Precision Medicine in Action: Pharmacogenomics & Exome Sequencing
Audra Bettinelli, MS, CGCGeneDx
Disclosures
• I am an employee of GeneDx, Inc., a wholly‐owned subsidiary of OPKO Health, Inc.
• Basic Principles • Guidelines• Mechanisms of Action• Clinical Applications• Case Examples
Agenda
https://www.trueprocess.com/future‐healthcare‐precision‐medicine/
Pharmacogenetics/Pharmacogenomics (PGx)
• The study of how gene(s) affect an individual's response to medications
• Use genetic information to guide drug targeting and dosing to maximize efficacy and reduce toxicity
• Genetic testing for SNPs/CNVs predicts enzymatic activity for:• Drug targeting: whether a different category of
medication would be better to prescribe for the patient’s symptoms
• Drug efficacy: how well the medication has the intended effect in treating the patient’s symptoms
• Drug toxicity: how likely the patient will have an adverse reaction to the medication
Pharmacogenomics (PGx) ‐ definitions
PGx Nomenclature
• *(star) Alleles
• Name of the allele not the variant
• *1 is wild type or fully functional allele
• *2, *3, *4, etc. are haplotypes containing one or more variants
• Results are typically reported as a diplotype– Example: CYP2C19 *2/*17
• Sometimes nucleotide changes are used instead of * alleles, eg. rs4149056
Types of Genes Analyzed
• Drug Transporters (eg. channels)• Variants affect drug absorption, distribution, and elimination
– Example: SLCO1B1
• Drug Targets (eg. receptors)• Variants affect drugs ability to bind or interact
– Example: RYR1
• Drug Metabolizing Enzymes (DMEs)– Genes involved in the metabolism (breakdown) of a drug
• Examples: Cytochrome P450 (CYP) enzymes i.e. CYP2D6
Focus on clinical utility
• Variants tested are common SNPs found throughout the population
• Reports do not focus on variant interpretation
• How can results can be used in clinic?
Current Practice: Trial and Error
Adverse Drug Reactions
Spear et al., 2001; PMID: 11325631, Lazarou et al., 1998; PMID: 9555760, Foster et al., Ann Intern Med 2003; Moore & Mattison, JAMA Int Med 2016; https://assurexhealth.com/, Elzagallaai et al., 2017; PMID: 28295234
20% of readmissions
FDA
”Pharmacogenomics can play an important role in identifying responders and non‐responders … avoiding adverse events, and optimizing drug dose.”
https://www.fda.gov/Drugs/ScienceResearch/ucm572698.htm
Hypersensitivity Skin Reactions: Carbamazepine
“Serious and sometimes fatal dermatologic reactions, including toxic epidermal necrolysis (TEN) and Stevens‐Johnson syndrome (SJS), have been reported with Tegretol treatment.”
• 1 to 6 per 10,000 Caucasians• ~10 times higher risk in some Asian countries• 15% of population in Hong Kong, 10% Taiwan, 4% North China• Strong association with HLA‐B*1502
http://www.pharma.us.novartis.com/product/pi/pdf/tegretol.pdf
Stevens‐Johnson Syndrome
https://hubpages.com/health/I‐Could‐Have‐Died‐Surviving‐Stevens‐Johnson‐Syndrome
https://drimanfirmansyah.com/tag/stevens‐johnson‐syndrome/
Carbamazepine: Serious Dermatologic Reaction
http://www.pharma.us.novartis.com/product/pi/pdf/tegretol.pdf
Data to support PGx use
• Applicable to everyone!– >90% of people carry at least one PGx‐relevant variant
• Of 1,000 FDA‐approved drugs, ~100 are candidates for PGx testing based on variants in 12 genes
Dunnenberger et al., Annu Rev Pharmacol Toxicol 2015Haga & Solomon, Pharmacogenomics 2016
Type of Medications
Cardiology Neurology OncologyAntiarrhythmics Antiepileptics Chemotherapeutics
Anticoagulants Antidepressants Corticosteroids
Antihypertensives Antipsychotics Immunosuppressants
Platelet Aggregation Inhibitors Corticosteroids Opioids
Statins Muscle Relaxants
Psychiatry General PracticeAntidepressants Antidiabetics
Antipsychotics General Anesthetics
Benzodiazepines Oral Contraceptives
Stimulants Proton Pump Inhibitors
Antivirals/Antiretrovirals
When Can PGx Testing be Used?
• Preemptively, prior to prescribing medications
• Guide drug therapy for conditions that fail to respond to treatment
• To alter the medication or dose in an effort to decrease side‐effects
Relling et. al., Clin. Pharmacol. Ther; 2011 Dunnenberger et. al., Annu. Rev. Pharmacol. Toxicol; 2015
Institutions implementing PGx Testing
Practice Guidelines
FDA has PGx information on the label of >100 medications• Example: Warfarin label contains specific dosing recommendations based on genotype
Black box warnings• Example: Codeine label contains warning for use in children
Table of PGx in drug labeling• fda.gov/drugs/scienceresearch/researchareas/pharmacogenetics/ucm083378.htm
www.fda.gov
Creates PGx clinical practice guidelines
19 guidelines for 33 gene‐drug pairs
Freely available, peer reviewed, evidence based, and routinely updated
cpicpgx.org
CPIC guidelines
PGx Prescribing information
CPIC
DPWG
CPN
Drug Labeling
FDA
Canada
Europe
Japan
Clinical Annotations
Summary of evidence
Quality rating for evidence
Other Clinical Tools
Pathways
Gene summaries
Variant annotations
www.pharmgkb.orgM. Whirl‐Carrillo, et al.. Clinical Pharmacol & Therapeutics (2012) PMID: 22992668
Strength of Evidence
https://www.pharmgkb.org/page/clinAnnLevels
Multiple Factors Affect Drug Response
Warfarin
https://www.pharmgkb.org/pathway/PA145011113
Warfarin Guidelines
Johnson et al. Clin Pharmacol Ther. 2017www.WarfarinDosing.org
Mechanisms of Action
Pharmacology
• Absorption• Distribution• Metabolism• Excretion
http://blog.gyrosproteintechnologies.com/spinblog/adme‐of‐therapeutic‐proteins
Drug Activity
Active Drug• Active parent drug• Immediate effect• Enzymes convert to inactive for excretion
Prodrug
• Inactive parent drug• Enzymes convert to active metabolite• Additional enzymes may convert the drug for excretion
• Example: Codeine
Properties of Both
• Active parent drug and active metabolite• Example: some SSRIs
http://www.pharmatips.in/Articles/Pharmaceutical‐Prodrug.aspx
Drug Metabolizing Enzymes (DMEs)
Normal Metabolizers
http://www.pharmatips.in/Articles/Pharmaceutical‐Prodrug.aspx
Active Drugs• Average risk of side effects• Average risk of treatment failure
Prodrugs• Average risk of side effects• Average risk of treatment failure
Normal Metabolizers
Rapid/Ultrarapid Metabolizers
Active Drugs• Less active drug in system• At risk for treatment failure
Prodrugs• More active drug in system• At risk for side effects/toxicity
Intermediate/Poor Metabolizers
Active Drugs• More active drug in system• At risk for side effects/toxicity
Prodrugs• Less active drug in system• At risk for treatment failure
Case study: Phenytoin
Used in treatment of epilepsy
Dosing can be complex
Caudle et al., 2014 25099164
Case Example2 year old female with history of epilepsy
Initially received valproate, then later oxcarbazepine
Admitted to the ED in status epilepticus
Treated with diazepam and phenytoin
Develop dizziness, nystagmus, ataxia, and excessive sedation
Plasma PTH levels were higher than expected
Patient was a CYP2C9 Poor MetabolizerDorado et al., 2013 22641027
CYP2C9
Expressed in the liver
Highly polymorphic
2 common alleles associated with decreased enzyme activity
Caudle et al., 2014 25099164
Phenytoin and CYP2C9
Phenytoin is metabolized by
CYP2C9
Poor metabolizers have reduced
function
Higher plasma concentrations of
phenytoin
At risk for dose related side effects
Sedation, ataxia, dizziness, nystagmus, nausea, cognitive
impairment
Caudle et al., 2014 25099164
Dosing Guidelines: Phenytoin
CYP2C9
Normal Metabolizer
Recommended maintenance
dose
Intermediate Metabolizer
25% reduction in starting dose
Poor Metabolizer
50% reduction in starting dose
Caudle et al., 2014 25099164
What to look for in a report
Which gene‐drug pairs are included?
Is your patient’s drug(s) included?
How are results returned? Are they understandable and clear?
Does the report include the level of evidence for recommendations?
Does the patient have access to the reports and patient‐friendly materials?
What Does a Report Look Like?
Page 1 of 28!
Don’tPanic!
PGx Reports: Elements to Look for
1. Table of Medications– metabolizer status or phenotype
2. Summary of the genotype3. Detailed prescribing guidance
PGx Reports: Table of Medications
• Often use a stop light approach for prescribing guidance
Green: prescribe as directed
: prescribe with caution
Red: prescribe with extreme caution / consider an alternative
Example Report
Prescribing GuidanceCodeine: Level of Evidence: Strong
CPIC guideline: consider alternative analgesic not affected by CYP2D6 (morphine, nonopioid) FDA Label: Codeine containing products should not be used in children younger than 12
Medication TableMedication Comments
Codeine Prescribing Alert
Genotype/Phenotype Summary
Gene Diplotype Phenotype
CYP2D6 *1/*1xN Ultrarapid Metabolizer
Case Example: Codeine
Boy with history of snoring and sleep apnea
Underwent elective adenotonsillectomy
Sent home on acetaminophen syrup with codeine
Found unresponsive and resuscitation efforts failed
Genotyping revealed a duplication of the CYP2D6 gene
Ultrarapid metabolizer phenotype
Morphine at autopsy exceeded therapeutic levels
Ciszkowski et al., 2009 PMID: 19692698
Codeine• Codeine: opioid analgesic used for relief of mild to severe pain– Prodrug converted by CYP2D6 to morphine
Crews et al., 2014; 24458010
CYD2D6
Crews et al., 2014; 24458010; guidelines video on pharmgkb.org
Allele Duplications
Allele Deletions
Loss of function Alleles
Reduced function Alleles
Increased Enzymatic Function Decreased Enzymatic Function
Ultrarapid Metabolizers Intermediate and Poor Metabolizers
Codeine Dosing Guidelines
CYP2D6 Ultrarapid Metabolizers
•Metabolize codeine quickly to morphine
•More morphine than expected
•At risk for toxicity•Guideline: consider alternative analgesic not affected by CYP2D6 (morphine, nonopioid)
CYP2D6 Intermediate Metabolizer
•Slowly metabolize codeine to morphine
•Reduced levels of morphine than expected
•At risk of treatment failure •Guideline: Use label recommended age/weight dosing monitor for nonresponse
CYP2D6 Poor Metabolizers
•Slowly metabolize codeine to morphine
•Greatly reduced levels of morphine than expected
•Likely risk of treatment failure
•Guideline: consider alternative analgesic not affected by CYP2D6 (morphine, nonopioid)
Crews et al., 2014; 24458010;
CPIC Guidelines
look up guidelines at pharmgkb.orghttps://cpicpgx.org/genes‐drugs/
Codeine and Children
Aka et al., 2017; PMID 29099060
Codeine with acetaminophen was approved by the FDA for use in children over 3 years
In April of 2017, the FDA included a black box warnings:
Do not use in children younger than 12
Do not use in adolescents 12‐18 with obesity, obstructive sleep apnea, or severe lung disease
Warning against use in breast feeding mothers
PharmacoDx Reports: ADHD
PharmacoDx Reports: Detailed Summary
Evidence Summary
Prescribing Guidance
Strength of Evidence
Predicted Genotype
PharmacoDx Reports: Statins
PharmacoDx Reports: Antidepressants
PharmacoDx Reports: Detailed Summary
Evidence Summary
Prescribing Guidance Strength of
EvidencePredicted Genotype
PharmacoDx Reports: Genotype/Phenotype Summary
Prescribing Guidance
Strength of Evidence
Predicted Genotype
Benefits and Limitations of PGx testing
Benefits• Reduces trial and error• Applicable to everyone• Reduces the genetic variable in drug response• Prescribing guidance is well‐vetted by independent, empiric data
Limitations• Genetics is not the only factor influencing drug‐response• No PGx test on the market captures all relevant medications or genes• Very little research to date on efficacy in pediatric care• Need more research on specific ethnic groups• Clinical Implementation is challenging
Exome Sequencing
• What is Exome Sequencing (ES)?– Massively parallel sequencing (Next Generation sequencing) of
the protein‐coding regions of the human genome• What is ES used for?
– Can be used to identify the underlying molecular basis of a genetic disorder in an affected individual
– May also identify secondary or incidental findings, clinically significant variants not obviously related to the patient’s current phenotype
• What are some advantages to ES? – Cast a wider net, inclusion of candidate genes– Free reanalysis– High diagnostic yield
Case Example15yo boy presents with ALL, hepatosplenomegaly and liver dysfunction
Trio exome sequencing performed
Initial result non‐diagnostic
Bone marrow aspirate sent for molecular testing
Results showed homozygous multi‐exon deletion in FANCA
Interpretation complicated by mixture of blasts and normal cells
Providers reached back out to GeneDx
Patient consent obtained
Case Example continuedRush del/dup for FANCA requested
Exome data from blood showed heterozygous paternally inherited deletion
Del/dup testing performed and confirmed het deletion in buccal DNA
Updated exome report released <1 week after request
Providers now working with lab that sequenced blasts
Does the patient have a somatic loss of heterozygosity in FANCA?
If so, he is a candidate for a PARP inhibitor if he experiences a relapse
Patient consent obtained
Questions?