Genome signal case
study
SNPs in disease gene mapping, medicinal drug development and
evolution
Single nucleotide polymorphism
(SNP)
• Single nucleotide polymorphism (SNP) technologies can be used to identify disease-causing genes
in humans and to understand the inter-individual variation in drug response.
• These areas of research have major medical benefits. By establishing an association between the
genetic make-up of an individual and drug response it may be possible to develop a genome-based
diet and medicines that are more effective and safer for each individual.
• Additionally, SNPs can be used to understand the molecular mechanisms of sequence evolution. It
has been found that throughout the given gene, the rate, type and site of nucleotide substitutions
as well as the selection pressure on codons is not uniform.
• The residues that evolve under strong selective pressures are found to be significantly associated
with human disease.
• Deleterious mutations that affect biological function of proteins are effectively being rejected by
natural selection from the gene pool. If substituted nucleotides are fixed during evolution then they
may have selection advantages, they may be neutral, or they may be deleterious and cause
pathology. Therefore, it is possible that disease-associated SNPs (or pathology) and evolution can
be related to one another.
Single nucleotide polymorphism
(SNP)
• The completion of the human genome project provided the necessary tools to understand the genetic
basis of diversity among individuals, the most common familial traits, evolutionary processes, complex
and common diseases such as diabetes, obesity, hypertension and psychiatric disorders, and to develop
genome-based medicinal drugs
• Scientists generally think that the genomes between two randomly selected individuals contain
approximately 0.1% differences or variations. This variation is called polymorphism, and it arises because
of mutations.
• Several comparative studies on identical and fraternal twins (Martin et al. 1997) and siblings suggest that
DNA polymorphism is one of the factors associated with susceptibility to many common diseases (Table
1), every human trait such as curly hair, individuality and inter-individual difference in drug response.
• DNA sequence variation is also considered to be responsible for genome evolution. Based on these
observations, it has been proposed that by cataloging the DNA polymorphisms in different populations
and in different species, it may be possible (a) to develop genome-based knowledge on the susceptibility
of an individual to many common diseases, (b) to manufacture safer and more effective individualized
diet and medications for patients, and (c) to understand evolutionary processes.
• However, many experts believe that this single nucleotide polymorphism (SNP) technology has to face
several challenges before it makes its impact on medicine.
Detection
• The simplest form of DNA variation among individuals is the
substitution of one single nucleotide for another. This type of change
(Fig. 1A) is called SNP.
• It is estimated that SNPs occur at a frequency of 1 in 1,000 bp
throughout the genome.
• approximately 50% of SNPs are in the noncoding regions, 25% lead
to missense mutations (coding SNPs or cSNPs), and the remaining
25% are silent mutations (they do not change encoded amino acids).
• These silent SNPs are called synonymous SNPs, and it is most likely
that they are not subject to natural selection
• On the other hand, nonsynonymous SNPs (nSNPs, change-encoded
amino acids) may produce pathology and may be subject to natural
selection.
• SNPs (both synonymous and nonsynonymous) influence promoter
activity and pre-mRNA conformation (or stability). They also alter the
ability of a protein to bind its substrate or inhibitors (Kimchi-Sarfaty
et al. 2007) and change the subcellular localization of proteins
(nSNPs).
• Therefore, they may be responsible for disease susceptibility,
medicinal drug deposition and genome evolution.
• Although several of them affect the
functions of genes, many of them are not
deleterious to organisms and must have
escaped selection pressure.
• For the purpose of identifying SNPs,
several private and public organizations
have undertaken massive efforts to
develop high-throughput SNP genotyping
methods over the past 20 years
(reviewed in Shastry 2002, 2005).
• As a result of these efforts, a large
collection of SNPs is now available from
the human genome project
SNPs in gene discovery
• Because some diseases are hereditary, one immediate goal of the human genome project is to
find out which genes predispose people to various disorders and how the sequence variation in
a gene affects the functions of its product.
• As mentioned previously, SNPs occur frequently throughout the genome. Therefore, they can be
used as markers to identify disease-causing genes by an association study (Gray et al. 2000).
• In such studies, it is assumed that two closely located alleles (gene and marker) are inherited
together. Therefore, a simple comparison of patterns of genetic variations between patients and
normal individuals may provide a method of identifying the loci responsible for disease
susceptibility (Hirschhorn and Daly 2005).
• One advantage of this method is that it does not need a large family. However, several
limitations such as population structure, different levels of linkage disequilibrium (LD) (see
below) in loci, and epistatic interaction of alleles may impose difficulties.
• Despite these limitations, there has been some success in identifying the association between
polymorphisms and diseases (Table 1).
• however, this type of whole-genome approach to
mapping requires the genotyping of thousands of
samples.
• Therefore, a different procedure called haplotype
(collection of SNPs on a single chromosome at a
locus that is inherited in blocks, Fig. 1B) analysis A hypothetical haplotype and drug
has been used to identify common disease genes response. Individual A shows no response,
(Hirschhorn and Daly 2005). Because the genome individuals B and D show an increased
undergoes recombination involving large response, whereas individual C shows a
decreased response to a drug. The
stretches of DNA, there may be several SNPs horizontal arrows denote no change in
linked together in this large region of DNA. These gene activity, whereas upward and
closely linked SNPs may then be cotransmitted downward arrows represent increased and
from generation to generation in these large decreased gene activity, respectively.
blocks (Reich et al. 2001). Haplotype analysis may give a more
accurate prediction of drug response
• Single nucleotide polymorphism technologies are also applicable in the development of individualized
medicine.
• Over the past 20 years it has become increasingly clear that genetic polymorphism in genes encoding drug-
metabolizing enzymes, drug transporters and receptors contribute, at least in part, to the inter-individual
variability in drug response (reviewed in Shastry 2003, 2004; Evans and Johnson 2001).
• These factors affect drug absorption, distribution, metabolism and excretion. As a result, some drugs work
better in some patients than others, and some drugs may be highly toxic to certain patients (Ansari and
Krajinovic 2007). This type of anti-drug reaction has been observed in several diseases, such as pulmonary
hypertension, epilepsy, cardiac arrhythmia, renal cell carcinoma, leukemia and liver cancer (reviewed in Shastry
2006a, 2006b; Roses 2000).
• In order to understand the relationship between heritable changes in genes and inter-individual variations to
drug response, two related fields namely pharmacogenetics and pharmacogenomics (Dervieux and Bala 2006)
emerged and gained popularity in the late 1990s.
• They have undertaken massive studies on the genetic personalization of drug response (McLeod and Evans
2001). As a result, there are several high-density SNP maps of genes encoding proteins of medical importance
(Iida et al. 2002, 2003), and now there is strong evidence (Table 2) that links SNPs to inter-individual differences
in drug response (Nothen and Cichon 2002; Ansari and Krajinovic 2007).
• Patients with more active drug-metabolizing enzymes may require higher doses of the drug, and those who do
not have an active enzyme may exhibit toxicity (Fig. 1C).
• However, it should be noted that there are many negative results regarding the association
of gene polymorphism and drug efficacy and toxicity.
• In addition to these negative results there are other problems. For example, drug
metabolism or variation in drug response includes dozens of genes, and many of these
often have multiple polymorphisms.
• Moreover, there are inducible genes, signaling molecules and environmental factors that
may also contribute to variable drug response. The greatest challenge for the future (Roden
et al. 2006) is to understand the genotypic–environmental factor interaction, ethnicity,
inheritance patterns in drug response and how genetic variance responds to medicine.
• If the goals of pharmacogenetics and pharmacogenomics are fulfilled, it may allow
clinicians to genetically subdivide and profile individual patients and treat each patient
according to their genetic make-up.
• This type of medical practice may gradually replace the current trial-and-error-based
selection of medicine in the future. However, at present, studies do not unambiguously
prove the clinical value of pharmacogenetic testing.
SNPs in evolution
• Genetic variants are not only considered to be responsible for disease
risk and inter-individual differences, but also molecular evolution.
• Genetic evolution in part depends upon a balance between natural
selection and environmentally driven mutation. The natural selection will
maintain and retain the amino acid type and position among species
because these amino acids are critical for the protein function.
• Therefore, in a given set of homologous genes, certain amino acids are
highly conserved, even among distantly related species that diverged
hundreds of million years ago (Fig. 3).
• These conserved residues are evolving under strong selective pressure.
Deleterious mutations that affect the biological functions of proteins are Protein sequence alignment of the mutant
effectively eliminated by natural selection from the gene pool.
part of the human frizzled-4 with that of
• The selection pressure against deleterious SNPs depends upon the
molecular functions of proteins and those genes that encode other species. A conservative change in codon
transcriptional regulatory proteins are generally found to be under the 256 causes pathology in the patient (A)
strongest selective pressure (Ramensky et al. 2002). whereas a radical change in a less conserved
residue is nonpathogenic (B). h, human; m,
mouse; r, rat; X, xenopus; Z, zebra fish; and g,
chicken
• Because SNPs are present at all levels of evolution, including the branch
point of speciation, they can be used to study sequence variation among
species.
• Additionally, the rate, type and site of substitution as well as the selection
pressure on codons are not uniform throughout the given gene. T
• herefore, if genetic variants are fixed during evolution, then they may
have either selection advantages for the organism, they may be neutral
regarding the fitness, or they may be deleterious and thus cause
pathology. Hence, a comparative genomic study of disease-associated
SNPs can be used to understand the relationship between the pathology
and evolution.