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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
Q

How long are foetal DNA fragments?

A

150 bases long

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26
Q

What procedure does NIPT aim to replace?

A

Amniocentesis - very risky

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27
Q

Examples of conditions that can be tested for using NIPT

A

Trisomies

Sex aneuploidy

Rare/inherited alterations

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28
Q

What, regarding NIPT, must be ensured?

A

No ability to determine the phenotypic qualities of the embryo like eye colour and height

This brings out the possibility of designer babies

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29
Q

What has been a fear with the rise of more advanced embryonic genomic testing?

A

That termination rates would increase amongst parents

This has not been the case however

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30
Q

What other application can NIPT be used for?

A

Cancer

Since these cells also release fragments of their DNA into the circulation when they apoptose

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31
Q

What is the area where genomics has had the biggest benefits?

A

Cancer

32
Q

Applications of genomics in cancer

A

Diagnosis - earlier gives better treatment outcomes

Stratification - cost reduced since less patients are on unnecessary treatments

Personalised therapy - tailoring therapy to individual patients

33
Q

Examples of genomic technologies used in cancer

A

Mammaprint

ConfirmMDx

OncomineDx test

34
Q

Describe how a mammaprint is carried out

A

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
Q

Which cancer is ConfirmMDx used for?

A

Prostate cancer

36
Q

Which patient cohort is ConfirmMDx targeted for?

A

False-negative and false-positive biopsies

37
Q

Describe how a ConfirmMDx test is carried out

A

This is a epigenetic test which looks at the methylation status of genes known to be linked to cancer

38
Q

What genes are looked at in ConfirmMDx?

A

GSTP1

APC

RASSF1

39
Q

How are prostate cancer results confirmed currently?

A

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
Q

Why are false negative test results from biopsies so common?

A

The possibility of extracting tissue with cancer using a thin needle is relatively small

41
Q

What is an OncomineDx test?

A

Personalised therapy genomic test involving stratisfying patients to therapy groups depending on their genomic changes

42
Q

Why is it important to appropriately administer the correct medication to the correct patient group?

A

A lot of therapies are high risk and can do more harm than good

43
Q

What was the first FDA-approved test used for stratifying patient groups to correct therapies?

A

OncomineDx test for non-small cell lung cancer

Selects which patients with lung cancer are eligible for treatment with specific FDA-approved drugs

44
Q

What is the current method for monitoring a patients’ response to therapy?

A

CT scan

45
Q

What are the disadvantages of using CT scans to monitor the patients’ response to a therapy ?

A

Small risk through increased X-ray exposure

Expensive

Takes time report

46
Q

How can genomic technologies be used to replace CT scans in monitoring the response of a patient to a treatment?

A

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
Q

How are cfDNA sequencing techniques better at looking at the progression of a tumour that single markers?

A

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
Q

What are the cells that originate from the original event called?

A

Clonal cells

49
Q

What are the cells that originate from secondary events leading to intatumoural heterogeneity called?

A

Subclonal cells

50
Q

What drives the heterogeneous response of a tumour to therapy?

A

Intratumour heterogeneity

51
Q

Why is it important to understand the difference between clonal and subclonal mutations?

A

Because this determines the use of targeted therapies

Targeted therapies are less successful against subclonal mutations compared to clonal mutations

52
Q

Examples of hormone receptors targeted for cancer therapy

A

BCR-ABL

EGFR

Oestrogen receptors

53
Q

What drug targets the BCR-ABL muation?

A

Imatinib

Tyrosine kinase inhibitors

54
Q

What drug targets the EGFR mutation?

A

Gefitinib

Tyrosine kinase inhibitors

55
Q

What drug targets the oestrogen receptor?

A

Tamoxifen

56
Q

What is the only way that targeted therapies can be effective?

A

If all the tumour cells express the mutation you are targeting

57
Q

In which cancer is the BCR-ABL mutation found?

A

Chronic myeloid leukemia

58
Q

What cancer is BRCA asscociated with?

A

Breast cancer

59
Q

Where is BRCA normally expressed?

A

Breast and other tissue

60
Q

What type of gene is BCRA?

A

Tumour suppressor gene

Involved in repairing damaged DNA

61
Q

What is the inheritance of BRCA?

A

Inherited

62
Q

What is the probability of developing breast cancer if you have abnormal BRCA genes?

A

80% risk by the age of 90

63
Q

What is the probability of developing ovarian cancer if you have abnormal BRCA genes?

A

55%

64
Q

Which company patented BRCA testing?

A

Myriad

In 1994

65
Q

What has happened following Myriad’s patent on BRCA testing?

A

In 2013, the US supreme court ruled that a naturally occurring DNA segment is not able to be patented

66
Q

What was the problem with Myriad’s patent on BRCA testing?

A

It was almost impossible to get a second opinion of the test result as no other lab could independently test for BRCA mutations

67
Q

What act protects against insurance discrimination?

A

GINA

Genetic information nondiscrimination act

68
Q

Describe the case of Pet Reilly

A

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
Q

What is gene therapy?

A

The introduction of normal genes in place of missing or defective ones in order to correct the germline or genetic disorders

70
Q

What is an adenovirus?

A

Inserts a new gene into a cell

If integrated, the new gene will make a functional protein to treat a disease

71
Q

In which diseases is gene therapy particularly useful?

A

In single-gene diseases

72
Q

When was the first time gene therapy provided first somatic treatment?

A

1993

73
Q

Diseases cured through gene therapy

A

ADA-SCID

CLL

Retinal dystrophy

Melanoma

74
Q

What, apart from gene therapy, is another targeted therapy being developed?

A

CAR-T cells

The future of cancer treatment

75
Q

Potential disease to be treated by gene therapy

A

DMD

First gene therapy trials have been approved

76
Q

How have chickens been used to make vaccines?

A

Chickens modified to make IFN a 2a

Can be extracted from eggs and used for therapy

Genomics (9 decks)

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