Overview of Pharmacogenomics, Genetic Variations, Biomarkers and Genetic Diagnostic Techniques

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Overview of Pharmacogenomics
Faraza Javed
PhD Pharmacology

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Pharmacogenomics
Pharmacogenomics is the study of how genes
affect a person’s response to drugs. This
relatively new field combines pharmacology (the
science of drugs) and genomics (the study of
genes and their functions) to develop effective,
safe medications and doses that will be tailored
to a person’s genetic makeup.
Its name (pharmaco- + genomics) reflects its
combining of pharmacology and genomics.

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Pharmacogenetics VS. Pharmacogenomics
Pharmacogenetics: Study of variability in drug
response determined by single genes.
Pharmacogenomics: Study of variability in drug
response determined by multiple genes within the
genome.

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Pharmacogenetics has been defined as the study
of variability in drug response due to heredity.
More recently, with the fashion for adding the
suffix ‘… omics’ to areas of research, the term
‘pharmacogenomics’ has been introduced. While
the former term is largely used in relation to
genes determining drug metabolism, the latter is
a broader based term that encompasses all genes
in the genome that may determine drug
response. The distinction however, is arbitrary
and both terms can be used interchangeably.

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The International Conference on Harmonization
(ICH) finalized a set of definitions that were
published as a guidelines in 2008:
Pharmacogenomics: The study of variations of DNA
and RNA characteristics as related to drug
response.
Phamacogenetics: A sub-set of pharmacogenomics,
for the study of variations in DNA sequence as
related to drug response.

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Background
The history of pharmacogenetics stretches as far
back as 510 B.C. when Pythagoras noted that
ingestion of fava beans resulted in a potentially
fatal reaction (Hemolytic Anemia and oxidative
stress) in some, but not all, individuals.
Interestingly, this identification was later
validated and attributed to deficiency of 6GDP
in the 1950s and called favism.

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 The traditional Chinese medicine with
acupuncture and herbs takes individual
variations into consideration and this system is
still practiced in new China.
 Sysang topology, a Korean traditional
medicinal system explains the individual
differences in behavioral patterns, physical
characteristics, and susceptibility to a certain
disease based on their biophysiological trait.

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 Since then there have been numerous landmarks
that have shaped this field of research, and have
led to the current wave of interest.
 Reports of prolonged paralysis and fatal
reactions linked to genetic variants in patients
who lacked butyrylcholinesterase
(‘pseudocholinesterase’) following
administration of succinylcholine injection
during anesthesia were first reported in 1956.

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 The term pharmacogenetic was first coined in
1959 by Friedrich Vogel, while the term
pharmacogenomics first began appearing around
the 1990s and the first FDA approval of a
pharmacogenetic test was in 2005 (for alleles in
CYP2D6 and CYP2C19).

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Genetic variation:
Primarily two types of genetic mutation events
create all forms of variations:
 Insertion or deletion of one or more nucleotide(s)
--Tandem Repeat Polymorphisms
--Insertion/Deletion Polymorphisms
 Single base mutation which substitutes one
nucleotide for another
--Single nucleotide polymorphisms (SNPs)

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Insertion or deletion of one or more nucleotide(s)
Tandem Repeat Polymorphisms
Tandem repeats occur in DNA when a pattern of
one or more nucleotides is repeated and the
repetitions are directly adjacent to each other.
Insertion/Deletion Polymorphisms
An insertion/deletion polymorphism, commonly
abbreviated “indel,” is a type of genetic variation
in which a specific nucleotide sequence is present
(insertion) or absent (deletion). While not as
common as SNPs, indels are widely spread across
the genome.

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Single Nucleotide Polymorphism
Variation within the human genome is seen about
every 500–1000 bases, although there are a
number of different types of polymorphic markers,
most attention recently has focused on single
nucleotide polymorphisms (SNPs, pronounced
snips), and the potential for using these to
determine the individual drug response profile.

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“A single-nucleotide polymorphism, often
abbreviated to SNP (pronounced snip;
plural snips), is a variation in a single
nucleotide that occurs at a specific position
in the genome, where each variation is
present to some appreciable degree within a
population”

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Many drugs that are currently available are “one
size fits all,” but they don't work the same way for
everyone. It can be difficult to predict who will
benefit from a medication, who will not respond at
all, and who will experience negative side effects
(called adverse drug reactions).

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With the knowledge gained from the Human
Genome Project, researchers are learning how
inherited differences in genes affect the body’s
response to medications. These genetic differences
will be used to predict whether a medication will
be effective for a particular person and to help
prevent adverse drug reactions.

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 A consortium between the pharmaceutical
industry and charities such as the Wellcome
Trust was formed to create a library of 300000
SNPs; this project was always well ahead of the
intended schedule, and has recently resulted in
the publication of a SNP map comprising 1.42
million SNPs at an average density of one SNP
every 1.9 kilobases.

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 Theoretically, this could be used to create
individual SNP profiles that correlate with
individual drug response. Currently, we
prescribe drugs according to the model that
‘one dose fits all’. Using SNP profiling, it may
possible to tailor drug prescription and drug
dosage to the individual, thereby maximizing
efficacy and minimizing toxicity.

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A Case Study in Pharmacogenetics
 6-mercaptopurine, 6-thioguanine, azathioprine
 Used to treat lymphoblastic leukemia, autoimmune
disease, inflammatory bowel disease
 Interferes with nucleic acid synthesis
 Therapeutic index limited by myelosuppression
6-thioguanine azathioprine6-mercaptopurine

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Pharmacogenetics: A Case Study

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Pharmacogenetics: A Case Study

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Pharmacogenetics: A Case Study

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Codeine and Cytochrome P450 CYP2D6
 Codeine is a commonly used opioid
--Codeine is a prodrug
--It must be metabolized into morphine for
activity
 Cytochrome P450 allele CYP2D6 is the
metabolizing enzyme in the liver
 7% of Caucasians are missing one copy of the
Cytochrome P450 CYP2D6 gene
 Codeine does not work effectively in these
individuals.

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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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Personalized Medicine
A form of medicine that uses information about a
person’s genes, proteins, and environment to
prevent, diagnose, and treat disease.
Examples of personalized medicine include using
targeted therapies to treat specific types of cancer
cells, such as HER2-positive breast cancer cells, or
using tumor marker testing to help diagnose
cancer. Also called precision medicine.

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Personalized Drugs
Herceptin (breast cancer, target: Her2/neu)
Erbitux (colorectal cancer, target: EGFR)
Strattera (attention-deficit/hyperactivity
disorder, Metabolism: P4502D6)
6-MP (leukemia, Metabolism: TPMT)
and the list is growing rapidly ...

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The promise of personalized medicines is also
of obvious interest and importance to the
pharmaceutical industry since it may allow
streamlining of the drug development, drug
testing and drug registration process, reducing
the time from chemical synthesis to
introduction into clinical practice, and
therefore the cost of the drug development
process.

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Faster Clinical Trials
 Different researchers reported that therapeutic
approaches using precision medicine, which
emphasizes the use of individual genetics to refine
cancer treatment, showed improved response and
longer periods of disease remission, even in phase
I trials.
 In a sub-analysis of 234 arms testing targeted
drugs, the authors found that using biomarkers
to assign patients to treatments led to response
rates of 31.1 percent compared to 5.1 percent for
those that did not.

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This shows the importance of pairing targeted
therapy with a biomarker.
 Another sub-analysis of the precision medicine
trials showed that while the use of both genomic
and protein biomarkers improved outcomes,
genomic biomarkers performed better.
Targeting genomic alterations resulted in a 42
percent response rate compared to a 22.4 percent
response if the biomarker was directed at a
protein overexpression.

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FDA Requires Genetic Tests for Certain Therapies

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Research in the area of pharmacogenomics is
now gaining importance due to the invention of
different techniques that can be used to identify
genetic variation.
Recombinant DNA Techniques
Joining together of DNA molecules from two
different species that are inserted into a host
organism to produce new genetic combinations
that are of value to science, medicine, agriculture,
and industry.

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DNA Amplification Technique i.e. PCR
The polymerase chain reaction (PCR) is a technique
used in molecular biology to amplify a single copy or
a few copies of a piece of DNA across several orders
of magnitude, generating thousands to millions of
copies of a particular DNA sequence.
Hybridization Techniques
Fluorescence In Situ Hybridization (FISH)
FISH is applied to provide specific localization of
genes on chromosomes. This technique is used to
check the cause of trisomies, microdeletion
syndromes, etc.

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Comparative Genomic Hybridization (CGH)
CGH, a special FISH technique (dual probes), is
applied for detecting all genomic imbalances.
The basics of technique is comparison of total
genomic DNA of the given sample DNA (e.g.
tumor DNA) with total genomic DNA of normal
cells. Copy number of genetic material (gains
and losses) is calculated by evaluation software.

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Multiplex Ligation-Dependent Probe
Amplification (MLPA)
MLPA is commonly applied to screen deletions
and duplications of up to 50 different genomic
DNA or RNA sequences.
On the immediate horizon are even more
powerful techniques, techniques that scientists
expect will have a formidable impact on the
future of both research and clinical genetics.

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DNA Chip Technology
Also called DNA microarray technology, is a
revolutionary new tool designed to identify
mutations in genes or survey expression of tens
of thousands of genes in one experiment.
e.g. Roche Chip for
Cytochrome P450 Genes:
CYPC19 and CYP2D6

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Better Treatment, Fewer Side Effects
William Phelps, the director of preclinical and
translational cancer research at the American
Cancer Society says:
With targeted approach, The overall toxicity to
patients should be reduced because you are more
likely to use the best collection of drugs the first
time around. When it comes to cancer,
personalization can take several different forms
currently.

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It might mean:
 testing a person’s cancer to find out if a certain
type of treatment will work on it
 looking at a person’s genetics to decide whether
he or she can handle a specific medicine, or
conducting a genetic test to determine if a person
has certain genetic mutations that could put
them at a higher risk for developing cancer
 Pretherapeutic screening does help to reduce the
risk of treatment related toxicities through
adaptive dosing strategies

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Challenges
Although there appears to be a general
acceptance of the basic tenet of
pharmacogenomics amongst physicians and
healthcare professionals, several challenges exist
that slow the uptake, implementation, and
standardization of pharmacogenomics. Some of
the concerns raised by physicians include:
 Limitation on how to apply the test into clinical
practices and treatment

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 A general feeling of lack of availability of the test
 The understanding and interpretation of
evidence-based research and
 The cost-effectiveness of pharmacogenomics
 Ethical, legal and social issues
Although other factors contribute to the slow
progression of pharmacogenomics (such as
developing guidelines for clinical use), the above
factors appear to be the most prevalent.

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Future
Computational advances in pharmacogenomics
has proven to be a blessing in research. In order
for the field to grow, rich knowledge enterprises
and business must work more closely together
and adopt simulation strategies. Consequently,
more importance must be placed on the role of
computational biology with regards to safety and
risk assessments.

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The field of pharmacogenomics is still in its
infancy. Its use is currently quite limited, but new
approaches are under study in clinical trials. In
the future, pharmacogenomics will allow the
development of tailored drugs to treat a wide
range of health problems, including
cardiovascular disease, Alzheimer disease, cancer,
HIV/AIDS, and asthma.

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References
 Maria Schwaederle, Melissa Zhao, J. Jack Lee, Vladimir Lazar, Brian
Leyland-Jones, Richard L. Schilsky, John Mendelsohn, Razelle
Kurzrock. Association of Biomarker-Based Treatment Strategies With
Response Rates and Progression-Free Survival in Refractory Malignant
Neoplasms. JAMA Oncology, 2016; DOI:10.1001/jamaoncol.2016.2129
 Wolff AC, Hammond ME, Hicks DG, et al. Recommendations for human
epidermal growth factor receptor 2 testing in breast cancer: American
Society of Clinical Oncology/College of American Pathologists clinical
practice guideline update. J Clin Oncol. 2013;31:3997–4013.
 Altshuler DL, Durbin RM, Abecasis GR, et al. A map of human genome
variation from population-scale sequencing. Nature. 2010;467(7319):1061–
1073.

43. 43
 Sim SC, Ingelman-Sundberg M. Pharmacogenomic biomarkers: new
tools in current and future drug therapy. Trends Pharmacol
Sci. 2011;32(2):72–81.
 Hoggatt J. Personalized medicine–trends in molecular diagnostics:
exponential growth expected in the next ten years. Mol Diagn
Ther. 2011;15(1):53–55.
 Norton P. Peet and Philippe Bey Pharmacogenomics: challenges and
opportunities. Drug Discovery Today. 2001;6:495–498.
 Hoskins JM, Carey LA, McLeod HL. CYP2D6 and tamoxifen: DNA
matters in breast cancer. Nat Rev Cancer. 2009;9(8):576–586.
 Kiechle FL, Holland CA. Point-of-care testing and molecular
diagnostics: miniaturization required. Clin Lab Med. 2009;29(3):555–
560

44. 44
 Rabbani B, Khanahmad H, Bagheri R, et al. Characterization of minor
bands of STR amplification reaction of FVIII gene by PCR cloning. Clin
Chim Acta. 2008;39(12):114–5.
 Levsky JM, Singer RH. Fluorescence in situ hybridization:Past, present and
future. J Cell Sci. 2003;116(Pt14):2833–8.
 Houldsworth J, Chaganti RS. Comparative genomic hybridization:An
overview. Am J Pathol.1994;145(6):1253–60.
 Shaffer LG, Kashork CD, Saleki R, et al. Targeted genomic microarray
analysis for identification of chromosome abnormalities in 1500
consecutive clinical cases. J Pediatr. 2006;149(1):98–102.
 Mullis KB, Faloona FA. Specific synthesis of DNA in vitro via a
polymerasecatalyzed chain reaction. Methods Enzymol 1987;155:335–50.