Define intention to treat analysis
A comparison of the treatment groups which includes all patients as originally allocated, post-randomisation. Inclusion occurs regardless of deviations occurring post-randomisation.
Preserves the prognostic balance generated by allocation
Calculate the QALY for someone with 2 years, with full QoL
2 x 1 = 2 QALYs
What is the DAVID software used for?
Shows patterns in families of genes, and the statistical probability that RNA is involved in the process
How would you confirm which gene is the mutant gene?
Another cell should be transfected
Outline the stages of a drug trial
1. Idea 2. Basic research 3. Drug development 4. Clinical trials- phases 1-3 5. Regulatory approval 6. Patient care
What are the two parts of CRISPR
Guide RNA that recognizes specific traces of viral DNA and attaches to it The enzyme Cas9 that cuts the DNA
The aim of phase 1 clinical trials
-ensure there are no major safety issues -ensure it can reach the targeted body area -ensure it can remain long enough to deliver treatment -gain preliminary evidence that it could offer therapeutic value
What is the declaration of Helsinki?
Ethical principles for medical research involving human subjects.
Describe the method of PCR
- select the unique sequence and form a forwards and reverse primer with it
- mix primers and DNA sample
- Heat to 96*C and cool to 60*C
- Add DNA polymerase and dNTPs to synthesise new DNA strand
- Heat to 72*c for DNA polymerase to bind
- Repeat (x30)
- Separate DNA using electrophoresis on agarose gel
How would you calculate sensitivity
Give 2 benefits of RCT
- Good randomization will “wash out” any population bias
- Easier to blind/mask than observational studies
- Results can be analysed with well-known statistical tools
- Populations of participating individuals are clearly identified
Definition: Gene Therapy
The introduction of genes into an afflicted individual for therapeutic reasons
Give 2 benefits of a case report
- Can help in the identification of new trends or diseases
- Can help detect new drug side effects and potential uses (adverse or beneficial)
- Educational – a way of sharing lessons learned
- Identifies rare manifestations of a disease
Describe the animal model for synthetic heroin
1. MPTP given to marmozets destroying dopaminergic neurons 2. can then study effects of Parkinson's in animals 3. several therapies consequently discovered 4. drugs/treatments then tested
Give 2 benefits of a systematic review
- Exhaustive review of the current literature and other sources
- Less costly to review prior studies than to create a new study
- Less time required than conducting a new study
- Results can be generalized and extrapolated into the general population more broadly than individual studies
- More reliable and accurate than individual studies
- Considered an evidence-based resource
Define Case Report
An article which describes and interprets an individual case
Randomly assigns participants to groups (intervention or control). The only expected difference should be the condition
If the A average cost is £2,000, and the B average cost is £3,000, and the A average QALY is 2 and the B average QALY is 4, calculate the £ per QALY gained
3,000/4 - 2,000/2 = 1,000/4 = £500 per QALY gained
True or false: SNPs are a cause of disease
False- they are associated with it
cDNA coding for any gene introduced into a cell
Trisomies are ....
conditions where there are 3 chromosomes present instead of 2
What is the purpose of RNA sequencing
Measures changes in gene expression
Difference Between Knockout and Transgenic
- knock-out animals is to eliminate functional copies of a gene, we must specifically target the natural copy of the gene - unlike the transgenics, where insertion can be at a random location
What is the difference between PCR and qPCR
RT-PCR used to amplify RNA to cDNA. Quantitative PCR- used to measure the specific amount of target DNA (or RNA) in a sample
Define Pedigree of Family
A diagram that shows the occurrence and appearance or phenotypes of a particular gene or organism and its ancestors from one generation to the next,
How are imaging methods used in diagnostic tests/screens
• All use combinations of parameters: shape, size, number, specific molecule • Scoring systems often used, subjectivity can be an issue, expert opinion often required
What are the two assumptions PCR depends on?
- viral sequence <300 bp long
- 18-20 bp of viral DNA not found elsewhere in the human genome
Give 2 disadvantages of a case report
- Cases may not be generalizable
- Not based on systematic studies
- Causes or associations may have other explanations
- Can be seen as emphasizing the bizarre or focusing on misleading elements
Explain how the Wakefield MMR study contravened ethical guidelines and demonstrated a conflict of interests
- ‘MMR vaccine gives you autism’
- Falsified by several papers who disproved this
- ‘All media lies’
- VERY limited paper- strong conclusions drawn from weak evidence
- The lancet then proved no correlation, but the doubt was already in the public mind
- Wakefield was being funded through solicitors seeking evidence to use against vaccine manufacturers
- So entirely biased/flawed from the start
- Children were picked by Wakefield to try and support his hypothesis, but he misreported his findings i.e. some kids he said had diseases didn’t
What do GWAS look for?
Single nucleotide polymorphisms (SNPs) which are over-represented in diseased patients.
Give one aim of gene therapy
to insert a normal allele of the defective gene into the somatic cells of the tissue affected by the disorder traceable to a single defective gene
Patients or physicians do not know which treatment group they are assigned too- helps to prevent bias
What is Karl Popper’s theory of falsification
1. Come up with an idea/hypothesis 2. Test it to destruction 3. You cannot prove a hypothesis is true- you can corroborate it 4. If you can prove a hypothesis is false- this is falsification.
Which type of study would be best for identifying potential causes of disease?
Give 2 benefits of a case-control study
- Good for studying rare conditions or diseases
- Less time needed to conduct the study because the condition or disease has already occurred
- Lets you simultaneously look at multiple risk factors
- Useful as initial studies to establish an association
Describe what is meant by a paradigm shift
Contradictory evidence builds up, so a new paradigm is proposed and tested.
Who is included in an intention to treat analyses
Everyone- no one is excluded
What are the steps in a trio analysis
- deep sequence both parents
- deep sequence proband
- observe differences- heterozygotic change
give 2 disadvantages of a systematic review
- Very time-consuming
- May not be easy to combine studies
Drugs can also be tested in vitro- but why is in vivo better?
in the body there are -cell to cell contacts/co-culture -3D not 2D matrix structure -complex signals e.g. hormones -matrix flexibility -normoxic conditions
What is GWAS
an approach used in genetics research to ASSOCIATE specific genetic variations (genotype) with particular diseases (or phenotype)
Describe trio analysis
Sequence the affected proband and both unaffected parents to look for de novo changes in the child.
Definition: Transgenic Animals
an organism whose genome contains DNA introduced from another organism of the same or a different species
State Koch's 4 postulates
- The germ is present in all with the disease (not healthy)
- Microorganisms must be isolated from a diseased organism and grown in pure culture
- Cultured microorganisms should cause disease in healthy tissue
- The specific disease must be reproduced when a pure culture of the bacteria is inoculated into a healthy susceptible host.
Define case-control study
compares patients/those with disease or outcome of interest with controls who don't. Retrospectively looks at how frequently exposure to a risk factor is present.
Define cohort study
One or more samples followed prospectively and status evaluations with respect to a disease are measured
How does a NIPS work
Via next generation sequencing- e.g. counts number of reads on chr21 (compare fetal and maternal ratios)
Give 3 disadvantages of using a disease model
- strain of mouse will affect genes
- different circadian rhythms
- scientists stress mice
- cage is hyper-hygienic -animals not human so not same mechanisms
What is the cut-off value per person for an ICER to be accepted?
What are Single nucleotide polymorphisms (SNPs)
single base pair differences in the sequences of a particular region of DNA from one individual compared to another of the same species or population
Section of the genome coding for a protein
How would you calculate specificity
patients are assigned to groups recieving different treatments- helps to reduce bias whether intentional/unintentional
Give 2 disadvantages of a cohort study
- Cohorts can be difficult to identify due to confounding variables
- No randomization, which means that imbalances in patient characteristics could exist
- Blinding/masking is difficult
- Outcome of interest could take time to occur
Define single blind
usually refers to the patient being blinded but not the administering clinician
Explain how and why the Nuremberg trials, the Tuskegee Study and the Alder Hey tissue scandal contributed to modern ethical guidelines and the Human Tissue Act
- -New guidelines were introduced as a result
- -ethics approval committees were established
- -Huge public mistrust of the scientific community/conspiracy theories
Give 2 disadvantages of RCT
- Expensive in terms of time and money
- Volunteer biases: the population that participates may not be representative of the whole
- Does not reveal causation
If blinding is not possible, what could happen instead
observers not involved in the patient's care may be used
Define True Positives
have the disease and correctly test positive
What does GWAS stand for?
Genome wide association studies
5' GGCTATCCG 3' 3' CCGATAGGC 5'
If both strands of this DNA could be transcribed:
- the two strands would be transcribed from left to right
- the two strands would be transcribed from right to left
- The upper strand would be transcribed from left to right and the lower strand would be transcribed from right to left
- The upper strand would be transcribed from right to left and the lower strand would be transcribed from left to right
d) The upper strand would be transcribed from right to left and the lower strand would be transcribed from left to right
Describe Phase 2 clinical trial
Only if phase 1 is successful.
Occurs in a larger group of people, and often contains patients who have the targeted condition.
Drug performance may be compared against pre-existing treatment/placebo
Steps to Develop a Transgenic Animal
- Remove eggs and fertilize them in vitro
- Clone the desired gene from the donor organism
- Inject the cloned DNA directly into the nuclei of the fertilized eggs
- Some of the cells express the foreign gene
- Developed embryos are implanted into the surrogate mother, once born are transgenic animals
What is a NIPS
Non-invasive prenatal screen (NIPS) for trisomy
Define systematic review
provides a comprehensive review of all relevant studies on a clinical/health related topic question
State the 3 NICE economic considerations
- Cost-effectiveness is determined by an analysis of the ratio of cost to health effect (QALY)
- Considers how many people are affected by the condition and the dehabilitation
- Pharma/Biotech industry must mitigate the risk of a negative recommendation of NICE
What are volatile organic compounds (VOCs)
Metabolic products present in sweat, faeces, urine and breath
Define genetic linkage
a measure of how resistant to recombination a genetic marker and phenotype are
The aim of phase 3 clinical trials
- demonstrate safety and effectiveness of new medicine/vaccine
- confirm dosage levels
- identify side-effects/contraindications
- compare against existing treatments
How to calculate a QALY
Life Expectancy x HR-QoL
Purpose of Transgenic Animals
(1) make proteins in large amounts for pharmaceutical purposes (2) study gene expression (3) GMO (longer self life, bigger animals, more food)
What are the steps of GWAS
- 1. DNA purified from both controls and patients
- Polymorphisms should be individually mapped
- These can then then be analysed and over-representations (SNPs) spotted
Define False positives
do not have the disease but incorrectly test positive
What are the 7 declarations of Helsinki
- Societal/Scientific Value
- Scientific validity
- Fair subject selection
- Favourable risk-benefit ratio
- Respect for subjects
- Informed consent
- Independent review
Define False negatives
have the disease but incorrectly test negative
Describe the purpose of the SCID-NOD mouse
no immune system, so allows tissue grafting can also inject human bone marrow
Define knock-out model
genes can be removed to identify their effects/physiological functions -this can test treatments + reveal developmental role
Give 2 disadvantages of a case-control study
- Problems with data quality because they rely on memory/recall
- Not good for evaluating diagnostic tests because it’s already clear that the cases have the condition and the controls do not
- It can be difficult to find a suitable control group
What is a conditional knock out
those in which a gene is lost only in particular tissues and/or at a particular time
Define knock-in model
Specific changes in a gene can be added to an organism/introduce specific mutations
Give 2 benefits of a cohort study
- Subjects in cohorts can be matched, which limits the influence of confounding variables
- Standardization of criteria/outcome is possible
- Easier and cheaper than a randomized controlled trial (RCT)
what are some advantages to CRISPR
quicker, cheaper and more efficient
What is cell free DNA
• DNA released into the blood • Tumour and normal cells • Non-invasive test
What is combined to generate a trisomy risk score
nuchal translucency, [PAPP-a], [HcG] and mothers age
a gene editing tool which uses the Cas 9 system
How to calculate Incremental Cost Effectiveness Ratio (ICER)
Difference in costs/Difference in QALYs = Cost per QALY gained
True or False: Pseudoscience provides falsifiable hypotheses; science does not.
False- Science provides falsifiable hypotheses; pseudoscience does not.
Purpose of Knockout Animals
Remove both alleles of a normal gene the animal express to compare the value of the gene - done to understand the purpose of the gene and its effect on the phenotype
Define double blind
Neither patient or clinician know which treatment is randomised to
What are the steps of RNA sequencing
- RNA isolated RNA reverse
- transcribed into cDNA
- DNA sequenced
- Analysed as a graph to see which genes are expressed
Why are accurate diagnostics tests important
• Correct therapy can be used • Early detection of diseased can give a better prognosis • We need good tests and know how to interpret them
Give 3 benefits of using a disease model
- small/fast breeding
- easily edit genes
- can replicate human symptoms/phenotype
- share a similar genome
- 3D model
determine the primary structure of nucleotides
When would an amniocentesis be offered?
risk is >1 in 150
Define True negatives
do not have the disease and correctly test negative
If it takes 18 cycles of qPCR to detect a RAS signal in a control line, and 14 cycles in a cancerous line, how many cycles difference is there? and what does this mean?
4 cycles- so cancerous has more RAS signals than control
What are some uses of PCR
- Detection of viral and bacterial DNA in tissue samples.
- Determining the size of a sequence of DNA between two ‘primers’.
- Production of DNA for making genetic tools (e.g. expression vectors) or DNA sequencing.
Give some uses of qPCR
- Quantifying viral load.
- Comparing amounts of DNA.
- Comparing amounts of specific mRNA (following conversion to DNA by RT)
Give some uses of RNA sequencing
- Comparative gene expression.
- Finding out which genes are regulated in a particular disease or in response to a specific stimulus.
- An un-biased method.
Give some uses of DNA sequencing
- Mutation detection
- Pathogen identification
- Gene identification
What are some uses of Genome sequencing
- Gaining all data on genetic variation.
- Identification of spontaneous mutations
Give some uses of GWAS
- Understanding pathways involved in complex diseases.
- Assessment of individual’s disease risk.
What is Trio analysis used for
Identification of the cause of rare genetic diseases.
What is a use of Western Blotting
- Determine changes in protein level.
- Disease/ tissue specific expression.
What is a genetic screen for?
Identification of genes important for a particular physiological or developmental process.
What is ELISA used for