Pharmacogenomics Exam 3 Flashcards
What is an allele?
An allele is one pair of genes. It is commonly used to describe alternative forms of a gene at a given locus (locus is the location of a gene or DNA marker on a chromosome).
What is a genotype?
The genotype refers to the set of alleles for a particular gene or locus. A genotype describes two alleles on homologous chromosomes. Like A/a, B/b etc.
What is a haplotype?
This is a combination of set of alleles that are inherited on the same chromosome. It is the set of alleles or SNPs on the chromosome.
What is a diplotype?
A diplotype describes two haplotypes on homologous chromosomes. It is a pair of haplotypes. Two haplotypes (one from each parent) form a diplotype. For example, an individual might inherit a maternal haplotype of A B C D and a paternal haplotype of a b c d, forming a diplotype of A B C D/a b c d.
What does homozygous mean?
Homozygous refers to the genotype. It means that there are two identical alleles.
What does heterozygous mean?
Heterozygous refers to the genotypes. It means that are two different alleles.
What are the different types of genetic variations?
Polymorphisms, mutations, and single nucleotide polymorphisms (SNPs)
What is a polymorphism?
This is a type of genetic variation. A polymorphism is an allele present in more than 1% of the population. It contributes to diversity within a population and is not usually associated with severe disease.
What is a mutation?
This is a type of genetic variation. This is a rare allele found in less than 1% of the population. It is commonly due to environmental factors or DNA copying errors.
What is the difference between a polymorphism and a mutation?
Polymorphisms occur in more than 1% of the population while mutations occur in less than 1% of the population.
What is an SNP?
This is a type of genetic variation when one nucleotide or base pair is substituted for another at a particular position within the genome.
What are the types of coding region variants?
- Synonymous variant
- Nonsynonymous variant
- Missense (part of nonsynonymous)
- Nonsense (part of nonsynonymous)
What is a synonymous variant?
This is a coding region (exon) variant. It is a silent polymorphism. It is when a single nucleotide changes in the coding region of the DNA sequence and it does not lead to changes in the AA sequence.
What is a nonsynonymous variant?
This is a coding region (exon) variant. It is a nonsynonymous polymorphism. This is when a single nucleotide change in the coding region now specifies a different AA that may lead to a potential change to protein activity or function.
What is a missense variant?
This is a type of nonsynonymous variant where there is a single nucleotide change leading to a different AA in the protein.
What is a nonsense variant?
This is a type of nonsynonymous variant where there is a single nucleotide change resulting in a stop codon.
What are the functional outcomes for nonsense coding region variants?
Nonsense variants in coding regions introduce premature stop codons, leading to truncated, nonfunctional proteins or mRNA degradation via nonsense-mediated decay, often resulting in loss of gene function.
What are the functional outcomes for an insertion frameshift mutations?
Insertion frameshift mutations disrupt the reading frame, leading to altered amino acid sequences and often premature stop codons, resulting in dysfunctional or nonfunctional proteins.
nsertion frameshift mutations occur when one or more nucleotides are added to the DNA sequence, disrupting the reading frame of the gene. This shift alters how the codons are read during translation, often leading to a completely different and usually nonfunctional protein, with possible premature stop codons.
What are the functional outcomes for a deletion frameshift mutations?
A deletion frameshift mutation occurs when one or more nucleotides are removed from the DNA sequence, disrupting the reading frame of the gene. This causes a shift in how codons are read during translation, leading to altered amino acid sequences and often a nonfunctional protein with possible premature stop codons.
What do variants in the coding region do to genes?
Variants in the coding region can alter the protein sequence, potentially affecting its function. They may lead to changes like missense mutations, truncations, or altered expression levels.
What do variants in the noncoding region do to genes?
Variants present in the noncoding regions may alter transcription factor binding to either increase or decrease transcription.
What do variants in the promoter region do to genes?
Changes in promoter and enhancer sequences can impact transcription factor binding and subsequent gene transcription.
What are the major types of chromosomal variants?
Inversion and translocation
What is inversion?
This is a chromosomal mutation where a small or large amount of bases in DNA are reversed. It can result in loss of function.
What is translocation?
This is a chromosomal mutation where a segment of one chromosome is transferred to another non-homologous chromosome (not the same chromosome).
What is pharmacogenetics?
How a variation in one single gene influences a response to a drug.
What is pharmacogenomics?
How all of the genes (the genome) can influence response to a drug. This is more of a global term.
What part of PK can genetic variants influence?
Pharmacokinetics genetic variants influence all of ADME! Genetic variants in metabolizing drug enzymes can impact the rate of drug metabolism. Genetic variants in transporters could impact the rate of drug absorption, distribution, and excretion
What part of PD can genetic variants influence?
Pharmacodynamic variants can modify drug targets.
What is the number of clinically actionable germline genes?
Only 30 genes are considered to be clinically actionable germline genes.
What is a germline genetic variation?
Germline genetic variations are inherited genetic variants that are present in every cell in the body that have a nucleus.
What is a somatic genetic variation?
Somatic genetic variations are not inherited but acquired. They are not present in every cell.
What is the difference germline and somatic genetic variation?
Germline variants are inherited and present in every cell while somatic variants are not inherited but acquired and not present in every cell.
What are X-linked dominant inheritance patterns?
Females have 2 X chromosomes so a mutation in one copy is enough to cause that disorder. Males have 1 Y and 1 X so a mutation in only one copy of the gene causes the disorder.
What are X-linked recessive inheritance patterns?
In females, the mutation would need to be present on both copies to have the disease but for males only one copy needs to be present for the disease. This is why males have a higher prevalence of X-linked variants.
Male are XY and females are XX. How are Y-linked inheritance patterns passed down?
Only males have the Y chromosome so mutations can only be passed from father to son.
What is the main goal of the CPIC?
CPIC’s goal is to address the barrier to clinical implementation of pharmacogenetic test by creating, curating, and posting freely available, peer-reviewed, evidence-based, updatable, and detailed gene/drug clinical practice guidelines. It gives evidence on how to apply pharmacogenetic results into patient care.
What are the basic levels of evidence for PharmGKB?
Level 1A- high evidence of variant-drug combination
Level 1B- high evidence of variant-drug combination
Level 2A- moderate evidence
Level 2B- moderate evidence
Level 3- Low evidence
Level 4- preliminary evidence
What is the drug Rasburicase?
Rasburicase is a recombinant urate oxidase enzyme that breaks down excess uric acid seen in tumor lysis syndrome present in hematological cancers where rapidly dividing cells lyse rapidly and release uric acid.
Why is glucose-6-phosphate dehydrogenase important when taking the drug rasburicase?
Rasburicase breaks down the uric acid from dying cancer cells into H202 and CO2. These products will enter the pentose phosphate pathway and glucose-6-phosphate dehydrogenase (G6PD) will break them down into NADPH and protect cells from oxidative stress.
How do variants in glucose-6-phosphate dehydrogenase result in rasburicase drug toxicity?
Variants in G6PD make the enzyme decrease or loss its function. Loss of this enzyme due to variations leads to increased susceptibility to stressors.
What types of samples are collected for genomic DNA testing?
- Blood (DNA from lymphocytes)
- Saliva/ cheek brushing
- Whole saliva
What are the main steps of PCR?
The goal of PCR is to made a bunch of DNA!
- Denaturing
- Annealing
- Extension
DAE
Explain the denaturing steps of PCR.
This is when the mixture of DNA with other components like primers, nucleotides, Taq polymerase, and mix buffer, are heated and it makes the double stranded DNA come apart into single strands.
Explain the annealing steps of PCR.
This is when the DNA mixture for the PCR is cooled down so the primeres can anneal a complementary DNA sequence for the single strand of DNA.
Explain the extension steps of PCR.
This is when the DNA mixture is warmed up to activate the DNA polymerase Taq enzyme. It will find the primer bound to single strand DNA and begin adding base pairs to create newly formed double stranded DNA.
What is Sanger Sequencing?
This is a method to detect differences in individual alleles. It uses dideoxynucleotide chain terminators in the PCR to create specific size PCR products. It has to be user defined gene target. The results will produce those exact DNA sequence.
What is the TAQMAN AS reaction?
This is a method to detect differences in individual alleles. This uses a combination of DNA primer and allele specific fluorescent probes to detect the specific alleles. It is fairly easy, cost effective, medium throughput, and allows you to tell the presence or absence of specific base pair variants.
What is a genechip/microassay?
This is a method to detect differences in individual alleles. This is also called hybridization. It uses allele specific oligonucleotides hybridization and allows looking at thousands of polymorphisms at one time. It promotes discovery this way.
What is Next-generation sequencing?
This is a method to detect differences in individual alleles. This is also known as high-throughput screening or massive parallel sequencing. It allows for sequencing of DNA and RNA very quickly and cheaply.
What are the 4 main steps of next-generation sequencing?
- Library preparation
- Cluster amplification
- Sequencing
- Alignment and data analysis
What is GWAs?
This is a genome wide association study that seeks statistical associations between genetic loci and a phenotype of interest. Basically, a phenotype is selected and the DNA data set is made from all different people and SNPs associated with those phenotypes can be identified.
What is the basic requirement needed to perform a GWA study?
GWAs need to use well defined cohorts of subjects with and without the qualitative trait.
How is an activity score from a functional variant calculated?
The activity score of a variant is calculated by adding up the values associated with each allele present.
How is the activity score for functional variants ranked?
> 1= increased function
1 or >1= normal or increased function
1= normal function
0.5= decreased function
0= no function
What is the definition of the metabolic phenotype UM?
UM is an ultra-rapid metabolizer that can occur due to an increased number of copy variants and/or polymorphisms increasing function.
What is the definition of the metabolic phenotype EM/NM?
EM/NM used to be called normal metabolizer but is now called extensive metabolizer. This is considered normal or wild-type with 1* alleles.
What is the definition of the metabolic phenotype IM?
IM is an intermediate metabolizer where enzyme function is decreased but still present. One allele could be decreased or non-functional and the other allele is normal.
What is the definition of the metabolic phenotype PM?
PM means poor metabolizer meaning that enzyme function is severely decreased or non-functional. This typically occurs when there are no functional alleles present.
What is the interaction between CYP2C9 and Celecoxib?
Around 75% of the metabolism of Celecoxib is done by CYP2C9.
How do the CYP2C9*2 and 3 variants impact Celecoxib metabolism, efficacy, and toxicity?
CYP2C9*2 and *3 result in decreased function of the enzyme that metabolizes Celecoxib. This results in higher blood concentrations of the drug resulting in a higher chance for toxicities like GI bleeds.
What is unique about CYP2D6?
CYP2D6 is the main non-inducible CYP450 enzyme meaning certain drug can not upregulate or downregulate it. Most changes in the activity of this enzyme is due to genetic variations.
What is the drug Isoniazid?
This is an antibiotic used to treat tuberculosis. It is an inactive prodrug that is activated inside of bacteria.
What are the interactions between NAT2 and Isoniazid?
Isoniazid is metabolized in via two pathways; NAT2 and hydrolysis. The products formed in the hydrolysis pathway are toxic metabolites to the liver.
How do slow NAT2 variants impact Isoniazid metabolism, efficacy, and toxicity?
Slow acetylators will have higher concentrations of Isoniazid and metabolism of the drug will more likely follow the hydrolysis pathway leading to the production of more toxic metabolites. It is better to give slow acetylators less of this drug.
How do fast NAT2 variants impact Isoniazid metabolism, efficacy, and toxicity?
Fast acetylators are more prone to fail treatment as the body is rapidly inactivating the drug to be excreted. In order to TX to be effective, more of this drug should be given to the person.
What is unique about the phase 2 metabolism enzyme UGT1A1?
It is the sole enzyme responsible for the breakdown of bilirubin.
How does atazanavir interact with UGT1A1?
Atanzanir, an HIV protease inhibitor, actually inhibits UGT1A1 which will increase plasma bilirubin levels.
How do extensive metabolizers for UGT1A1 impact those prescribed Atazanavir?
It does not impact them much as the Atazanavir will not shut off all function.
How do poor metabolizers for UGT1A1 impact those prescribed Atazanavir?
Additional suppression of UGT1A1 by Atazanavir can drive bilirubin concentrations high enough to cause bilirubin related disorders like jaundice.
What are ABC transporters?
One of the major superfamilies of transporters. This is an ATP dependent EFFLUX transporter. They can go against concentration gradients.
What are SLC transporters?
One of the major superfamilies of transporters. It can be both active and passive transport and is the major INFLUX transporter (some can act as efflux though).
What are the 3 types of SLC transporters?
- Membrane channels- large proteins that function as pores
- Facilitative transporters- facilitated diffusion that follows the concentration gradient
- Secondary active transporters- similar to facilitated diffusion but has two substances binding. It can be symport or antiport.
What are the characteristics of SLCO1B1 (OATP1B1)?
It is an organic anion transporter that functions in influx that is mainly expressed in hepatocytes. It transporters compounds from the blood into the liver.
How do common variants in SLCO1B1 impact its functional effect?
Variations that change the function of this transporter will reduce the transport function.
What is unique about the *5 allele for SLCO1B1?
With the *5 allele, there is a decrease in the number of transporters on the cell surface which inhibits their ability to transport substances into hepatocytes.
What is the MOA of statin drugs?
Statins are used to treat primary hypercholesterolemia. It inhibits the production of endogenous cholesterol production by inhibiting HMG-CoA reductase.
How is the TCA drug amitriptyline metabolized?
Amitriptyline itself is active and it selective for serotonergic neurons. It can be converted to another active molecule called nortriptyline by CYP2C19 which is more selective for NE neurons. Amitriptyline can also be converted to inactive by CYP2D6.
What does vismodegib target in the SHH signaling pathway?
Vismodegib is a SMO antagonist that stops the constant cellular proliferation signalling of Sonic Hedgehog Pathway. This works in cells that have their mutation at the PTCH1 site which would normally negative feedback and stop SMO.
