The Role of Pharmacogenetics in
Safety Assessment
Michael Mosteller, Arlene R. Hughes,
Sara H. Hughes, and Matthew R. Nelson
32nd Midwest Biopharmaceutical Statistics Workshop
Ball State University, May 19, 2009
Slide 2
What is Pharmacogenetics?
Some Basic Genetics
Single Nucleotide Polymorphism (SNP)
– A single nucleotide polymorphism (SNP) with two sequences
that differ at a single position:
ATCGC and ATTGC
Allele - Any of two or more alternative DNA sequence patterns that occur at a
given location in the genome.
– For the SNP above, the possible alleles would be: C and T
Genotype - The alleles present in a particular person at a particular location in
the genome.
– For the above SNP, the possible genotypes are:
C/C, C/T, or T/T
Genetic Markers – Locations in the genome at which people have differing
DNA sequences.
– Can be used as genetic landmarks (SNPs are an example)
Phenotype – A general term that refers to any non-genetic feature of an
organism.
U.S. Department of Energy Genome Research Programs: genomics.energy.gov
Available at: www.ornl.gov/sci/techresources/Human_Genome/publicat/primer2001/primer11.pdf
What is Pharmacogenetics?
Some Historic Highlights
Slide 3
1950’s - Drug responses linked to known genetic deficiencies
– G6PD deficiency + primaquine = hemolysis
– “Pharmacogenetics” proposed in 1959
1980’s - Dawn of the molecular genetics/genomics era
– The number of genetic markers increased dramatically
– “Pharmacogenomics” coined in 1986
1990’s - Human Genome Project and the SNP Consortium
– More (and more) genetic markers
2000’s - The HapMap Project
– Over 3 million SNPs studied in 270 individuals of European, African,
Japanese and Chinese ancestry
2000’s - Advances in DNA Microarray Genotyping Chips
– Rapid, relatively inexpensive, genome-wide genotyping of ~1 million
SNPs with commonly occurring alleles.
The stage is set to explore the possibilities of pharmacogenetics.
Slide 4
What is Pharmacogenetics?
Definition & Essence of a Pharmacogenetic Analysis
Pharmacogenetics: The study of the influence of genetics (variations
in DNA sequence) on drug response.
Statistical Bottom Line:
Does a genotype (or allele)
have a significant effect on
how an individual responds
to a drug?
% of Patients with Bilirubin Change > 2 mg/dl
Enzymes
Cell Surface Receptors
Antibodies
Medicine Response
Adverse Reaction Symptoms
Abnormal Lab Values
…or
binary. can
The
endpoint
be continuous…
P = 2 x 10-22
6,6
6,6
6,7
UGT1A1 Genotype
6,7
7,7
7,7
(Danoff et al., The Pharmacogenomics Journal (2004) 4, 49–53)
UGT1A1 Genotype (rs3064744)
(Adapted from Danoff et al., The Pharmacogenomics Journal (2004) 4, 49–53)
Slide 5
Drug Safety: Key Role in Personalized Medicine
The Vision of Personalized Medicine:
–
–
–
–
The right medicine to the right patient at the right dose
Optimize the benefit/risk ratio for the individual
Reducing safety risk is critical
Lots of collaborative activity…
Slide 6
Drug Safety: A Special Focus for FDA
Numerous initiatives to improve drug safety
International Serious Adverse Events Consortium (SAEC)
– Formed in 2007, with
strategic and scientific
support from FDA
– Initial projects:
Phase 1 ― SAEC Membership (11)
Spanish DILI
Drug induced liver injury
Stevens Johnson Syndrome
EUDRAGENE
– Future projects under
consideration include:
QT Prolongation
Hypersensitivity Rxn
Rhabdomyolosis
Edema
Renal Failure
DILIGEN
Top 5 SAEs
External Collaborators/Contributors
SAE Consortium
Slide 7
A Safety Pharmacogenetics Success Story
HLA-B*5701 status predicts susceptibility to hypersensitivity reaction
to abacavir sulfate.
Good uptake into clinical practice; referenced in US product label:
Steps Leading to Full Clinical Implementation
of a Safety Pharmacogenetics Association
From Marker Discovery to Clinical Implementation
– Discovery of the statistical association
– Confirmation of the statistical association
– Proposal of a biological hypothesis
– Demonstration of clinical utility
– Demonstration of generalizability among ethnically
diverse patients
– Provision of a pharmacogenetic marker test
– Demonstration that cost effectiveness is likely
– Incorporation of pharmacogenetic information in
product label
– Education of patients, physicians, regulators, and
payers
Slide 8
Slide 9
Abacavir Hypersensitivity Reaction
Abacavir (ABC): Effective HIV medicine
Hypersensitivity reaction (HSR) in 2-9%
Symptoms: Fever, rash, malaise, GI symptoms
Symptoms resolve with permanent discontinuation
Rechallenge can result in a life-threatening or fatal
reaction
Effective clinical management program developed
Pharmacogenetics program initiated to improve
benefit/risk
– Candidate genes (PK and immune)
– Genome Scan
Slide 10
Discover An Association
CNA30027, a retrospective case/control
study in 100 HSR Cases, 200 Controls
2001: Unprecedented results seen
in an interim analysis of CNA30027
Association later refined to HLA-B*5701
Based on data in Hetherington, et al., Lancet 2002; 359: 1121–22.
Slide 11
Confirm the Association
Dr. Simon Mallal was also conducting PGx research on
ABC HSR
2001: Mallal et al., independently identified the association
between HLA-B*5701 and ABC HSR
Therefore, association was seen in two independent
sample sets
Results from a later report:
Western Australian HIV Cohort Study*
HSR
No HSR
B*5701+
17
4
B*5701-
1
226
Sensitivity
94%
Specificity
98%
* Martin, et. al, PNAS 2004; 101:4180-4185.
Slide 12
Reasonable Biological Hypothesis
Biological
mechanism
not critical for
prediction
purposes,
but…
Bolsters
evidence
provided by
other findings
Abacavir
Aldehyde
(ABC Metabolite)
B*5701
Naisbitt DJ, Pirmohamed M, Park BK, Current Allergy and Asthma Reports 2003;3:22-29
Slide 13
Show Clinical Utility is Likely
No universal criterion for utility
One criterion: AE incidence reduction
Using retrospective data…
Genotype
Result
ABC Hypersensitivity
Present
Absent
True 17 False 4
B*5701+ Positive
Positive
False
B*5701Negative
Total
1
18
True 226
Negative
227
• HSR, screening:
1/227 = 0.4%
230
248
• HSR, no screening:
18/248 = 7.3%
What if HLA-B*5701+ patients were screened out?
Based on these results Martin et al. (2004) concluded
HLA-B*5701 could be useful in reducing HSR incidence
Slide 14
Demonstration of Clinical Utility in a Prospective,
Randomized Clinical Trial: PREDICT-1
PREDICT-1: Large, prospective GSK clinical study to assess the
utility of HLA-B*5701 screening
ABC-containing regimen with
HSR monitoring according to
Standard of Care
(~900)
ABC Naïve
Randomize (1:1)
Subjects
(~1800)
ABC-containing regimen
Exclude Subjects
who are B*5701
positive
Prospective HLA-B*5701
Screening
(~900)
Compare HSR incidence in Standard of
Care Arm and HLA-B*5701 Screening Arm
Enroll Subjects
who are B*5701
negative
Hughes S, Hughes A and Brothers C et al. PREDICT-1 (CNA106030): The first powered, prospective trial
of pharmacogenetic screening to reduce drug adverse events. Pharmaceutical Statistics 2007
PREDICT-1:
The First Pharmacogenetic Study of its Kind
Slide 15
Slide 16
PREDICT-1: Primary Study Endpoints
Co-primary endpoints comparisons between study arms of:
– Incidence of clinically-suspected ABC HSR
– Incidence of immunologically-confirmed ABC HSR
Major symptoms of clinically-suspected hypersensitivity
Hetherington S, et al. Clin Ther 2001; 23: 1603-14
Slide 17
PREDICT-1 Incorporated Skin Patch Testing:
A tool to refine HSR phenotype
Adhesive surface
1% abacavir
10% abacavir
Petrolatum control
Excipient control
Research tool used to identify
patients with immunemediated ABC HSR
Requires prior ABC exposure
Phenotype refinement without
need for rechallenge
Phillips et al. AIDS 2002 and 2005
Phillips et al. IAS 2007 Abstract MOPEB001
24-hour reading (48 hour reading)
Slide 18
PREDICT-1: Design & Analysis Details
Sample size of 1806 provided ≥90% power to detect
– 50% reduction in clinically suspected HSRs
– 80% reduction in immunologically confirmed HSRs
Power for immunologically confirmed HSR endpoint >99%; power for
clinically suspected HSR endpoint = 90%
 overall study power approx. 90% (>0.99 x 0.90)
Closed test approach for analysis of co-primary nested endpoints
(immunologically confirmed HSRs are a subset of clinically suspected
HSRs)
– if significant reduction in immunologically confirmed HSRs then test for
reduction in clinically suspected HSR endpoint
HSR rates compared between study arms using logistic regression,
adjusting for randomisation strata and other prognostic factors
Slide 19
PREDICT-1 Key Results: Comparing HSR Rates in
PGx Screening Arm versus Standard of Care Arm
Prospective Screen
Evaluable N=802
Standard of Care
Evaluable N=842
0/802 (0%)
23/842 (2.7%)
Immunologically Confirmed HSR
Statistical Results
Exact Odds Ratio[1] (95%CI): 0.03 (0.00, 0.18)
P-value: p<0.0001
Clinically Suspected HSR
Model Based Proportions [2]
Statistical Results
Evaluable N=803
Evaluable N=847
27/803 (3.4%)
66/847 (7.8%)
3.3%
7.9%
Odds Ratio[1] (95%CI): 0.40 (0.25, 0.62)
P-value: p<0.0001
[1] Odds ratio adjusted for actual strata of race, ART status, introduction of NNRTI and concurrent PI use.
[2] Model-based proportions calculated using parameter estimates and subject characteristics in the overall
population.
ART = Antiretroviral therapy
NNRTI = Non-nucleoside reverse transcriptase inhibitor
PI = Protease inhibitor
Slide 20
PREDICT-1 Key Results: Test Characteristics for
Predicting Immunologically Confirmed HSR
Immunologically
Confirmed HSR
No Immunologically
Confirmed HSR
Total
HLA-B*5701 Positive
23
25
48
HLA-B*5701 Negative
0
794
794
23
819
842
Total
Specificity:
Sensitivity:
PPV:
NPV:
794/819 = 96.9%
23/23 = 100%
23/48 = 47.9%
794/794 = 100%
95% CI (95.5%, 98.0%)
95% CI (85.2%, 100.0%)
95% CI (33.3%, 62.8%)
95% CI (99.5%, 100.0%)
Calculated using the Standard of Care arm data only
Slide 21
PREDICT-1 Key Results: Covariate Assessment
Model Covariates
Prospective Screen Arm
vs. Standard of Care Arm
Immunologically
Clinically
Confirmed HSR Suspected HSR
p < 0.0001
p < 0.0001
White vs. Non-White
p = 0.11
p = 0.02
ART Naive vs. ART Experienced
p = 0.66
p = 0.26
Introduction of NNRTI (Yes vs. No)
p = 0.57
p = 0.001
Concurrent PI Use (Yes vs. No)
p = 0.91
p = 0.009
Clinically suspected HSR was influenced by several covariates
Refined phenotype (patch test confirmed HSR) was independent of
these covariates
The SHAPE Study:
Are Findings Relevant only to Caucasians?
M Saag, et al. Clinical Infectious Diseases 2008; 46:1111-1118.
Slide 22
Slide 23
SHAPE Study Key Results:
Frequency of HLA-B*5701 by Patient Subgroups
Percentage of Subjects with HLA-B*5701 (95% CI)
For clinically
suspected HSR, the
frequency of
HLA-B*5701 was
lower in Black
subjects
For immunologically
confirmed HSR, all
case individuals
carried the HLAB*5701 allele,
regardless of race
The utility of HLAB*5701 appears to
generalize to US
Black patients
100
100%
100%
80
60
40
44%
20
14%
4%
White
Black
CS-HSR CS-HSR
n=130
n=69
Clinically
Suspected
Cases
White
IC-HSR
n=42
Black
IC-HSR
n=5
Immunologically
Confirmed
Cases
White
Control
n=202
1%
Black
Control
n=206
Abacavir
Tolerant
Controls
(Adapted from: M Saag, et al. Clinical Infectious Diseases 2008; 46:1111-1118.)
Develop / Access an Assay
for Pharmacogenetic Marker Detection
In general, development of laboratory based assays
or test kits may be needed
For HLA-B*5701:
HLA typing was widely available for tissue typing purposes
Several centralized clinical laboratories now offer
HLA-B*5701 evaluation for abacavir hypersensitivity
Lai-Goldman & Faruki, Genetics in Medicine 2008; 10: 874-78.
Slide 24
Slide 25
Evaluate Cost Effectiveness
A Cost Effectiveness Analysis of HLA-B*5701 Screening
– Results depend on realistic assumptions
– Usually, achieving a healthcare benefit comes with a cost
– However, under many scenarios, screening with HLA-B*5701
was predicted to reduce HSRs and average cost of care
(referred to as a “Dominant” outcome)
Hughes, DA, et al., Pharmacogenetics 2004, 14:1–8
Slide 26
Educate & Inform
Patients, Physicians, Regulators, and Payers
Benefits & limitations of using the pharmacogenetic
marker
How to order the marker assay
How to interpret the assay results
For HLA-B*5701 key messages are:
– Discontinue abacavir permanently if HSR cannot be ruled out,
regardless of the HLA-B*5701 result.
– HLA-B*5701 testing should never be performed diagnostically to
support a decision to rechallenge with abacavir.
– HLA-B*5701 testing must not be used as a screening test after
someone has started treatment with abacavir. If a hypersensitivity
reaction is suspected abacavir must be immediately and
permanently discontinued.
Slide 27
Challenges for Safety Pharmacogenetics
Association of HLA-B*5701 with abacavir hypersensitivity
effectively illustrates the potential of pharmacogenetics to
improve drug safety, however…
There are many challenges for safety pharmacogenetics:
– Limited sample sizes in early clinical development
– Very low rates of some serious adverse events
– Monitoring safety of newly approved drugs
– Acquiring DNA samples from cases
– Accurate diagnosis of adverse drug reactions in the
presence of symptoms from other causes
– Finding causal markers that occur with low frequency
– Finding multiple genetic markers contributing to risk of
an adverse drug reaction
Slide 28
Questions and Discussion