Pharmacogenomics 2 Flashcards
What are the different types of variations in the genome ?
Single nucleotide polymorphisms - most common
Deletion/insertion
Tand em repeat
Copy variation number
What is a single nucleotide polymorphism ?
It is a single nucleotide alteration
- sometimes they don’t make any difference
The frequency at whihc they occur is 12000000a this is good because they can be used to determine why someone has a disease or if they have a genetic predisposition to a disease
What is a deletion/insertion variation ?
Deletion or insertion of 1-1000 nucleotides
The frequency at which they occur is >1000000
What is tandem repeat variation ?
Repeat of 2-1000 nucleotides
Eg like the CAG repeat in huntingtons
Occurs at a frequency of >500000
What is a copy number variation ?
Deletion/multiplication of regions >1kb - occurs in large regions
- this often occurs in cancer and this causes the cell to stop growing
What are synonymous SNP ?
Is a nucleotide difference in mRNA coding sequence that doesn’t alter the amino acid encoded
What is a non-synonymous SNP?
Is a nucleotide difference in mRNA coding sequence that does alter the amino acid sequence
What are the methods to study polymorphisms ?
Candidate gene approach
Candidate pathway gene approach
Genome wide association studies
Next generation sequencing
What are the advantages of candidate gene approach ?
Focuses on genes with known or proposed biological functions if resources are limited
Capable of identifying polymorphisms with low allele frequency
Allows deep ressequencing on interesting candidate genes in the post GWAS phase
What are the disadvantages of candidate gene approach ?
May potentially miss important genes
A priori knowledge of candidate gene is required
What are the advantages of candidate pathway gene approach ?
Only genes of biological functions are tested
Only requires a small number of samples
Association information obtained on genes known to be relevant to drug
What are the disadvantages of candidate pathway gene approach ?
Not comprehensive
A priori knowledge of candidate genes and/or pathways required
What are Gs advantages of genome wide association studies ?
A complete unbiased picture of the genome
No prior hypotheses required
What are the disadvantages of genome wide association studies ?
Large numbers of samples required
Lack of info about gene function
Insensitive to both structural and rare variants
What are the advantages of next generation sequencing ?
Least expensive for genome wide coverage per variant
Individual needs only to be sequenced once
Can identify causative snp
What are the disadvantages of next generation sequencing ?
Missing variations within large stretches of highly duplicate DNa High levels of noise Large numbers of samples are required Lack info about gene function Cost
What is a major issue with candidate gene approach and candidate pathway gene approach ?
They are biased
What exactly is next generation sequencing ?
Enables HTS to sequence genomes
- enables you to look at the whole genome to find changes
What is transformational technology -iPSC?
Induced pluripotent stem cells
Can take human cells from adults and convert the, to stem cells - these can then be differentiated into other cells
They vm be used to model diseases
It will help to develop better treatments and test them safely
What does full sequencing of a patients genome and then computer analysis of all the SNPs allow ?
It can help determine the causes of diseases
Help to determine whether a patient has an increased susceptibility to disease
Help to determine whether a patient will have aversive or therapeutic response to a treat,net
It would enable tailor made prescriptions
Why are SNPs so important ?
Account for 90% of all human genetic variation
Occur every 100 to 300 bases along the 3 billion base human genome
May have no effect but could be used as a marker
May have different effects
- coding region- may affect proton function or stability
- non coding region of RNA can affect processing or stability of mRNA
- promoter region - can affect where expressed when expressed or the level of expression
What is microarray analysis currently been used in ?
Used as part of cancer research
- easy to get tumour samples
- therefore normal cell samples and tumour samples can be compared, deomonstrating changes in genes expressiion levels
What could the research using microarray anayaldis in cancer be helpful for ?
Because all cancers are different, different drugs should be better to treat different ones
- therefore it could be used to determine the best drugs to treat a patient based upon the genome sequence of their tumour
What is the example where specific treatment for a tumour has been carried out ?
Identified adenocarcinoma proliferation was driven activity of the protooncogen RET
Stabilised the disease using protein kinase pathway inhibitors for 7 months
New lesions then appeared
Nine new mutations discovered and therapeutic resistance seen because of activation of the MAPK and AKt pathway
- there was upregulation of he genes involved in producing ERK1 whihc is involved in cell proliferation - therefore they inhibited the overactive pathway which initially worked but then another tumour was produced
What was the RET inhibited used ?
Sunitnib
After the formation of the new tumour what treatmemt was then used ?
Once new lesions formed then hey changed treatment to sorafenib and sulindac
Stabilised for a few months and then another tumour developed - further upregulation of of the RET pathway and increases on the AKT pathway
What did the expression of genes in tumours tell us?
Showed us it is feasible to sequence patient and tumour DNA and to look at gene expression levels
- analyse the changes in gene expression
We can interrogate the vast amount of data we get back
And make sensible conclusions
What are the variabilities between individuals and our bodies repsonses to a drug ?
Metabolism/removal- we can have variations in enzymes that metabolise drugs which can affect half life of drugs - therefore this affects the dosing in different individuals
Effect- individuals will have variations in receptors and enzymes - the targets for drugs to interact with - this will affect the response
What are cytochrome p450s important for ?
Important for phase 1 drug metabolism
- oxidations, hydroxylation, carboxylation and reduction - genes can affect the rates of these reactions
What is included in phase 2 metabolism !
Acetylation Methylation Sulphation Glucuronidation These are different types of modification
What are cytochrome p450s involved in ?
Involved in metabolism of over 100 drugs
What does the cytochrome CYPD26 enzyme cause ?
It is highly polymorphics - over 75 different alleles and frequency varies with ethnicity Therefore individuals can be - poor metabolisers - intermediates metabolisers - normal - extensive metabolised - normal - ultra rapid metabolisers
In humans what are the variations in drug metabolism caused by CYP2D6 ?
Pm - the concentration rises to very high levels that’s are toxic and can remain in the body for a long time
Im- drug reaches relatively high levels for quite a long time and can cause some toxic effects
Em- they reach the therapeutic window and then it drops quite quickly
Um- metabolisers it too quickly so it doesn’t reach therapeutic window
How could we provide a personalised drug regime ?
If we knew each point at which an individual’s genome sequence varied from the norm and if we knew the affect of each variation on the drug response
- individuals will be required to take more or less of a drug dependent upon the genome to enable them e gain the most beneficial effects
