Content

 Introduction to SNP
 Pharmacogenomics
 Role of SNPs in Pharmacogenomics
 Review of Literature
 Case Study
 Future Approach
 References
 INTRODUCTION
Various scientific endeavours had already started even before the completion of the first
human genome reference sequence to identify unique genetic differences between
individuals. 99.9% of one individual DNA sequences will be identical to that of another
person. Of the 0.1% difference, over 80% will be single nucleotide polymorphisms (SNPs).
Single nucleotide polymorphisms, or SNPs (pronounced "snips"), are DNA sequence variations that
occur when a single nucleotide (A, T, C, or G) in the genome sequence is altered. For example a SNP
might change the DNA sequence AAGGCTAA to ATGGCTAA. Hence SNP is a single base
substitution of one nucleotide with another, and both versions are observed in the general
population at a frequency greater than 1%. Human DNA is comprised of only four chemical
entities, e.g. A, G, C, T, whose specific chemical order is the alphabet of the genome. An
example of a SNP is individual "A" has a sequence GAACCT while individual "B" has
sequence GAGCCT, the polymorphism is a A/G. The most recognized public effort was
spearheaded by The SNP Consortium (TSC) whose mission was to determine and map about
300,000 evenly spaced single nucleotide polymorphisms within the human genome

……..G G T A A C
T T G …...
……..G G C A A C
Single nucleotide Polymorphism
T T G …...

Current estimates are that SNPs occur as frequently as every 100-300 bases. This implies in
an entire human genome there are approximately 10 to 30 million potential SNPs. More than
4 million SNPs have been identified and the information has been made publicly available
through the efforts of TSC and others. Many of these SNPs have unknown associations.
Compilation of public SNPs by NCBI has produced a subset of SNPs defined as a non-
redundant set of markers that are used for annotation of reference genome sequence and are
thus referred to as reference SNPs (rsSNPs). Over 2.6 million SNPs have currently been
assigned as "rsSNPs".

Recent work has suggested that about 10 million SNPs that are common in human population
are not inherited independently; rather, sets of adjacent SNPs are present on alleles in a block
pattern, so called haplotype. Many haplotype blocks in human have been transmitted through
many generations without recombination. This means although a block may contain many
SNPs, it takes a few SNPs to identify or tag each haplotype in the block.

Pharmacogenomics:
Pharmacogenomics is the branch of pharmacology which deals with the influence of genetic
variation on drug response in patients by correlating gene expression or single-nucleotide
polymorphisms with a drug's efficacy or toxicity. By doing so, Pharmacogenomics aims to
develop rational means to optimize drug therapy, with respect to the patients' genotype, to
ensure maximum efficacy with minimal adverse effects. Such approaches promise the advent
of "personalized medicine"; in which drugs and drug combinations are optimized for each
individual's unique genetic makeup. It holds the promise that drugs might one day be tailor-
made for individuals.

Role of SNPs in Pharmacogenomics:

SNPs can occur in coding (gene) and noncoding regions of the genome. Many SNPs have no
effect on cell function, but scientists believe others could predispose people to disease or
influence their response to a drug. Although more than 99% of human DNA sequences are
the same, variations in DNA sequence can have a major impact on how humans respond to
disease; environmental factors such as bacteria, viruses, toxins, and chemicals; and drugs and
other therapies. This makes SNPs valuable for biomedical research and for developing
pharmaceutical products or medical diagnostics. SNPs are also evolutionarily stable—not
changing much from generation to generation—making them easier to follow in population
studies Single Nucleotide Polymorphisms (SNPs) holds the key in defining the risk of an
individual’s susceptibility to various illnesses and response to drugs. There is an ongoing
process of identifying the common, biologically relevant SNPs, in particular those that are
associated with the risk of disease. The identification and characterization of large numbers
of these SNPs are necessary before we can begin to use them extensively as genetic tools. As
SNP allele frequencies vary considerably across human ethnic groups and populations, the
SNP consortium has opted to use an ethnically diverse panel to maximize the chances of SNP
discovery. Currently most studies are biased deliberately towards coding regions and the data
generated from them therefore are unlikely to reflect the overall distribution of SNPs
throughout the genome. The SNP consortium protocol was designed to identify SNPs without
any bias towards these coding regions. Most Pharmacogenomics studies were carried out in
heterogeneous clinical trial populations, using case-control or cohort association study
designs employing either candidate gene or Linkage disequilibrium (LD) mapping
approaches. Concerns about the required patient sample sizes, the extent of LD, the number
of SNPs needed in a map, the cost of genotyping SNPs, and the interpretation of results are
some of the challenges that surround this field. While LD mapping is appealing in that it is an
unbiased approach and allows a comprehensive genome-wide survey, the challenges and
limitations are significant. An alternative such as the candidate gene approach does offer
several advantages over LD mapping. Ultimately, as all human genes are discovered, the
need for random SNP markers diminishes and gene-based SNP approaches will predominate.
The challenges will then be to demonstrate convincing links between genetic variation and
drug responses and to translate that information into useful Pharmacogenomics tests.
 Review of literature
SNPs are the major of all the human DNA polymorphisms. SNPs are single base pair
positions in genomic DNA at which different sequence alternatives (alleles) exist in normal
individual in some populations (11). SNPs have a great commercial potential for
pharmaceutical community and is evident by the fact that-the SNP Consortium was founded
In 1999 by 10 of the world’s top pharmaceutical companies – Astra Zeneca, Bayer AG,
Briston-Myers Squibb Co., Hoffman – La Roche Ltd., Glaxo Wellcome, Hoechst Marion
SmithKline Beecham and is committed to identifying and mapping at least 300,000 SNPs
from the human genome and releasing them into the public domain (12).

The two “genomes” that each of us carry, inherited from our parents most often differ from
each other & from the genomes of other humans – in terms of single base changes or it can be
said that our genes have ancestors & analyzing shared patterns of SNP variation can identify
them. These base changes are the SNPs frequent type of variation in the human genome, and
they provide powerful tools for a variety of medical genetic studies.

More than 1.4 million single nucleotide polymorphisms (SNPs) in the human genome have
been identified. This collection should allow the initiation of genome-wide linkage
disequilibrium mapping of the genes in the human population. The density is even higher in
the region containing genes. The international SNP map-working group estimates that they
have identified 60,000 SNPs within genes (coding SNPs) or one coding SNP per 1.08-kilo
bases of gene sequences. For the first time, nearly every human gene and genomic region is
marked by a sequence variation sequence.

These data provide interesting first glimpses into the pattern of variation across the genome.
Variation is generally assessed by nucleotide diversity by evaluating the number of base
differences between two genomes, divided by the number of base pairs compared. Creating
associations between SNPs and disease is achieved by Genotyping. Genotyping is the key
process by which SNPs are harvested into the commercially useful information in the form of
biological associations. These studies are based on the technologies like DNA micro arrays,
mass spectrometry, and high efficiency fluorescence polarization and utilized for industrial –
scale SNP genotyping.

The variations or polymorphism are markers of genes and genome with which researchers
perform genetics analysis in an outbreed species. As the single base differences that
genetically separate individuals within a population, SNPs could act as markers in the search
for the origins of diseases caused by the interaction of multiple genes. A large SNP library
could help researchers pin point the genetic origins of diseases, and potentially, the most
appropriate drugs to treat them.

The main use of human SNP map will be in dissecting the contributions of individual genes
to diseases that have a complex, multi gene basis. Knowledge of genetic variation directly
affects patient care to some degree for example, gene variation leads to tissue and organ
incompatibility, affects the success of transplant and the main stay of medical genetics has
been the study of rare gene variations that lie behind inherited diseases such as cystic fibrosis.
But variation in genome sequences underlies differences in our susceptibility to, or protection
from all kind of diseases, in the age of onset and severity of illness; and in the way your
bodies respond to treatment for example, we already know that single base difference in the
APOE gene are associated with Alzheimer’s disease that a simple deletion within the
chemokinin receptor gene CCR5 leads to resistance to HIV and AIDS. The benefits of the
SNP map are that it covers the entire the genome. So by comparing the patterns and
frequencies of SNPs in patients and controls, researches can identify which SNPs are
associated with which diseases (11,12).

The SNPs of clinical medicine is gaining increasing attention in the most efficient way of
identifying genetic region or genes implicated common complex diseases and traits such as
CNS disorders, cancer and cardiovascular diseases. Many laboratories tacking complex gene
mapping have focused on autoimmune diseases, such as type I diabetes, multiple sclerosis,
and lupus erythematosus because these diseases are often early adult onset, easily diagnosed,
and can be studied in different ways (13).

A major application of SNP efforts is on using small variations in genes sequences as

markers for defining populations exhibiting a given phenotype. In other words cohorts-
population or groups using a set of SNPs and this set of SNPs defines the set of individuals
that biologically are indistinguishable with respect to a given trait. Thus the major derivers
for the SNP efforts in health care are-

  1. Defining genetic regions and targets for therapeutics,

  2. Stratifying patient populations according to expression of SNP markers (and

corresponding biological phenotype), and

  3. Positioning drugs into the appropriate sub sectors of patient populations.

Fortunately, knowledge concerning the pharmacogenetics of drug metabolism, when applied

to drug selection and dosing, could help physicians prevent adverse effects and therapeutic
failures, and therefore enhance therapeutic efficiency and reduce costs. According to Dr. Fred
Ledley knowing whether a drug will produce a response is important so that the best
treatment can be given straight away and major cost saving could come from genetic testing
for genetic variations. Predictive genetic test will be more developed and will be first
applicable in the situations where individuals have a strong family history of a particular
condition. Such testing is available for several conditions, such as breast and colon cancer.
With increasing genetic information about common illness, this kind of risk assessment will
be more generally available.

Polymorphisms in the human genome contribute to wide variations in how individuals respond to medications,
either by changing the pharmacokinetics of drugs or by altering the cellular response to therapeutic agents. The
goal of the emerging discipline of pharmacogenomics is to personalize therapy based on an individual's
genotype. Due to the relatively large frequency of single-nucleotide polymorphisms (SNP) in the human genome,
synonymous SNPs are often disregarded in many pharmacogenomic studies based on the assumption that these
are silent. We have shown recently that synonymous SNPs in ABCB1 (P-glycoprotein), which is implicated both
in determining drug pharmacokinetics and multidrug resistance in human cancer cells, can affect protein
conformation and function. We discuss the importance of polymorphisms in drug metabolizing enzymes and
transporters in anticancer therapy and suggest that synonymous polymorphisms may play a more significant role
than is currently assumed.[5]
 REFERENCES
 Giacomini, K. M., et al. "The Pharmacogenetics Research Network: From Snp Discovery to
Clinical Drug Response." Clin Pharmacol Ther 81.3 (2007): 328-45.

 Zilfalil Alwi, (2005) The Use of SNPS in Pharmacogenomics Studies. Malaysian Journal of
Medical Sciences, 12 (2). pp. 4-12. ISSN

 www.ornl.gov/hgmis

  11. F.S. Collins, M.S. Guyer and A. Chakravarti,

Science,278, 1580 (1997).

 12.E.S.Lander,Science,274, 539 (1996).

  13.F.S. Collins,JAMA, 278, 1285 (1997).

  17. N.S. Halim,The Scientist14, 20 (2000).

  18. F.S. Collins and V.A. Mc Kusick,JAMA, 285, 540 (2001).
 3 Mango R, Vecchione L, Raso B, Borgiani P, Brunetti E, Mehta JL, Lauro R, Romeo F,

Novelli G. Pharmacogenomics in cardiovascular disease 2005

Dec;6(15):2565-76.

 H C Erichsen1 and S J Chanock1,2

1. 1
Section on Genomic Variation, Pediatric Oncology Branch, Center for Cancer Research,
Advanced Technology Center, National Cancer Institute, National Institutes of Health, 8718
Grovemont Circle, Bethesda, MD 20892-4605, USA
2. 2
Core Genotyping Facility, National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA. Journal of Cancer (2004) 90, 747–751. doi:10.1038/sj.bjc.6601574
http://www.bjcancer.com/
Published online 17 February 2004

5 Sauna ZE, Kimchi-Sarfaty C, Ambudkar SV, Gottesman MM. Silent polymorphisms speak:
how they affect pharmacogenomics and the treatment of cancer
15;67(20) 2007
 

Case Study

How can SNPs be used as risk factors in disease development?

 SNPs do not cause disease, but they can help determine the likelihood that someone
will develop a particular illness. One of the genes associated with Alzheimer's
disease, apolipoprotein E or ApoE, is a good example of how SNPs affect disease
development. ApoE contains two SNPs that result in three possible alleles for this
gene: E2, E3, and E4. Each allele differs by one DNA base, and the protein product of
each gene differs by one amino acid.

Each individual inherits one maternal copy of ApoE and one paternal copy of ApoE. Research
has shown that a person who inherits at least one E4 allele will have a greater chance of
developing Alzheimer's disease. Apparently, the change of one amino acid in the E4 protein
alters its structure and function enough to make disease development more likely. Inheriting
the E2 allele, on the other hand, seems to indicate that a person is less likely to develop
Alzheimer's.

Of course, SNPs are not absolute indicators of disease development. Someone who has
inherited two E4 alleles may never develop Alzheimer's disease, while another who has
inherited two E2 alleles may. ApoE is just one gene that has been linked to Alzheimer's. Like
most common chronic disorders such as heart disease, diabetes, or cancer, Alzheimer's is a
disease that can be caused by variations in several genes. The polygenic nature of these
disorders is what makes genetic testing for them so complicated [1]

 In numerous cases, the polymorphic expression of drug-metabolizing enzymes has

provided an explanation as to why some patients do not obtain the expected benefits from
drug therapy. The most important of the polymorphically expressed P450 enzymes is
CYP2D6. It is responsible for the metabolism of many older tricyclic antidepressant
medications, such as desipramine. The wide inter individual variation in the steady – state
plasma concentrating or therapeutic effect of these medications after a similar dosage is
primarily attribute to differences in their metabolism by CYP2D6. The wide inter individual
variation in the steady-state plasma concentration or therapeutic effect of these medications
after a similar dosage is primarily attributable to differences in their metabolism by
CYP2D6. Ironically, these are some of the most frequently prescribed drugs on the market.
The resulting inter individual variability in the pharmacokinetic profile of these drugs make
it difficult to predict the clinical response to a given dose. A similar situation exists with the
enzyme CYP2D9 (contributing to the metabolism of anxiolytics and antiulcer drugs) and
phenytoin (a standard anticonvulsant medication).[13]
 The role of single nucleotide polymorphisms in improving drug therapy
Pharmacogenomics is the study of how an individual's genetic inheritance affects the body's
response to drugs. Pharmacogenomics holds the promise that drugs might one day be tailor-
made for individuals and adapted to an individual's genetic makeup. Several studies have
shown that both adverse and beneficial responses to cardiovascular drugs can be influenced
by single nucleotide polymorphisms in genes coding for metabolising enzymes, drug
transporters and drug targets. Despite the large amount of data about gene-drug interactions,
the translation of pharmacogenomics in clinical practise is slow. To improve this, there is a
need of new technology and large prospective trials allowing for simultaneous analysis of
multiple genetic variants in molecular pathways that could affect drug disposition and
action.[3]
 SNPs in cancer research and treatment
Genetic variation in the human genome is an emerging resource for studying cancer, a
complex set of diseases characterized by both environmental and genetic contributions. The
number of common germ-line variants is great, on the order of 10–15 million per person,
and represents a remarkable opportunity to investigate the aetiology, interindividual
 differences in treatment response and outcomes of specific cancers. The study of genetic
variation can elucidate critical determinants in environmental exposure and cancer, which
could have future implications for preventive and early intervention strategies. However, we
are in the initial stages of characterizing the tools (i.e., the single-nucleotide polymorphism,
SNP) to rigorously analyze the genetic contributions to complex diseases, such as cancer. If
the promise of the genomic era is to be realized, we must integrate this information into new
strategies for implementation in both public health measures and, most importantly,
provision of individual cancer-related care.

Future Approach

The impact of genetics on medicine will be even more widespread. The pharmacogenomics
approach for predictive drug responsiveness will be standard practice for quite a number of
disorders and drugs. New gene based “designer drugs” will be introduced in the market for
diabetes mellitus, hypertension, mental illness and many other conditions. Improved
diagnosis and treatment of cancer will likely be the most prominent clinical consequences of
genetics. A vast amount of molecular information can be collected about the genetic basis of
malignancy and on that basis every tumor will have a precise molecular fingerprint.
Cataloging the genes and therapy will be individually targeted to that fingerprint (17). Many
of the diseases can be identified where common variants in genes involved in drug
metabolism or drug action are associated with the likelihood of a good or bad response (18).

Harping on the human genome, single nucleotide polymorphism and better understanding of
potential discipline – the pharmacogenomics, will give a fruitful return in the form of better
understanding of complex diseases by deciphering metabolic pathways, reduction of drug
toxicity, development of predictive genetic test and this will lead ultimately to the
development of individualized medicine prescribing practices