Exam 1 Flashcards
Clopidogrel gene of interest
CYP2C19
Warfarin gene of interest
CYP2C9, VKORC1
Statins gene of interest
SLCO1B1
Phenytoin gene of interest
CYP2C9, HLA-B
TCA/SSRI gene of interest
CYP2C19, CYP2D6
Thiopurines gene of interest
TPMT
Tacrolimus gene of interest
CYP3A5
Atazanavir gene of interest
UGT1A1
Pharmacogenomics definition
The study of whole genomic effects on drug response
Pharmacogenetics definition
The study of individual gene-drug interactions
How many nucleotide bases are in the Human Genome
3 billion
How many nucleotide bases are in the average gene
3000
Estimated total number of genes
20-30 thousand
Reasons for a pharmacogenetic treatment
Improve efficacy, reduce toxicity, predict non-responders, and minimize the burden on the healthcare system
Precision medicine definition
Tailored disease prevention and treatment taking into account differences in an individual’s genes, environment, and lifestyle
Precision Therapeutics definition
Customizing medications to patients, categorized by molecular and cellular biomarkers in order to improve treatment outcomes
Amount of variation between individuals’ genetic makeup
0.1-0.5%
When did Mendel publish his work on inherited factors (genes)
1866
When was DNA identified by Friedrich Miescher
1869
When did Watson & Crick identify the structure of DNA
1953
When did Vogel introduce the term pharmacogenomics
1959
When did Marshal Nirenberg crack the genetic code for protein synthesis
1961
When was DNA sequencing invented
1975
When was PCR invented
1983
When was the Human Genome launched
1999
When was the Human Genome completed
2003
When was next generation sequencing developed
2007
When was Clinical Pharmacogenetics Implementation Consortium established
2009
When was personalized healthcare initiative announced
2015
Pharmacokinetics definition
What the body does to the drug (defines the exposure to a drug)
Pharmacodynamics definition
What the drug does to the body (defines drug effect)
Intrinsic variables
Pregnancy, race, organ function, lactation, sex, disease, age, genetics
Extrinsic variables
Drug-drug interaction, environment, diet, EtOH, Medical practice, smoking
What is drug response determined by
Genetics, disease, environment, lifestyle, concomitant drugs
What does genetic variation lead to
Changes in drug ADME
Enzyme variation results in
Activation or deactivation
Transporter variation results in
Absorption, distribution, or elimination rates
Receptor variation results in
Drug effect (pharmacodynamics)
Amount of prescription drugs in the US affected by actionable pharmacogenes
18%
Amount of FDA-approved medications affected by actionable pharmacogenes
7%
Possible outcomes of drug therapy
Effective with minimal toxicity, effective with toxicity, failure with minimal toxicity, failure with excessive toxicity
Textbook model: Genome
The book
Textbook model: Chromosome
The chapter
Textbook model: Gene
The sentence
Textbook model: Nucleotide
The letters
Chromosome definition
Cellular structures containing genes
Gene definition
A segment of DNA that contains information for making a protein or RNA molecule
Phenotype definition
The outward characteristic of an individual - the measurable trait
Synonymous SNP
No change in AA previously termed “silent” can alter mRNA stability. Does not change the AA.
Non-synonymous SNP
A nucleotide mutation that alters the AA sequence of a protein
Missense SNP
A change in one DNA base pair that results in the substitution of one AA for another in the protein made from a gene
Nonsense SNP
Insertion of a stop codon truncated incomplete, and usually, nonfunctional protein product –> inactive
CYP2B6*4A - CYP2
Family gene name
CYP2B6*4A - CYP2B
Subfamily gene name
CYP2B6*4A - CYP2B6
Enzyme gene name
CYP2B6*4A - 4
Allele
CYP2B6*4A - A
Suballele
Drug metabolizing enzymes normal/extensive metabolizer phenotype
Combination of normal function and decreased function alleles (fully functional enzyme)
Drug metabolizing enzymes intermediate metabolizer phenotype
Combination of normal function decreased function, and/or no function alleles (decreased enzyme activity)
Drug metabolizing enzymes poor metabolizer phenotype
Combination of decreased function and/or no function alleles (decreased or no enzyme activity)
Drug metabolizing enzymes rapid metabolizer phenotype
Combination of normal function and increased function alleles (increased enzyme activity)
Drug metabolizing enzymes ultra-rapid metabolizer phenotype
Combination of increased function alleles (increased enzyme activity)
What offers genotype-based guidance for drug dosing
Clinical pharmacogenetics implementation consortium (CPIC)
What offers PGx knowledge base (literature, annotation guidance)
PharmGKB
What offers nomenclature resource
PharmVar - Pharmacogene variation concortium
What offers PGx clinical annotation tool
PharmCat
Goal of CPIC
Address the barrier to clinical implementation of PGx tests by creating, curating, and posting freely available, peer-reviewed, evidence-based, updateable, and detailed gene/drug clinical practice guidelines
CPIC grading system - gene/drug pair Rx actionability
A - D
CPIC grading system - Guideline Rx recommendation
Strong, moderate, optional, none
Diplotype definition
Results of a PGx that includes one maternal and one paternal allele
Prodrug slow metabolizer
Poor efficacy
Prodrug rapid metabolizer
Good efficacy, rapid effect
Active drug slow metabolizer
Good efficacy, accumulation of drug
Active drug rapid metabolizer
Poor efficacy
CPIC key assumption
Genotyping will become more widespread where all patients will get PGx tested
Anticoag for CYP2C19: 1/17, 17*/17, 1/1
Clopidogrel standard dose
Anticoag for CYP2C19: 1/2, 1/3, 2/17, 2/2, 2/3, 3/3
Alternative (prasugrel, ticegrelor)
`Anticoag for CYP2C19 UM/RM, NM
Clopidogrel standard dose
Anticoag for CYP2C19 IM, PM
Alternative (prasugrel, ticegrelor)
Pharmacist’s responsibilities in PGx
Educate patient about PGx principles
Advocate for rational and routine use of PGx testing
Elements of a basic understanding of PGx should enable pharmacists to
Recommend PGx testing to aid in drug and dose selection
Design a patient-specific medication regimen based on a patients profile
Educate patients and other healthcare providers on the principles of PGx and indications for testing
Communicate PGx-specific medication recommendations to the healthcare team
PGx online database: PharmGKB detail
Robust: Rx information, drug label, variant, and clinical annotations. Provides links to guidelines
Clinical Practice Guidelines detail
Published annually, worldwide acceptance. Do not advise on who to test, aid in “what to do” with the results of PGx
FDA recourse details
Limited: dated material, lack of clinical utility, interpretation by clinician necessary
Sanger sequencing
Chain termination method. Needs the whole sequence - PCR with radioactive dideoxynucleotides, then gell electrophoresis to separate PCR, then decode the sequence of interest
Sanger sequencing benefits
Conformation of variants
Detects rare or novel SNPs
Sanger sequencing limitations
Low throughput
Not targeted
Next generation sequencing
The standard in clinical dx and research
Pyrosequencing, ion semiconductor sequencing (pH based), and dye sequencing (by ligation) - SOLiD
Next generation sequencing benefits
High throughput
Detects rare or novel SNPs
Able to be targeted
Next generation sequencing limitations
Higher cost
More sophisticated
Informatics needed
Allelic discrimination and detection method
Mostly PCR-based
Discrimination: primer extension, hybridization, ligation, enzymatic cleavage
Detection: Mass spectrometry, fluorescence, chemiluminescence
qPCR benefits
Low cost
High throughput
qPCR limitation
Small # of SNPs/genes
Small # of samples
Known varients only
Microarray/chip benefits
Low cost
High throughput
Many SNPs/genes
Microarray/chip limitations
Known variants only
Small # of samples
What certification is required for clinical labs
Clinical Laboratory Improvement Amendments
Which PGx method would be best to identify a patient’s CYP2C19 status to guide clopidogrel tx
Quantitative PCR
GINA
Genetic Information Nondisclosure Act
GINA definition
Title I: protects individuals against genetic discrimination with respect to health insurance
Title II: Protects individuals against employment discrimination on the basis of genetic information
- employers are prohibited from requesting, requiring, or purchasing genetic information about applicants or employees
- employers prohibited from using genetic information for pay, promotion or job assignments
What does whole exome sequencing not identify
Regulatory and intronic variants
