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Molecular Pathology Flashcards

1
Q

What is molecular pathology

A

The use of molecular techniques in pathology to help diagnose

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2
Q

What is genomics

A

Part of molecular pathology which involves using only sequencing to look for abnormality in dna or rna

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3
Q

What are the 3 ways in which molecular pathology impacts patients

A
  1. Diagnostic
  2. Prognostic
  3. Predivtive- to help personalise treatment
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4
Q

How do we diagnose tumours with molecular techniques

A
  1. Look down the microscope - will show if high grade or low grade
  2. Apply a immunohistochemistry- show what the tumour is e.g sarcoma
  3. Molecular testing- can tell the type of sarcoma
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5
Q

How does molecular pathology help to determine prognosis in high stage of low stage breast cancer

A
  • High stage breast cancer is treated with surgery and then chemotherapy
  • low stage breast cancer needs oncotype dx testing which will show how likely the tumour will come back

If low risk: no chemotherapy- good prognosis
If highr risk: chemotherapy needed- bad prognosis

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6
Q

What are the 3 ways in which we can personalise treatment with molecular pathology

A
  1. Molecular marker helps determine type chemotherapy to give
  2. Molecular markers help tell is the patient will benefit from immunotherapy
  3. molecualr markers help determine if they can recieve targeted molecular therapy
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7
Q

What are the 3 types of molecule alteration that we can look at

A
  1. Large scale abnormalities of chromosome structure
  2. Small scale abnormalities of the DNA sequence e.g point mutations
  3. Abnormalities of protein expression
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8
Q

What are the small scale sequence changes in a dna

A

Substitution
Insertion
Deletion

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9
Q

What is substitution

A

Replacing a base to a different one

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10
Q

What is insertion

A

Imserting a base into the sequence

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11
Q

What is deletion

A

Deleting a base

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12
Q

What is a oncogene

A

A gene that when is activated can cause cancer

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13
Q

What is a tumour supressing gene

A

Gene that will prevent from developing a cancer

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14
Q

What will happen if a mutation occurs in a tumour supressing gene

A

It can predispose to developing cancer

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15
Q

What are the 2 ways in which we can detect small scale sequence changes

A
  1. Targeted pcr

2. Sequencing

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16
Q

What is a targeted pcr

A

Using probes that are specific to the pre-determined mutations of interest

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17
Q

In targeted pcr what mutation will you detect

A

Specifc mutation of that probe

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18
Q

What is sequencing

A

Sequencing the tumour dna and comparing to a normal reference

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19
Q

What are the 2 types of large scale chromosomal abnormalities that can occur

A

Translocation

Amplification

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20
Q

What is translocation

A

Swapping segments of chromosome

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21
Q

What is amplification

A

When you amplift a gene segment of dna so there are extra copies of it that you shouldnt have

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22
Q

What are the 2 ways of identifying large scale chromosomal abnormalities

A

FSH

Sequencing

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23
Q

What is FSH (fluorscence in situ hybridisation)?

A

When we use fluroscener markers to look at the location of specific genes within the genome
If they are in normal locations there isnt translocation
If there are in abnormla location we know there has been translocation

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24
Q

What is sequencing

A

Sequence the gene and compare with the reference gene

25
How does sequencing tell us translocation has occured
You go to the humna genome reference and look up the abnormal sequence which should belong to a different gene
26
What does a real time pcr involve
Using probes that detect specific pre-specified mutations we are looking for
27
What are the disadvantage of real time pcr
You cant detect mutations that you are not looking for therefore can miss mutations
28
What does FISH help us to detect
Translocation | Amplification
29
What does FISH involve
Using fluorescently labelled probes to look for specific DNA sequences that you are interest in
30
What is a next genereation sequencing
1. You start with extracted patient dna from the tumour 2. We amplify the dna so there are many copies 3. Randomly chop the dna into little fragments 4. We sequence the little fragments in parallel and see if there are mutations
31
What are the disadvantage of next generation sequencing
Time consuming | Requires more tissue
32
To carry out NGS what do we need
Bioinformatics
33
What does bioinformatics help with
What out if the variant is geuine and is the mutation drivew cancer growth
34
How many copies of alleles are there for one gene
2 - one from mother and one from father
35
In sporadic cacner how are the alleles knocked out
By random chnave throughout life
36
When does sporadic cancer usually occur
Later on in life
37
What happens to the alleles in genetic cancer syndrome
You inherit a defective copy of one allele, you then get a sporachic change to knock out the second allele
38
When does genetic cancer syndrome occur in life
Early life
39
In genetic cancer syndrome what becomes defective
Dna repair | Apoptosis
40
What can be involved in dna repair
Mismatch repair | Homologous recombination
41
What is involved in apoptosis
P53
42
What syndrome do you get if there is a problem with the mismatch repair system
Lynch syndrome
43
What problem do you get there is a problem with homologous recombination
BRCA
44
What syndrome do you get if there is a defective p53 in apoptosis
Li fraumeni syndrome
45
What is lynch syndrome
When you inherit a mutation in the mmr gene | You then acquirew the second mutation in mmr gene
46
How do we diagnose lynch syndrome
Mmr immunohistochemistry
47
What can lynch syndrome occur in
Colorectal and endometrial cancer
48
What is the management of lynch syndrome
Surveillance: regular 2 yearly colonoscopy to detect early | Prevention- extended colectomy
49
Which genes are involved in homologous recombination for dna repair
BRCA1 | BRCA2
50
What is homologous repair
Reparing dna stranded breaks
51
What cancer does BRCA1 mutation predispose you to
Breast | Ovarian
52
What cancer does BRCA2 predispose you to
Pancreatic Prostate Ocular Melonoma
53
What are the ways in detecting BRCA1/2 mutations
1. Tumour testing: sequencing tumour which will detect spordic and germ line mutation 2. Non tumour testing: sequencing BRCA1/2 gene from patient dna and will only show germline mutation and not sporadic (this is present in tumour)
54
What is the management of BRCA1/2
- annual mammogram | Prevention; prophylactic bilateral mastectomy ans salpingo-oopherectomy to eliminate risk of breast and ovarian cancer
55
What is li fraumeni syndrome
Mutation in the TP53 gene that encodes P53 protein
56
What is the normal role of P53
1. Become activated when the cell is under stress e.g dna damage 2. P53 causes the cell cycle to stop and activated dna repair mechanims or apoptosis if it cant be repair
57
If p53 is not working properly due to mutations what can occur
Develop cancer
58
How do we diagnose tp53 mutation/ li fraumeni syndrome
- tumour testing- sequence for tp53 in the tumour | - non tumour testing: sequence tp53 in patients dna (blood)
59
What is the management of li fraumeni syndrome
- survelliance | - prevention: prophylactic bilateral mastectomy

Cellular Pathology (19 decks)

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