What the body does to drug [conc. v time]

[image]

WHAT THE DRUG DOES TO THE BODY [conc v effect]

study of relationship between rx conc. at site of action & ther & adverse effx

difference in min effective dose and minimum toxic dose

[image]

Determining actual target site conc = difficult

Drug targets not in blood/plasma(found in tissue/organs)

Plasma conc cn be used to optimize dose regimen

Plasma concentrations correlate well w/ those in tissue

Therapeutic drug monitoring

[TDM]

Use assays to determine drug plasma conc and interpret/apply resulting conc to retrospectively develop safe and effective regimen

[for narrow ther index rx's]

1. Dx , Rx selection

2. Start ther. w/ standard dose

3.Rx levels monitored

4. PK model applied to obtain individ. dosing reg.

5. Individ. dosing reg

Demographics 

Drug-Drug intrxn

Genes

Environment

Lifestyle habits

Abacavir

Plavix

Strattera

CISplatin

Coumadin

Codeine

Actionable = 44%

Required = 24%

Recommended = 4%

Informative = 28%

Pharmacogenetics vs Pharmacogenomics

influencing response to drugs

Pharmacogenetics = genetic dif at single variation/locus(gene)

Pharmacogenomics = genetic dif in multiole genes(genome wide) 

Optimizes rx therapy

using tech for personalized rx

optimize rx development

Metabolism and receptor types 

WT-WT

WT-V

V-V

WT-WT = normal profile [min toxicity, great ther effect]

WT-V = inc drug exposure 2x [toxic, min ther effect]

V-V = inc drug exposure 4x [too toxic,no ther effect]

1. Dose rec: Warfarin, atomoxetine

2. Indication: trastuzumab, imatinib, dasatinib

3. Increased serious ADR or Tx failure risk: carbamazepine, valproic acid

4. Contraindictaion: abacavir, fluorouracil

5. General warning/precautionary statements/ need for dose reductions based on rx metabolizing phenotype : atomoxetine, mercaptopurine, modafinil, clopidogrel, codeine

6. others with explicit/implicit evidence that no dose adjustment required by phenotype

WARFARIN LABEL

CYP2C9 & VKORC1

KNOWLEDGE OF GENOTYPE CAN INFORM INITIAL DOSE SELECTION

-iNDIVID. DOSE PER PT

- INR OBTAINED DAILY TILL STABLE THER. RANGE ACHEIVED (THEN EVERY 1-4 WEEKS)

Varient CYP2C9 in warfarin use results in...

SNP to VKORC1 result in....

decreased metabolism of s-warfarin (7-HYDROXYLATION)

variable warfarin dose reqs.

SUGAR-PHOSPHATE backbone

4 nucleotides (adenine, thymine, cytosine, guanine)

1990-2003

Goals= 

-identify all enes in human DNA

-store info in database

-determine sequences of 3 billion BPs

-address issues

average gene has ______ base pairs (varies greatly)

Human chromosomes have ______ BPs

Less than ____ of genome codes for protien 

average gene has 3,000 base pairs (varies greatly)

Human chromosomes have 150,000 BPS

Less than 2%of genome codes for protien 

DNA to DNA [replication]

DNA   to   RNA  [transcription]

RNA   to   protein [Translation]

*****HIV>>>>RNA bac to DNA (retrovirus)

EXONS ARE......

INTRONS ARE......

UTR

EXONS ARE protein coding regions that are SPLICED together

INTRONS ARE noncoding/ SPLICED out

UTR = untranslated regions

START CODON= 

STOP CODONS = 

CODON = 

START CODON(1st nucleotide) = AUG

STOP CODONS(2nd nucleotide) = UAA,UAG, UGA

CODON = 3 NUCLEOTIDES

GENOME = entire genetic makeup [genes,exonx,introns]

EXOME = only the exons of our genes [protein coding parts]

REGULOME = DNA elements that modulate gene expression

-single nucleotide polymorphism

-change in single BP

-Occurs approximately every 300 BPs

ex: GATCT

     GATTT

Insertion/Deletion [IN/DELS]

-insertion or deletion of one or more BPs

ex: GATCTGA

       GATCCTGA

-variable number of tandem repeats

-consecutive BP groups that are differentially repetitive

-Microsatelite, minisatellites

ex: AG(TA)_n

     AG(TA)₅

vs  AG(TA)₇

Copy number Variation

-whole gene copies or varirations

Nonsense SNP = premature stop codon[nonfunctional protein]

Nonsynonymous = Change in codon causing dif amino acid [change in protein]

Intronic or UTR = changes in mRNA level or stability

Promotor or enhancer region = chnages in gene expression/ how much RNA/protein is made

 SNP NOMENCLATURE 

CYPC2C19 681 G>A

GENE  POSITION   ALLELE1>ALLELE2

-SNP can be given rs # [reference SNP#]

ALLELE NOMENCLATURE 

CYPC2C19 681 G

GENE  POSITION   ALLELE

[can have * CYP2C19*1]

p = Freq (A)

q = Freq (a)

p + q = 1

p² + 2pq + q² = 1

NOT occur at any point in the HUMAN GENOME

[recombination occurs between blocks]

Block sizes 

European =

African = 

European = 44 kilobases

African = 22 kilobases

tendancy for pairs of alleles at nearby loci

to be associated with each other more often than

expected by chance if the loci were segregating indipendently in the pop

Measure of LD [linkage disequilibrium]

values greater than or equal to 0.70-0.80 is considered in "high" LD

D'

from 1 (complete LD;no ancestral combo)

to 0 (no LD;independent assortment)

r²

from 1 (perfect LD,no ancestral recombo, and the 2 SNPs have the same allele frequency)

to 0 (no LD;independent)

Factors that influence LD

[LD provides basis for most association disease strategies]

REcombination [time,distance]

Mutation

Admixture,pop stratification/structure

pop growth, nat selec., gene drift

Haplotype

Diplotype

Haplotype = combo of alleles or SNPs along chromosome that tend to be inherited together.

Diplotype= 2 haps inherited for certain gene, or combo of alleles or SNPs

LD and Haplotypes 

Theory vs Reality

Theory = lots of SNPS

Reality = Fewer haplotypes are actually observed

-access

-feasibility

-cost

-level of evidence

-ancestral pop SNPs were discovered in

-# of SNPs tested

-average population risk used

-Algorithm used to predict your risk based on genetic information

-Single SNP vs Haplotype based analyses

-lack of clinical utility for pharmacogenetic testing

-health info tools need pharmacogenetic info at point of care for clinical decision support

-healthcare professionals need edu

(field growing fast w/ new discoveries = PRACTICE GAP)

Lit review>>PUBMED>>

1.SNP info

[NCBI SNP,HapMap]

2.Gene info

[NCBI gene,UCSC genome browser,PharmGKB]

3.Disease Info

[NCBI OMIM, Huge Navigator]

Boolean operators =

AND

NOT

OR 

 or COMBINATION of these

Goal was to find most genetic variant that have frewuencies of at least 1% in the populations studied

-tool used for

1. look at allele frequencies (BEST PLACE***)

2.pop. [ancestry groups]

-PharmGKB 

-KEGG

Haploreg

SNPs 3d

NCBI dbGaP

NHGRI

GENE & DISEASE

SNP

PATHWAY INFO

GENOME WIDE ASSOCIATION STUDIES

GENE & DISEASE [NCBI Gene,OMIM, HuGE, UCSC]

SNP [NCBI SNP,1000 Genomes, Haploreg & SNPs 3D]

PATHWAY INFO [PharmGKB,KEGG]

GENOME WIDE ASSOCIATION STUDIES [NCBI dbGaP, NHGRI catalog of Genome Wide Association Studies]

NCBI SNP

1000 Genomes (allele freq)

NCBI Genome

UCSC Genome Browser (gene expression)

HuGE Navigator

OMIM

PharmGKB

KEGG

UCSC genome browser

HuGE Navigator 

dbGaP

GWAS catalog