A

Detect fetal abnormalities through the detection of fetal DNA in the mother’s blood

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24
Q

Rationale behind NIPT

A

When foetal cells apoptose, the DNA is released into the mother’s bloodstream

A small vial of blood can be obtained for the mothers arm, and the DNA can be sequenced through next generation sequencing

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25
How long are foetal DNA fragments?
150 bases long
26
What procedure does NIPT aim to replace?
Amniocentesis - very risky
27
Examples of conditions that can be tested for using NIPT
Trisomies Sex aneuploidy Rare/inherited alterations
28
What, regarding NIPT, must be ensured?
No ability to determine the phenotypic qualities of the embryo like eye colour and height This brings out the possibility of designer babies
29
What has been a fear with the rise of more advanced embryonic genomic testing?
That termination rates would increase amongst parents This has not been the case however
30
What other application can NIPT be used for?
Cancer Since these cells also release fragments of their DNA into the circulation when they apoptose
31
What is the area where genomics has had the biggest benefits?
Cancer
32
Applications of genomics in cancer
Diagnosis - earlier gives better treatment outcomes Stratification - cost reduced since less patients are on unnecessary treatments Personalised therapy - tailoring therapy to individual patients
33
Examples of genomic technologies used in cancer
Mammaprint ConfirmMDx OncomineDx test
34
Describe how a mammaprint is carried out
Analyses the activity of certain genes in early-stage breast cancer and stratifies patients depending on their likelihood of recurrence 10 years after diagnosis Group with increased risk of recurrence = more treatment Group with decreased risk of recurrence = mastectomy and nothing more
35
Which cancer is ConfirmMDx used for?
Prostate cancer
36
Which patient cohort is ConfirmMDx targeted for?
False-negative and false-positive biopsies
37
Describe how a ConfirmMDx test is carried out
This is a epigenetic test which looks at the methylation status of genes known to be linked to cancer
38
What genes are looked at in ConfirmMDx?
GSTP1 APC RASSF1
39
How are prostate cancer results confirmed currently?
Patients undergo a painful biopsy procedure to rule out risk Involves sticking up to 96 needles into the prostate and extracting tissue to be biopsied
40
Why are false negative test results from biopsies so common?
The possibility of extracting tissue with cancer using a thin needle is relatively small
41
What is an OncomineDx test?
Personalised therapy genomic test involving stratisfying patients to therapy groups depending on their genomic changes
42
Why is it important to appropriately administer the correct medication to the correct patient group?
A lot of therapies are high risk and can do more harm than good
43
What was the first FDA-approved test used for stratifying patient groups to correct therapies?
OncomineDx test for non-small cell lung cancer Selects which patients with lung cancer are eligible for treatment with specific FDA-approved drugs
44
What is the current method for monitoring a patients' response to therapy?
CT scan
45
What are the disadvantages of using CT scans to monitor the patients' response to a therapy ?
Small risk through increased X-ray exposure Expensive Takes time report
46
How can genomic technologies be used to replace CT scans in monitoring the response of a patient to a treatment?
Cell free DNA can be used to measure the size of the tumour The bigger the tumour, the more likely it is to shed DNA into the vascular system cfDNA sequencing can be used to look for tumour evolution, relapse and personalised treatment plans
47
How are cfDNA sequencing techniques better at looking at the progression of a tumour that single markers?
Not all cells may express the single marker, but the part of the cancer that secreted the specific gene might have been killed off, and the rest of the non-p53 secreting cancer may still be growing Measuring only this marker therefore gives false results
48
What are the cells that originate from the original event called?
Clonal cells
49
What are the cells that originate from secondary events leading to intatumoural heterogeneity called?
Subclonal cells
50
What drives the heterogeneous response of a tumour to therapy?
Intratumour heterogeneity
51
Why is it important to understand the difference between clonal and subclonal mutations?
Because this determines the use of targeted therapies Targeted therapies are less successful against subclonal mutations compared to clonal mutations
52
Examples of hormone receptors targeted for cancer therapy
BCR-ABL EGFR Oestrogen receptors
53
What drug targets the BCR-ABL muation?
Imatinib Tyrosine kinase inhibitors
54
What drug targets the EGFR mutation?
Gefitinib Tyrosine kinase inhibitors
55
What drug targets the oestrogen receptor?
Tamoxifen
56
What is the only way that targeted therapies can be effective?
If all the tumour cells express the mutation you are targeting
57
In which cancer is the BCR-ABL mutation found?
Chronic myeloid leukemia
58
What cancer is BRCA asscociated with?
Breast cancer
59
Where is BRCA normally expressed?
Breast and other tissue
60
What type of gene is BCRA?
Tumour suppressor gene Involved in repairing damaged DNA
61
What is the inheritance of BRCA?
Inherited
62
What is the probability of developing breast cancer if you have abnormal BRCA genes?
80% risk by the age of 90
63
What is the probability of developing ovarian cancer if you have abnormal BRCA genes?
55%
64
Which company patented BRCA testing?
Myriad In 1994
65
What has happened following Myriad's patent on BRCA testing?
In 2013, the US supreme court ruled that a naturally occurring DNA segment is not able to be patented
66
What was the problem with Myriad's patent on BRCA testing?
It was almost impossible to get a second opinion of the test result as no other lab could independently test for BRCA mutations
67
What act protects against insurance discrimination?
GINA Genetic information nondiscrimination act
68
Describe the case of Pet Reilly
23andMe showed she had high risk of developing Alzheimers So she changed her insurance policy and paid more to be guratanteed long term care
69
What is gene therapy?
The introduction of normal genes in place of missing or defective ones in order to correct the germline or genetic disorders
70
What is an adenovirus?
Inserts a new gene into a cell If integrated, the new gene will make a functional protein to treat a disease
71
In which diseases is gene therapy particularly useful?
In single-gene diseases
72
When was the first time gene therapy provided first somatic treatment?
1993
73
Diseases cured through gene therapy
ADA-SCID CLL Retinal dystrophy Melanoma
74
What, apart from gene therapy, is another targeted therapy being developed?
CAR-T cells The future of cancer treatment
75
Potential disease to be treated by gene therapy
DMD First gene therapy trials have been approved
76
How have chickens been used to make vaccines?
Chickens modified to make IFN a 2a Can be extracted from eggs and used for therapy

Genomics (9 decks)

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