pharmacogenomics Flashcards

Question

Which ethnicity has the most complex genetic composition (high numbers and high frequency of genetic variants)?

Answer 1

* African * Human origin?

Answer 2

* Ashkenazi Jews * Culture isolation, population bottleneck (~ 350 individuals

Answer 3

* Pharmacokinetic (PK) genes, particularly CYPs, are polymorphic and harbor many genetic variants. Around 8 CYP genes are clinically most important with CYP2D6 being most polymorphic. Star (*) alleles are used to name well-characterized (mostly common) CYP variants. Allele frequency of CYP alleles differ substantially across ethnicities and populations.

Answer 4

* Common * Have impact on activity of encoding enzymes - Decrease enzyme function (deceased function allele) - Abolish enzyme function (Loss-of-function allele) -Increase enzyme function (Gain-of-function allele)

Answer 5

it is dependent on where the enzyme acts, the produg to metabilise it into the active compound or to the drug deactivating it general dogma though is : Changes in allele function - Changes in enzyme activity - Changes in drug exposure

Answer 6

-Data source for the categorical function of star alleles Star allele functions are well-characterized and can be looked up in PharmVar PharmVar, short for Pharmacogene Variation Consortium, is a global initiative focused on cataloging and standardizing genetic variations within genes that encode proteins involved in drug metabolism and response. These variations can influence an individual's response to pharmaceutical drugs, affecting factors such as drug efficacy and potential adverse reactions. The PharmVar database provides curated information on pharmacogenetic variations, including their frequencies in different populations, clinical significance, and recommendations for drug dosing or selection based on an individual's genetic profile. This information is valuable for healthcare professionals in personalized medicine, allowing them to tailor drug treatments to individual patients based on their genetic makeup, ultimately leading to better therapeutic outcomes and reduced risks of adverse drug reactions.

Answer 7

CPIC (and others) publishes guidelines to translate genotypes into metabolizer phenotypes and provide therapeutic recommendations. *A group of international pharmacogeneticists who are interested in facilitating use of pharmacogenetic tests for patient care. * Curates pharmacogenetic data from the literature. - Allele definition -Allele function - Allele frequency -Evidence linking Genotype to Phenotype * Publishes detailed gene/drug clinical practice guidelines - From variant function to allele function to protein function to patient response to dose/drug recommendation Allele function and activity score, Translate an individual’s genotype into phenotype, From metabolizer phenotype to dose recommendations

Answer 8

0-2 but it can be more than 2 for ultrarapid metabolisers Ultrarapid metabolizers (UM),Rapid metabolizers (RM) =Duplicated allele or increase function allele Normal metabolizers (NM) Intermediate metabolizers (IM)= Decreased function allele or LOF allele Poor metabolizers (PM)=Two LOF alleles

Answer 9

* The Dutch Pharmacogenetics Working Group (DPWG) * The Canadian Pharmacogenomics Network for Drug Safety (CPNDS) * The French National Network of Pharmacogenetics (RNPGx) * Drug labels - FDA (Table of Pharmacogenetic Associations; Table of Pharmacogenomic Biomarkers in Drug Labeling) - EMA - Pharmaceuticals and Medical Devices Agency, Japan (PMDA) - Swiss Agency of Therapeutic Products (Swissmedic) - Health Canada (Santé Canada) (HCSC)

Answer 10

Section 1: Pharmacogenetic Associations for which the Data Support Therapeutic Management Recommendations e.g abacavir ( maybe the only one ) Section 2: Pharmacogenetic Associations for which the Data Indicate a Potential Impact on Safety or Response e.g codein Section 3: Pharmacogenetic Associations for which the Data Demonstrate a Potential Impact on Pharmacokinetic Properties Only e.g. amitriptyine

Answer 11

one might say that knowing the PGx an action should be taken while the other might only be recomending or not saying anything CPIC and DPWG - >20% differences in therapeutic recommendations were identified (Bank PCD. et al. Clin Pharmacol Ther. 2018) * DPWG, CPIC, CPNDS, and RNPGx - Discordances in fluoropyrimidines, irinotecan, clopidogrel, warfarin and statins (Abdullah-Koolmees H. et al. Front Pharmacol. 2021) * FDA and EMA - Only 54% overlap in drug-gene interactions (Ingelman-Sundberg M. Pharmacol Res. 2020) * FDA, EMA, CPIC and DPWG - Only 18% concordance Source of information considered - Clinical study/Preclinical study/Case report * Time point when the evidence was collected * Therapeutic recommendations vary between countries * Update of the gene-drug information - English version of DPWG recommendations hasn’t been updated since 2011 * Activity score assignment

Answer 12

PharmGKB is a comprehensive resource for pharmacogenomic information. * PharmGKB (The Pharmacogenomics Knowledgebase) collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relationships. it give you info form all databases , as it may vary it can also show you the pathways you can Browse Drugs with Variant Annotations

Answer 13

Associated with Adverse Drug Reactions Modulate Drug Efficacy

Answer 14

* Allele frequency - gnomAD - dbSNP - The literature * SNP information (genomic coordinate, variant type, nucleotide substitution) - dbSNP

Answer 15

In summary, while both gnomAD and dbSNP contain information about genetic variants in humans, gnomAD focuses on allele frequency data from large-scale sequencing studies, particularly rare variants, while dbSNP is a comprehensive database that catalogs various types of genetic variants and provides unique identifiers for each variant.

Answer 16

* Allele: *1, *2, *3… * Diplotype: *1/*1, *1/*2, *2/*3… * Assume in a cohort people are either wild-type or CYP2C19*2 carriers * Allele frequency: CYP2C19*2 = 0.2 * Diplotype frequency CYP2C19*2/*2 = ? CYP2C19*1/*1 = ? CYP2C19*1/*2 = ? for hoozygous we just do: 0,2^2 for example but for heterozygus we have to do: 2* 0,2*0,8

Answer 17

If the numbers dont add up to 1 then the *1 is missing add all the same variant functions together multiply and add together all the possible allele combinations that give you every functional group

Answer 18

* Pharmacogenes are polymorphic * Star alleles * Inter-population differences in star allele frequencies * Consequent metabolizer phenotypes

Answer 19

Forward genetics Phenotype to Genotype Reverse genetics the opposite

Answer 20

* Read length: 400 to 1200 bp * High accuracy * Easy to perform in a common genetic laboratory * Low-throughput * Time-consuming * Trained staff required * Still used today in small scale project or validate result from more advance sequencing technologies

Answer 21

* Defined by methods in which millions of DNA templates are sequenced spontaneously in a single reaction * Emerged around 1995 and commercially available since 2005 * Principle (Video) -DNA fragmentation -Amplification of DNA fragment by PCR - Short-read sequencing - Short reads assembly * Read length: 50 to 600 bp * High-throughput, cost-effective * Automation * Can be very accurate * Difficult to analyze complex genomic loci (repetitive regions, structure variants) * Widely-used in industry and academia

Answer 22

* Defined by methods that can produce substantially longer reads than second generation sequencing * Developed after 2011 * Two long-read sequencing platforms - Nanopore sequencing by Oxford Nanopore Technology - Single molecule real time (SMRT) sequencing by Pacific Biosciences (PacBio) * Read length: 5,000 to 30,000 bp * No amplification bias from PCR * Suitable to analyze complex genomic loci * Expensive * Much less downstream bioinformatic tools coupled * Getting more used in detecting genetic variations in disease genes and complex pharmacogenes, e.g. CYP2D6

Answer 23

Before: 3 billion USD, 13 years Now: 500 USD, half a day

Answer 24

multiple around the world , in many different palces

Answer 25

* 2,504 human genomes (1KGP, 2015) 88M variants, 76M variants with frequency < 5%, 64M variants with frequency < 0.5% * 76,156 human genomes (gnomAD v3, 2023) > 644M short nuclear variants, >390M variants with frequency < 0.1% * Pharmacogenomic variations rare variants are also important CYP2D6 has the most variants The majority of sequencing identified variants have low frequencies. gnomAD is a good resource to analyze these variants.

Answer 26

No cause we see that the phenotypic spectrum is overlapping between different diplotypes * Are star alleles sufficient to inform metabolizer phenotype? * No. Something is missing in genetic factors that can explain the variability in drug response (missing heritability). * What is missing? 20-30% genetic factors ~50% known variants ~50% missing heritability : rare variants log read sequencing of complex loci haplotypes of specific CYP genes Two variants in the same allele – we call that haplotype specific polimorphic gene regulation

Answer 27

* Searches for similar amino acid sequences * Chooses closely related sequences that may share similar function * Obtains the multiple alignment of these chosen sequences * Calculates normalized probabilities for all possible substitutions at each position from the alignment Normalized probabilities < cutoff : Deleterious Normalized probabilities >= cutoff : Tolerated Here's how SIFT works: Sequence Alignment: SIFT starts by aligning protein sequences from different species that are evolutionarily related to the protein of interest. This alignment helps identify conserved regions and residues within the protein. Calculation of Conservation Scores: SIFT calculates a conservation score for each amino acid residue in the protein based on the degree of conservation observed in the sequence alignment. Highly conserved residues are assigned higher conservation scores, indicating that changes to these residues are less likely to be tolerated without affecting protein function. Substitution Prediction: When presented with a query amino acid substitution (mutation), SIFT evaluates the conservation score of the wild-type (original) amino acid residue and predicts the impact of the substitution based on this score. If the substitution involves a highly conserved residue (high conservation score), SIFT predicts that it is likely to be deleterious or damaging to protein function. Conversely, if the substitution involves a less conserved residue (low conservation score), SIFT predicts that it is more likely to be tolerated without significant effects on protein function. Threshold Determination: SIFT uses a predetermined threshold (typically 0.05 or 0.1) to classify substitutions as tolerated or intolerant. Substitutions with a SIFT score below the threshold are predicted to be deleterious (intolerant), while substitutions with a score above the threshold are predicted to be tolerated (tolerant). Output: The output of SIFT typically includes the predicted impact of the substitution (tolerated or deleterious) along with a numerical SIFT score indicating the degree of conservation at the affected residue.

Answer 28

A method and server for predicting damaging missense mutations Based on a machine learning method (Naive Bayes classifier) Two training datasets: * HumDiv, 3,155 damaging variants, 6,321 nondamaging variants * HumVar, 13,032 damaging variants, 8,946 nondamaging variants

Answer 29

A general framework for estimating the relative pathogenicity of human genetic variants * Machine-learning method to train 14.7 million highfrequency human-derived variants and 14.7 million simulated variants * Integrating many diverse annotations into a single score for each variant (higher score à more deleterious)

Answer 30

Generate missense variant predictions from a collection of tools

Answer 31

Generate predictions from a collection of tools

Answer 32

NO Sequence conservation Allele frequency Disease-related features are not enough to find Disease causing variants around 75 % prediction accuracy for CADD

Answer 33

better results for ADME optimised * DPYD gene - DPYD-Varifier (variant function prediction) * CYP2D6 gene -Enzyme activity prediction based on sequences (long-read) - Hubble.2D6 (haplotype function prediction) * Few other tools

Answer 34

* Overfitting: overlap between training variants and testing variants * Lack of training data (for predictors designed for specific type of variants, e.g., PGx variants) * Method selection

Answer 35

through Aggregated frequency and then calculating and adding all the probabilities of every diffferent diplotype that is in this cagegory e.g. intermidiate metaboliser

Answer 36

* PD genes encode drug targets that can trigger therapeutic response upon drug binding * The number of drug targets are not well-defined.

Answer 37

* Vitamin K epoxide reductase (VKOR, encoded by VKORC1) is the target of warfarin * VKORC1 -1639G>A (rs9923231, G3673A) * Variant carriers have decreased activity of VKOR, thus are more sensitive to warfarin and require lower dose * MAF = 32.6%, dominant in East Asians CFTR * CFTR (cystic fibrosis transmembrane conductance regulator) encodes a chloride channel and play important role in ion and water secretion and absorption in epithelial tissues. * Abnormal CFTR function is the cause of cystic fibrosis (CF), a genetic disorder that induce sticky and thick mucus secretion and cause difficulty in breathing and frequent inflammation. * CF occurs in 1 in 2,500 to 3,500 white newborns * Five classes of CFTR mutation and corresponding therapies different functionalities of the protein e.g. missfolded , shortened etc

Answer 38

Two French families with an autosomal dominant form of familial hypercholesterolemia (FH) “gain-of-function” mutations identified in PCSK9 in these and other FH patients Development of PCSK9 inhibitor

Answer 39

1)Genetic variants in drug-target binding sites * GPCRs * 108 GPCRs targeted by 475 (34%) FDA-approved drugs * Natural occurring variants in GPCR binding site impact drug response and bias signaling 1 in 6 individuals carries at least one missense variant in the binding sites * Binding site variants can impact drug response and be used for drug development 2) Drug off-target effect: HLA genes related hypersensitivity reactions * HLA (Human Leukocyte Antigen) encodes major histocompatibility complex (MHC) * MHC molecules have peptide binding grooves binding sites affected: HLA-B*57:01 and abacavir induced abacavir hypersensitivity syndrome HLA-B*15:02 and carbamazepine induced Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) * Genetic variations in drug targets are important determinants of drug response * Genetic variations in HLA genes can trigger drug-induced hypersensitivity reaction * HLA-B*57:01 is a strong risk allele for abacavir hypersensitivity syndrome

Answer 40

Overall implementation of pharmacogenomic labels however remains poor particularly for CYP genes In total there are 25 guidelines with actionable recommendation affecting 140 medications. Of these, only 2-3 are implemented in clinical routine These are testing of: HLA-B*57:01 and abacavir DPYD and fluoropyrimidines HLA-B*15:02 and carbamazepine in patients of Asian ethnicity Abacavir hypersensitivity Manifests as Morbilliform/maculopapular rash Fever (often precedes rash) Myalgias, fatigue Mucosal ulceration More rarely (<5%) also as hepatitis and nephritis Fluoropyrimidine toxicity Up to 30% of patients have severe treatment-related toxicity, including diarrhea, mucositis, myelosuppression and hand foot syndrome. Anti-cancer drugs, such as fluorouracil and capecitabine Prospective trial showed that genotype-guided dose reduction was beneficial HLA-B*15:02 and carbamazepine-induced Steven-Johnson syndrome (SJS) SJS when <30% of skin surface area is affected Toxic epidermal necrolysis (TEN) when >30% are affected Very severe skin reaction Zhou et al., CPT 2020 Mortality rates: 2-15% for SJS and 25% for TEN

Answer 41

Overall implementation of pharmacogenomic labels however remains poor particularly for CYP genes Contributing factors: * Lack of reproducibility (underpowered studies dilute the literature) * Large variability within genotype groups; effects are stochastic rather than deterministic Many outliers in the studies make the results less deterministic * TDM instead of PGx * Strong effects on pharmacokinetics, weak effects on clinical outcomes/ADRs * Unclear added value (lack of clinical trials, alternative medications; e.g. DOACs) Pharmacogenetic expert groups are dominated by pharmacists and pharmacogeneticists but lack involvement of physicians Poor congruence between “expert” recommendations and regulatory guidance (SmPCs) * (Lack of pharmacogenetic education) * Practical limitations in clinical routine * Lack of cost and reimbursement considerations

Answer 42

Multi-center, multi-gene, multidrug, multi-ethnic, and multihealthcare system trial. The PREPARE trial involves recruiting patients from primary care practices and providing pharmacogenomic testing to guide medication selection and dosing for selected drugs. The PREPARE trial involves recruiting patients from primary care practices and providing pharmacogenomic testing to guide medication selection and dosing for selected drugs.

Answer 43

Incorporation of rare variability to increase the predictive power * Clinical trials to evaluate the added value * Fostering of inter-disciplinarity * Increased cost consideration and feasibility trials in primary care

Answer 44

1. CYP2C19 for clopidogrel and escitalopram 2. CYP2D6 for risperidone and tamoxifen 3. CYP2C9 for warfarin