PharmacoGenetics

Dr Bassi PU

MBBS Lecture Series

Types of Genetic Variants

• A polymorphism is a variation in the DNA sequence that is present at an allele frequency of 1% or greater in a population.
• Two major types of sequence variation are:

-single nucleotide polymorphisms (SNPs)

- insertions/deletions (indels).

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Indels are much less frequent in the genome and are of low frequency in

Single nucleotide polymorphisms (SNPs)

• SNPs are very common in the human population.
• Between any two people, there is an average of one SNP every ~1250 bases.
• Most of these have no phenotypic effect
• Venter et al. estimate that only <1% of all human SNPs impact protein function (lots of in “non-coding regions”)
• Some are alleles of genes.

Pharmacogenetic phenotypes

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• Genetic variations which affects the drug response can be divided in 3 categories:
• 1. Variations affecting Pharmacokinetics .
• 2. Variations affecting Drug receptor/target.

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Definition of Terms

• Tandem Repeat Polymorphisms: Tandem repeats or variable number of tandem repeats (VNTR) are a very common class of polymorphism, consisting of variable length of sequence motifs that are repeated in tandem in a variable copy number

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• Based on the size of the tandem repeat units:
• Microsatellites or Short Tandem Repeat (STR) : repeat unit: 1-6 (dinucleotide repeat: CACACACACACA)
• Minisatellites : repeat unit: 14-100

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Insertion/Deletion Polymorphisms: Insertion/Deletion (INDEL) polymorphisms are quite common and widely distributed throughout the human genome.

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• Mutations are heritable changes in the base sequence of DNA. This may, or may not,¹ result in a change in the amino acid sequence of the protein for which the gene codes

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Definition of Terms

• PHARMACOGENETICS: The effect of genetic variation on drug response, including disposition (PK), safety, tolerability and efficacy (PD).
• PHARMACOGENOMICS: It employs the tools for surveying the entire genome to assess multigenic determinants of drug response. 
• Pharmacogenetics Pharmacogenomics The study of genetic basis for variability in drug response Use of genetic information to guide the choice of drug and dose on an individual basis 

Goals of Pharmacogenetics�

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• The Right Dose of
• The Right Drug for
• The Right Indication for
• The Right Patient at
• The Right Time.

CYP2C19

• AR
• Aromatic hydroxylation of anticonvulsant mephenytoin
• Normal “extensive metabolizers” ( S )- mephenytoin is extensively hydroxylated by CYP2C19 before its glucuronidation and rapid excretion in the urine,
• whereas ( R )-mephenytoin is slowly N -demethylated to nirvanol, an active metabolite
• Poor metabolizers

1. Lack of stereospecific ( S )-mephenytoin hydroxylase activity, so both ( S )- and ( R )- mephenytoin enantiomers are N -demethylated to nirvanol, which accumulates in much higher concentrations.

2. Increase the therapeutic efficacy of omeprazole in gastric ulcer and gastroesophageal reflux diseases

CYP2C9

Relative contributions of different phase II pathways 

PLASMA CHOLINESTERASE DEFICIENCY�

• suxamethonium sensitivity is due to genetic variation in the rate of drug metabolism as a result of a Mendelian autosomal recessive trait.
• short-acting neuromuscular-blocking anaesthetic drug - is normally rapidly hydrolysed by plasma cholinesterase.
• 1 in 3000 individuals fail to inactivate suxamethonium rapidly and experience prolonged neuromuscular block if treated with it; this is because a recessive gene gives rise to an abnormal type of plasma cholinesterase.
• The abnormal enzyme has a modified pattern of substrate and inhibitor specificity.
• It is detected by a blood test that measures the effect of the inhibitor dibucaine, which inhibits the abnormal enzyme less than the normal enzyme.

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• Heterozygotes hydrolyse suxamethonium at a more or less normal rate, but their plasma cholinesterase has reduced sensitivity to dibucaine,
• intermediate between normal subjects and homozygotes.
• Only homozygotes express the disease: they appear completely healthy unless exposed to suxamethonium (or, presumably, closely related chemicals) but experience prolonged paralysis if exposed to a dose that would cause neuromuscular block for only a few minutes in a healthy person.

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�PLASMA CHOLINESTERASE DEFICIENCY�

• Variations affecting PK Suxamethonium and Pseudocholinesterase deficiency Genes affecting NAT2 Polymorphism of the TPMT (thiopurine S-methyltransferase) gene UGT polymorphism

•Due to mutation, there is formation of abnormal cholinesterase.

•The individuals fail to inactivate Suxamethonium rapidly and experience prolonged neuro- muscular blockade.

•Frequency: 1/3000 19

•Rate of drug acetylation varied in different population as a result of balanced polymorphism.

•Acetylation by N acetyltransferase (NAT 2) enzyme

•Slow acetylators: peripheral neuropathy

•Fast acetylators: Hepatotoxicity (wrt Isoniazid)

•AR trait

•Rapidly degraded mutant enzyme and consequently deficient S -methylation of 6-MP, thioguanine, and azathioprine, required for their detoxification.

•High risk of thiopurine drug-induced fatal hematopoietic toxicity.

•Toxic side effects due to impaired drug conjugation and/or elimination (eg, the anticancer drug irinotecan)

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A. Atypical Plasma Cholinesterase

• a rapid acting, rapid recovery muscle relaxant - 1951
• usual paralysis lasted 2 to 6 min in patients
• occasional pt exhibited paralysis lasting hrs
• cause identified as an “atypical” plasma cholinesterase

Hydrolysis by pseudocholinesterase

choline

succinylmonocholine

A. Atypical Plasma Cholinesterase��

• Atypical plasma cholinesterase has 1/100 the affinity for succinylcholine as normal enzyme
• occurs in 1:2500 individuals
• tested clinically via the abilityof dibucaine to inhibit esterase hydrolysis of benzoylcholine
• Family studies indicate variability in plasma cholinesterase activity consistent with 2 allelic, autosomal, codominant genes
• other variant forms exist as well

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DRUG ACETYLATION DEFICIENCY�

• drug acetylation varied in different populations as a result of balanced polymorphism
• The characteristic of fast or slow acetylation is controlled by a single recessive gene associated with low hepatic acetyltransferase activity.
• White populations contain roughly equal numbers of ‘fast acetylators’ and ‘slow acetylators’
• Other ethnic groups have different proportions of fast and slow acetylators

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Pharmacogenetics and drug receptor targets

• Pharmacogenetics and drug receptor targets
• Inactivation of MTHFR (methylenetetrahydrofoltate reductase) Serotonin receptor polymorphism
• Beta receptor polymorphism
• Polymorphism in HMG-CoA reductase
• Polymorphism in Ion channels
• Polymorphism in ACE
• GI toxicity in case of Methotrexate
• Responsiveness to Depression
• Responsiveness to Asthma
• Degree of lipid lowering following Statins
• Cardiac arrhythmias
• Renal Function Test

Polymorphism- modifying diseases �

• MTHFR polymorphism is linked to homocysteinemia, which in turn affects thrombosis risk. These polymorphisms do not directly affect the PK or PD of prothrombotic drugs, such as glucocorticoids, estrogens, and asparaginase, but may modify the risk of the phenotypic event (thrombosis) in the presence of the drug.
• Polymorphisms in ion channels (e.g., HERG, KvLQT1, Mink, and MiRP1) increase the risk of cardiac arrhythmias, which may be accentuated in the presence of a drug that can prolong the QT interval (e.g., macrolide antibiotics, antihistamines).

�Clinically available Pharmacogenomic tests ��

Various type of test are �

1. HLA gene tests

a) ABACAVIR & HLAB*5701

b) ANTICONVULSANTS & HLAB*1502

c) CLOZAPINE & HLA-DQ 1*0201

2. Drug metabolism related gene test

a) THIOPURINE & TPMT

b) 5-FLUOROURACIL (5-FU) & DPYD

c) TAMOXIFEN & CYP2D6

d) IRINOTECAN & UGT1A1*28

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Various type of test

3) Drug target related gene test

1. Trastuzumab & HER 2
2. b) DASATINIB, IMATINIB & BCR-ABL 1

4) Combined (metabolism & target) gene test

a) WARFARIN & CYP2C9 + VKORC 1 GENOTYPING

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• Pharmacogenetics & Drug development

Due to individual variation…

• 20-40% of patients benefit from an approved drug
• 70-80% of drug candidates fail in clinical trials
• Many approved drugs removed from the market due to adverse drug effects
• The use of DNA sequence information to measure and predict the reaction of individuals to drugs.
• Personalized drugs
• Faster clinical trials
• Less drug side effects Pharmacogenetics

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Pharmacogenomics/genetics in Drug Discovery & Development

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“A lot of the failures we had in the industry in Phase III were not because these molecules didn’t work but because they only work in a specific patient population ’’Mackay says.

Today, more than 60% of AstraZeneca’s drug development programs have some personalized component, such as a biomarker or diagnostic. Further more, a new medicine that is “safe, effective, and differentiated is not enough, ”Mackay says. “You need to be all of those three things and have somebody pay for your medicine.” C

Role of pharmacogenetics in drug development

1. Can identify new targets. For eg.

1. Genome wide assessment could identify genes whose expression differentiate inflammatory process.
2. A compound could be identified that can change expression of gene responsible for inflammatory process.
3. That compound can serve as starting point for anti inflammatory drug development

Role of pharmacogenetics in drug development

2) Pharmacogenetics may identify subsets of patients who will have a very high or a very low likelihood of responding to an agent.

- a) So drug can be tested on selected patients will respond & low possibility of ADRs.

- b) This will reduce the time & cost of drug development.

3) Pharmacogenomics can identify the subset of patient with higher risk of serious adverse effect.

- So these patients can be avoided in trials 

GeneSight

• GeneSight is a genetic test that helps healthcare providers take personalized approach to prescription
• Because gene influence the way a person responds to specific medications, the medication may not work the way for every body
• GeneSight uses DNA gathered with simple check swab. The analysis help to individualized medication example

GeneSight Psychotropic Drugs

• For people who have been on drugs diagnosed with depression, anxiety or other conditions
• The gest is able to individualize effects of respond to antidepressant

GeneSight Analgesics

• For patients who have been diagnosed with acute or chronic pain. Analgesic gene test can affect possible respond to to opioids, NSAIDs & Muscles relaxants
• Others incudes
• GeneSight ADHD
• GeneSight Folic acid conversion in the body
• GeneSight
• GeneSight Inform DUAL ISH

• FDA has approved new test to help determineif breast cancer patients are candidate for HERCEPTIN treatment
• These allows the test called DUAL ISH , allows for measurement of number of copies of HER2 in tumour tissues

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Personalized Drugs

• Herceptin (breast cancer, target: Her2/neu)
• Erbitux (colorectal cancer, target: EGFR)
• Tarceva (lung cancer, target: EGFR)
• Strattera (attention-deficit/hyperactivity disorder, Metabolism: P4502D6)
• 6-MP (leukemia, Metabolism: TPMT)
• Antivirals (i.e. resistance based on form of HIV)
• etc. and the list is growing rapidly ...

• Pharmacogenetic data can be submitted to FDA during IND & NDA application.

• If pharmacogenetics studies on animals are available then pharmacogenetic tests should be included in clinical trials.

• During NDA application sponsor should submit the pharmacogenetic data voluntarily, intended to put on label of the drug

• Chemogenomics, or chemical genomics, is the systematic screening of targeted chemical libraries of small molecules against individual drug target families (e.g., GPCRs, nuclear receptors, kinases, proteases, etc.) with the ultimate goal of identification of novel drugs and drug targets. Chemogenomics

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Pharmacogenetics in clinical practice

• Three major types of evidence that should accumulate to implicate polymorphism in clinical care.
• Screens of tissues from individuals linking the polymorphism to a trait.
• Complementary preclinical studies.
• Multiple supportive clinical phenotype/genotype association studies.

• Despite considerable research activity, pharmacogenetics are not yet widely utilized in clinical practice.
• Dose adjustment on the basis of renal or hepatic dysfunction can be accepted by clinician.
• But there is much more hesitation from clinician to adjust the dose on pharmacogenetic ground.
• This can be due to resistance to accept or can be due to unfamiliarity with the principles of genetics.

• Another hurdle in the path of Pharmacogenetics is
• Genetic Discrimination.
• Genetic discrimination occurs if people are treated unfairly because of differences in their DNA that increase their chances of getting a certain disease.
• For example, a health insurer might refuse to give coverage to a woman who has a DNA difference that raises her odds of getting breast cancer .
• Employers also could use DNA information to decide whether to hire or fire workers. 38

• Genetic Information Non- discrimination Act (GINA) 2008
•  It is a new federal law that protects Americans from being treated unfairly because of differences in their DNA that may affect their health.
•  The new law prevents discrimination from health insurers and employers.

Advantages of pharmacogenomics

• To predict a patient’s response to drugs
• To develop “customized” prescriptions  To minimize or eliminate adverse events
• To improve efficacy and patient compliance
• To improve rational drug development
• Pharmacogenetic test need only be conducted once during the life time.
• To improve the accuracy of determining appropriate dosage of drugs
• To screen and monitor certain diseases
• To develop more powerful, safer vaccines
• To allow improvements in drug discovery and development

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Barriers of Pharmacogenomics

1. Complexity of finding gene variations that affect drug response.

- Millions of SNPs must be identified and analyzed to determine their involvement in drug response

2. Confidentiality, privacy and the use and storage of genetic information

3. Educating healthcare providers and patients

- Complicates the process of prescribing and dispensing drugs

- Physicians must execute an extra diagnostic step to determine which drug is best suited to each patient

• 4. Disincentives for drug companies to make multiple pharmacogenomic products - Most pharmaceutical companies have been successful with their “one size fits all” approach to drug development

- For small market- Pharmaceutical companies hundreds of millions of dollars on pharmacogenomic based drug development.

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Clinomics

• Clinomics is the study of genomics data along with its associated clinical data.
• As personalized medicine advances, clinomics will be a bridge between basic biological data and its effect on human health. 

Guys, Take Note! One of the Pharmacogenetic Tools, No Escape any more

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CONCLUSION

• Genetic variation contributes to inter-individual differences in drug response phenotype at every pharmacologic step
• Through individualized treatments, pharmacogenetics and pharmacogenomics are expected to lead to:
• Better, safer drugs the first time
• More accurate methods of determining appropriate drug dosages
• Reduce healthcare expenditure
• Pharmacogenomics offers unprecedented opportunities to understand the genetic architecture of drug response
• HOWEVER IN MANY CASES NOT YET READY FOR PRIME TIME!!!

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Thank you

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??? Questions!

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