Exam 1 Flashcards
precision medicine
tailoring disease prevention and treatment taking into account differences in indv genes, environments, and lifestyles
precision therapeutics
customizing medications to pts categorized by molecular + cellular biomarkers to improve treatment outcomes
pharmacogenetics
study of individual gene-drug interactions, usually involving 1 or 2 genes that have a dominant effect on a drug response (simple relationships)
Pharmacogenomics
study of genomic effects on drug response, often using high throughput data (sequencing, SNP chip, expression, etc) - COMPLEX interactions
What determines drug response
genetics
disease
environment
lifestyle
concomitant medications
Effects of genetic variation on medication therapy
varied drug absorption
varied metabolism rates
varied elimination rates
variations in receptors leading to variation in drug effect
Genome
organism’s entire genetic material found in cells, including genes and regulatory elements
Chromosome
Cellular structure containing genes (composed of DNA + proteins)
Gene
segment of DNA that contains info for making protein or RNA molecule
Nucleotide
building block of DNA/RNA including 1 base, 1 phosphate, and 1 sugar molecule
Allele
one of 2+ alternate forms of a gene containing specific inheritance characteristics
Genotype
genetic constitution
Phenotype
outward characteristic
Single Nucleotide Polymorphisms
Common genetic single nucleotide variants resulting from a single base pair change
Synonymous SNP
no change in amino acids, can alter mRNA stability
Non-synonymous SNP
nucleotide that alters amino acid sequence of protein
Missense SNP
change in 1 DNA base pair that results in substitution of one amino acid for another in the resulting protein
Nonsense SNP
results in insertion of stop codon
SNP nomenclature
C for coding DNA sequence (c. 67A>T)
P for protein sequence (p. tryp24cys)
normal/extensive metabolizer phenotype
normal function/decreased function alleles -> fully functional enzyme
intermediate metabolizer phenotype
combo of normal function and decreased function/no function alleles -> slightly decreased enzyme activity
poor metabolizer phenotype
combo of decreased function and no function alleles -> significantly decreased or absent enzyme activity
rapid metabolizer phenotype
combo of normal function and increased function alleles -> increased enzyme activity
ultra-rapid metabolizer phenotype
combo of increased function alleles or >2 normal function alleles -> very increased enzyme activity
CPIC
Clinical Pharmacogenetics Implementation Consortium that posts gene/drug clinical guidelines
CPIC level A/B
have evidence for prescribing action
CPIC levels C/D
Do not have adequate evidence for prescribing action
CPIC recommendation levels
Strong, moderate, optional, none
Which drugs does CPIC provide guidelines for
- drugs with a PharmGKB clinical annotation level of evidence 1a,1b,2a,2b
- drug with PharmGKB level/FDA drug label recommendations of actionable PGX genetic testing
PharmGKB
pharmacogenomics knowledge base - more scientific than clincial
What population is used to determine pgx recommendations in package inserts
a “ballpark estimate” of the population
Benefits of PGX guided decision making
decrease adverse reactions
optimize med response
improve clinical outcomes
decrease length of treatment
decrease total healthcare costs
Gene chips
use panels of polymorphisms to calculate relative risk/benefit ratio of therapeutic course for individual patient
diplotype
includes one paternal and one maternal allele
Genes that affect warfarin metabolism
CYP 2C9
VKORC1
Cardiovascular drugs w/ PGX recommendations
clopidogrel
warfarin
simvastatin
Hypersensitivity reaction PGX testing recommendations
abacavir
allopurinol
carbamazepine
Neuro drugs with PGX recommendations
phenytoin
opioids
SSRIs
TCAs
Oncology drugs with PGX recommendations
TPMT
DPYD
Sanger sequencing benefits
confirmation of variants
detects rare/novel SNPs
high accuracy
Sanger sequencing limitations
low throughput
not targeted
Next Generation Sequencing
category of several different sequencing methods. Standard in clinical diagnostics and research
Examples of next generation sequencing
pyrosequencing
ion semiconductor sequencing
dye sequencing
Next Gen Sequencing benefits
high throughput
detects rare/novel SNPs
able to be targeted
Limitations of Next Gen Sequencing
high cost
more sophisticated
need informatics
Long Read Sequencing
reads 10,000-2,000,000 base pairs
Long Read Sequencing Limitations
lower accuracy
need improvement in sample preparation/DNA isolation protocols to produce ultralong HMW DNA
Analysis, mapping, and variant calling tools are less mature
scalability is an issue due to duration and # of samples needed
Genotyping
process of determining which genetic variants an individual possesses
QPCR and micro-array
Allelic discrimination strategies
primer extension
hybridization
ligation
enzymatic cleavage
Allelic detection methods
Mass spectrometry
fluorescence
chemiluminescence
qPCR
Quantitative PCR
a type of genotyping
qPCR benefits
low cost
high throughput
qPCR limitations
small number of SNPS/genes
small number of samples
works with known variants only
Microarray/Chip
type of genotyping in which specific probes are fixed to a solid surface and can detect SNPs, CNV, gene expression, and methylation
Microarray benefits
low cost
high throughput
recognizes many SNPs/genes
Microarray limitations
known variants only
small number of samples
FDA approved tests
include companion diagnostics and some direct to consumer tests
What does premarket review of FDA approved tests establish
analytical validity
clinical validity
complexity level
Companion diagnostics
medical device that provides information essential for the safe and effective use of a corresponding drug or biological product
Direct to consumer tests
marketed directly to consumers without involvement of healthcare professional
Direct to consumer test FDA review
tests only reviewed if for “moderate to high risk medical purposes”
Which direct to consumer tests has received FDA marketing authorization
23 and Me
Lab Developed Tests
in vitro diagnostic tests manufactured and used within a single lab
recent framework for oversight from the FDA
CLIA
Clinical Laboratory Improvement Amendments - goal to ensure quality lab testing and is regulated by CMS. CLIA certification is required for clinical PGX labs
CLIA certification levles
CLIA-Waived
Moderate Complexity
High Complexity
CLIA Accreditation (optional)
PGX Lab accredidation bodies
J. Co
College of American Pathologists
PGX professional organizations
College of American Pathologists
Association for Molecular Pathology
Phase 1 Metabolism
oxidation, reduction, hydrolysis
CYP450s
Phase 2 Metabolism
Conjugationreactions
UGTs, TPMT, NAT
Clopidogrel CYP
CYP 2C19
Clopidogrel MOA
pro-drug
binds to P2Y12 receptor to irreversible inhibit platelet aggregation
Clopidogrel ultra-rapid metabolizer
17/17 OR 1/17
Clopidogrel intermediate metabolizer
1/2
Clopidogrel poor metabolizer
2/2
Increased clopidogrel metabolism
increased active drug -> lower platelet aggregation
NAT2 gene
codes for N-acetyl transferase protein -> affects isoniazid acetylation
SLCO1B1 gene
codes for OATP1B1 uptake transporter - affects statin metabolism
521T>C polymorphism
reduces uptake of statin into hepatocytes, increasing serum level
