Molecular Pathology Flashcards
What is molecular pathology
The use of molecular techniques in pathology to help diagnose
What is genomics
Part of molecular pathology which involves using only sequencing to look for abnormality in dna or rna
What are the 3 ways in which molecular pathology impacts patients
- Diagnostic
- Prognostic
- Predivtive- to help personalise treatment
How do we diagnose tumours with molecular techniques
- Look down the microscope - will show if high grade or low grade
- Apply a immunohistochemistry- show what the tumour is e.g sarcoma
- Molecular testing- can tell the type of sarcoma
How does molecular pathology help to determine prognosis in high stage of low stage breast cancer
- 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
What are the 3 ways in which we can personalise treatment with molecular pathology
- Molecular marker helps determine type chemotherapy to give
- Molecular markers help tell is the patient will benefit from immunotherapy
- molecualr markers help determine if they can recieve targeted molecular therapy
What are the 3 types of molecule alteration that we can look at
- Large scale abnormalities of chromosome structure
- Small scale abnormalities of the DNA sequence e.g point mutations
- Abnormalities of protein expression
What are the small scale sequence changes in a dna
Substitution
Insertion
Deletion
What is substitution
Replacing a base to a different one
What is insertion
Imserting a base into the sequence
What is deletion
Deleting a base
What is a oncogene
A gene that when is activated can cause cancer
What is a tumour supressing gene
Gene that will prevent from developing a cancer
What will happen if a mutation occurs in a tumour supressing gene
It can predispose to developing cancer
What are the 2 ways in which we can detect small scale sequence changes
- Targeted pcr
2. Sequencing
What is a targeted pcr
Using probes that are specific to the pre-determined mutations of interest
In targeted pcr what mutation will you detect
Specifc mutation of that probe
What is sequencing
Sequencing the tumour dna and comparing to a normal reference
What are the 2 types of large scale chromosomal abnormalities that can occur
Translocation
Amplification
What is translocation
Swapping segments of chromosome
What is amplification
When you amplift a gene segment of dna so there are extra copies of it that you shouldnt have
What are the 2 ways of identifying large scale chromosomal abnormalities
FSH
Sequencing
What is FSH (fluorscence in situ hybridisation)?
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
What is sequencing
Sequence the gene and compare with the reference gene
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
What does a real time pcr involve
Using probes that detect specific pre-specified mutations we are looking for
What are the disadvantage of real time pcr
You cant detect mutations that you are not looking for therefore can miss mutations
What does FISH help us to detect
Translocation
Amplification
What does FISH involve
Using fluorescently labelled probes to look for specific DNA sequences that you are interest in
What is a next genereation sequencing
- You start with extracted patient dna from the tumour
- We amplify the dna so there are many copies
- Randomly chop the dna into little fragments
- We sequence the little fragments in parallel and see if there are mutations
What are the disadvantage of next generation sequencing
Time consuming
Requires more tissue
To carry out NGS what do we need
Bioinformatics
What does bioinformatics help with
What out if the variant is geuine and is the mutation drivew cancer growth
How many copies of alleles are there for one gene
2 - one from mother and one from father
In sporadic cacner how are the alleles knocked out
By random chnave throughout life
When does sporadic cancer usually occur
Later on in life
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
When does genetic cancer syndrome occur in life
Early life
In genetic cancer syndrome what becomes defective
Dna repair
Apoptosis
What can be involved in dna repair
Mismatch repair
Homologous recombination
What is involved in apoptosis
P53
What syndrome do you get if there is a problem with the mismatch repair system
Lynch syndrome
What problem do you get there is a problem with homologous recombination
BRCA
What syndrome do you get if there is a defective p53 in apoptosis
Li fraumeni syndrome
What is lynch syndrome
When you inherit a mutation in the mmr gene
You then acquirew the second mutation in mmr gene
How do we diagnose lynch syndrome
Mmr immunohistochemistry
What can lynch syndrome occur in
Colorectal and endometrial cancer
What is the management of lynch syndrome
Surveillance: regular 2 yearly colonoscopy to detect early
Prevention- extended colectomy
Which genes are involved in homologous recombination for dna repair
BRCA1
BRCA2
What is homologous repair
Reparing dna stranded breaks
What cancer does BRCA1 mutation predispose you to
Breast
Ovarian
What cancer does BRCA2 predispose you to
Pancreatic
Prostate
Ocular
Melonoma
What are the ways in detecting BRCA1/2 mutations
- Tumour testing: sequencing tumour which will detect spordic and germ line mutation
- Non tumour testing: sequencing BRCA1/2 gene from patient dna and will only show germline mutation and not sporadic (this is present in tumour)
What is the management of BRCA1/2
- annual mammogram
Prevention; prophylactic bilateral mastectomy ans salpingo-oopherectomy to eliminate risk of breast and ovarian cancer
What is li fraumeni syndrome
Mutation in the TP53 gene that encodes P53 protein
What is the normal role of P53
- Become activated when the cell is under stress e.g dna damage
- P53 causes the cell cycle to stop and activated dna repair mechanims or apoptosis if it cant be repair
If p53 is not working properly due to mutations what can occur
Develop cancer
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)
What is the management of li fraumeni syndrome
- survelliance
- prevention: prophylactic bilateral mastectomy
