**2. Application**

Many common diseases having high morbidity as well as mortality rates have now known with well-established genetic components. The degree of role of genetics has been predicted for diseases like obesity and diabetes according to their sibling analysis [26, 27]. In the same way, some rare gene mutations can provide a vision into the more complex biological processes [28]. For instance, when the subject possesses extreme levels of HDL in their blood, one can easily demonstrated the influence of CETP (cholesteryl ester transfer protein) on patients HDL levels [29–31]. In another case, a person having deactivating mutations due to the Janus kinase 3 (JAK 3) gene shows severe combination of immune-deficient syndrome, as sometimes inhibition of JAK3 was expected to affect the human immune suppression [32, 33]. Hence, this led to a new investigation on drugs having CETP inhibition and JAK3 inhibition with the help of pharmacogenetics [34]. Also, with the advent of pharmacogenomics, the path of relationships between disease state and human genes has now established which led to the suitable selection of therapeutic targets.

Nowadays, many academic institutions and Pharmaceutical companies are moving toward the investigation on the relationship between disease phenotypes and genetic variations to better categorize diseases [35, 36]. Although the collection of medical phenotypes having linkages with samples of DNA provides a prominent opportunity for examine the genetic variation which are present in patients. Investigation of genetic variation can be done by collection of DNA of particular patient. This is characterized in a study where DNA from a person involves in trails of lipid lowering demonstrated a swift connection between phenotypic novel lipase gene family and for HDL levels. As per literature reports, above mentioned studies are based on a sound hypothesis which is linked to candidate's biological gene selection. Now it is easy to cross-examine the genome selection which is solely depends on phenotypic criteria [10, 37]. These stages have now substituted around 300,000 SNPs across the genome, by exploiting only few haplotype-defining SNPs. Perlegen sciences have developed newly genotyping technologies which has with a capability of genotyping mass hundreds or thousands of markers with the help of high-density based oligonucleotide arrays linked with restriction enzyme-based genomic reduction. However, as these technologies advances, still exact number of haplotype-defining SNPs is uncertain. Some findings are recently reported relation to assess polymorphisms across selected gene regions recommends that, it is necessary to reach an r2 of >0.8% in order to detect more than 80% of all haplotypes. Due to HapMap project progression with defined LD patterns linkage, scientist working on genes will thorough assess to the degree of LD in a represented regions or selected regions. This will enable to explore more around selection of SNP regardless design of study [38, 39]. As genome approach does not depend upon selection of candidate genes, so understanding on complex diseases such as psychiatric or cardiovascular diseases will become more efficient. Some researchers believed that the new horizons on LD coverage about insights of human genome and SNP density will show the perception of a substantial genomic portion areas and its relation with interest of phenotype [40, 41]. To assess the Perlegen Sciences chip-based array-based platform and to justify the haplotype tagging approach for the identification of genetic associations, 7283 SNPs connecting 17.1 mega bases (Mb) of DNA were genotyped for detecting linkages with HDL levels. Further, SNPs were connected with 50 CETP haploblock gene were found out as the most valuable association in dataset. The companies like Perlegen and project like Hap Map project recently declared their purpose to provide it SNPs markers into public provinces to further advent to basis for such kind of experiments which help in the scientific community [42, 43].

**19**

condition [56, 57].

*Pharmacogenomics: Overview, Applications, and Recent Developments*

Pharmacogenetics significantly expands the therapy outcomes and drug uses. Medications may prescribe in low dose under strict monitoring to patients which shows genetically predisposed to their adverse events. This would probably helpful for drugs having narrow therapeutic index such as warfarin may be started gradually in patients having VKORC1 genotype linked with improved warfarin sensitivity. With the help of pharmacogenetics, it is now possible to reduce the number of subjects to conduct any experiment and chances of error may be eliminated for

On the contrary, clinicians may be able to minimize possible adverse effects with the aid of genetic information for matching suitable drug to suitable patient at an appropriate dose. For instances, traditional approach to the management of hypertension involves the trial of numerous anti-hypertensive drugs till the desired blood pressure achieved with adequate drug tolerability. In this case, few initial drugs/agents fail to produce lower blood pressure or shown intolerable adverse effects. This way of selection of drugs took long time which ultimately suffered by patients. On the contrary, Pharmacogenetics, based on the patients' DNA, offers the greatest response with the best tolerability of the drug. Based on genetic regulator of cellular functions, pharmacogenetics may be able to produce new drugs with less adverse effects. For example, chromosome translocation and its derived enzymes are responsible for causing life-threatening chronic myeloid leukemia (CML) which led to accelerate FDA approval of inhibitor of translocation-created enzyme Imatinib [46]. In the end, this core subject improves the quality and cutdown the total costs of healthcare by minimizing the number of adverse reaction and reduce treatment failures gives rise to the discovery of new genetic targets for

**3.1 Thiopurine therapy and TPMT (thiopurine methyltransferase) testing**

Thiopurine are the categories of drugs that are used to conquer the normal activity of the body's immune system. In short, these are called antimetabolites chiefly used as an antiproliferative as well as immunosuppressants such as mercaptopurine and azathioprine. 6-mercaptopurine daily administered for 3–4 years for treating childhood leukemia, while azathioprine which is a prodrug of 6-mercaptopurine prescribed for treating inflammatory bowel disease (also known as Crohn's disease) [50]. TPMT methylates thiopurine compounds. S-adenosyl-Lmethionine acts as methyl donor and converts it into S-adenosyl-L-homocysteine [51, 52]. So, TPMT metabolizes various thiopurine based drugs with mechanism of S-adenosyl-L-methionine while S-methyl acting as donor, while S-adenosyl-Lhomocysteine acting as a derivative. Genetic polymorphism which affects basically enzymatic activity has association with variations in toxicity and sensitivity within individuals due to such drugs. Nearby 1/300 individual is lacking for this enzyme. TPMT has not recognized to have any phenotype in the absence of encounter drug. TPMT is now enlists by FDA as a pharmacogenomic biomarker for various adverse drug reactions related to cisplatin such as cisplatin-induced

Patients having identical alleles at equivalent chromosomal loci accumulate unnecessary thioguanine nucleotides levels (up to 10-fold higher related with wild types) and treatment with standard dosages of drug and leading to a hematopoietic toxicity (pancytopenia and myelosuppression) which is life-threatening

*DOI: http://dx.doi.org/10.5772/intechopen.93737*

many diseases [44, 45].

disease management [47–49].

ototoxicity in teenagers [47, 53–55].

**3. Case studies**

*Pharmacogenomics: Overview, Applications, and Recent Developments DOI: http://dx.doi.org/10.5772/intechopen.93737*

Pharmacogenetics significantly expands the therapy outcomes and drug uses. Medications may prescribe in low dose under strict monitoring to patients which shows genetically predisposed to their adverse events. This would probably helpful for drugs having narrow therapeutic index such as warfarin may be started gradually in patients having VKORC1 genotype linked with improved warfarin sensitivity. With the help of pharmacogenetics, it is now possible to reduce the number of subjects to conduct any experiment and chances of error may be eliminated for many diseases [44, 45].

On the contrary, clinicians may be able to minimize possible adverse effects with the aid of genetic information for matching suitable drug to suitable patient at an appropriate dose. For instances, traditional approach to the management of hypertension involves the trial of numerous anti-hypertensive drugs till the desired blood pressure achieved with adequate drug tolerability. In this case, few initial drugs/agents fail to produce lower blood pressure or shown intolerable adverse effects. This way of selection of drugs took long time which ultimately suffered by patients. On the contrary, Pharmacogenetics, based on the patients' DNA, offers the greatest response with the best tolerability of the drug. Based on genetic regulator of cellular functions, pharmacogenetics may be able to produce new drugs with less adverse effects. For example, chromosome translocation and its derived enzymes are responsible for causing life-threatening chronic myeloid leukemia (CML) which led to accelerate FDA approval of inhibitor of translocation-created enzyme Imatinib [46]. In the end, this core subject improves the quality and cutdown the total costs of healthcare by minimizing the number of adverse reaction and reduce treatment failures gives rise to the discovery of new genetic targets for disease management [47–49].

### **3. Case studies**

*Drug Design - Novel Advances in the Omics Field and Applications*

Many common diseases having high morbidity as well as mortality rates have now known with well-established genetic components. The degree of role of genetics has been predicted for diseases like obesity and diabetes according to their sibling analysis [26, 27]. In the same way, some rare gene mutations can provide a vision into the more complex biological processes [28]. For instance, when the subject possesses extreme levels of HDL in their blood, one can easily demonstrated the influence of CETP (cholesteryl ester transfer protein) on patients HDL levels [29–31]. In another case, a person having deactivating mutations due to the Janus kinase 3 (JAK 3) gene shows severe combination of immune-deficient syndrome, as sometimes inhibition of JAK3 was expected to affect the human immune suppression [32, 33]. Hence, this led to a new investigation on drugs having CETP inhibition and JAK3 inhibition with the help of pharmacogenetics [34]. Also, with the advent of pharmacogenomics, the path of relationships between disease state and human genes has now established which led to the suitable selection of therapeutic targets. Nowadays, many academic institutions and Pharmaceutical companies are moving toward the investigation on the relationship between disease phenotypes and genetic variations to better categorize diseases [35, 36]. Although the collection of medical phenotypes having linkages with samples of DNA provides a prominent opportunity for examine the genetic variation which are present in patients. Investigation of genetic variation can be done by collection of DNA of particular patient. This is characterized in a study where DNA from a person involves in trails of lipid lowering demonstrated a swift connection between phenotypic novel lipase gene family and for HDL levels. As per literature reports, above mentioned studies are based on a sound hypothesis which is linked to candidate's biological gene selection. Now it is easy to cross-examine the genome selection which is solely depends on phenotypic criteria [10, 37]. These stages have now substituted around 300,000 SNPs across the genome, by exploiting only few haplotype-defining SNPs. Perlegen sciences have developed newly genotyping technologies which has with a capability of genotyping mass hundreds or thousands of markers with the help of high-density based oligonucleotide arrays linked with restriction enzyme-based genomic reduction. However, as these technologies advances, still exact number of haplotype-defining SNPs is uncertain. Some findings are recently reported relation to assess polymorphisms across selected gene regions recommends that,

of >0.8% in order to detect more than 80% of all

haplotypes. Due to HapMap project progression with defined LD patterns linkage, scientist working on genes will thorough assess to the degree of LD in a represented regions or selected regions. This will enable to explore more around selection of SNP regardless design of study [38, 39]. As genome approach does not depend upon selection of candidate genes, so understanding on complex diseases such as psychiatric or cardiovascular diseases will become more efficient. Some researchers believed that the new horizons on LD coverage about insights of human genome and SNP density will show the perception of a substantial genomic portion areas and its relation with interest of phenotype [40, 41]. To assess the Perlegen Sciences chip-based array-based platform and to justify the haplotype tagging approach for the identification of genetic associations, 7283 SNPs connecting 17.1 mega bases (Mb) of DNA were genotyped for detecting linkages with HDL levels. Further, SNPs were connected with 50 CETP haploblock gene were found out as the most valuable association in dataset. The companies like Perlegen and project like Hap Map project recently declared their purpose to provide it SNPs markers into public provinces to further advent to basis for such kind of experiments which help in the

**2. Application**

**18**

it is necessary to reach an r2

scientific community [42, 43].

#### **3.1 Thiopurine therapy and TPMT (thiopurine methyltransferase) testing**

Thiopurine are the categories of drugs that are used to conquer the normal activity of the body's immune system. In short, these are called antimetabolites chiefly used as an antiproliferative as well as immunosuppressants such as mercaptopurine and azathioprine. 6-mercaptopurine daily administered for 3–4 years for treating childhood leukemia, while azathioprine which is a prodrug of 6-mercaptopurine prescribed for treating inflammatory bowel disease (also known as Crohn's disease) [50]. TPMT methylates thiopurine compounds. S-adenosyl-Lmethionine acts as methyl donor and converts it into S-adenosyl-L-homocysteine [51, 52]. So, TPMT metabolizes various thiopurine based drugs with mechanism of S-adenosyl-L-methionine while S-methyl acting as donor, while S-adenosyl-Lhomocysteine acting as a derivative. Genetic polymorphism which affects basically enzymatic activity has association with variations in toxicity and sensitivity within individuals due to such drugs. Nearby 1/300 individual is lacking for this enzyme. TPMT has not recognized to have any phenotype in the absence of encounter drug. TPMT is now enlists by FDA as a pharmacogenomic biomarker for various adverse drug reactions related to cisplatin such as cisplatin-induced ototoxicity in teenagers [47, 53–55].

Patients having identical alleles at equivalent chromosomal loci accumulate unnecessary thioguanine nucleotides levels (up to 10-fold higher related with wild types) and treatment with standard dosages of drug and leading to a hematopoietic toxicity (pancytopenia and myelosuppression) which is life-threatening condition [56, 57].

In more concise way, patients having heterozygous gene variations are also at high risk in terms of toxicity and dosage reductions is prior in these cases up to their tolerate therapy. According to pharmacoeconomic studies, the determination of the TPMT genotype is cost-effective and it must be checked prior to the start of therapy. According to a review of the literature, it was found that TPMT testing with clinical performances for myelosuppression was estimated with specificity of 89%, sensitivity of 32%, 9% PPV and NPV of 97% (**Table 3**). The low estimated value represents low incidence of severity in myelosuppression especially in those patients who are carrier of not less than one defective allele. Researchers have estimated the net cost for avoidance of serious events of myelosuppression. Out of 1000 patients receiving azathioprine, only 3.2% (equivalent to 32 cases) have founded with severe leukopenia and TPMT screening avoided as third of those trials [50, 58].

Iorio and co-workers have analyzed drug responses on various human cancer cell lines. The mapping was done for around 11K tumors obtained from different 29 different human tissues as per Cancer of Genome Atlas (TCGA) enlisted from 1000 cancer cell lines as per Genomics of Drug Sensitivity in Cancer resource. In another event, TCGA patient gene expression was studied for drug response. In this, more than 140 gene drug interactions were studied with specific somatic biomarkers [59–61].

### **3.2 Abacavir therapy and HLA testing**

Abacavir which is HIV-1 nucleoside with reverse transcriptase inhibition is employed for management of HIV/AIDS. It is well tolerated but sometimes shows common to more severe side-effects which include lactic acidosis, hypersensitivity [62]. In some studies, it was observed that a genetic testing/marker can help in predicting whether a HIV-infected patient is at high risk of abacavir induced severe hypersensitivity reactions (approx. 5% of patients) [63, 64]. This hypersensitivity reaction accompanies with lethal gastrointestinal symptoms, rashes, and fever. This reaction is life threatening, particularly if drug is restarted and discontinued. One study has shown about an occurrence of human leukocyte antigen (HLA) B05701 is main cause of hypersensitivity [45, 65]. Based on the Australian cohort, patients were 114 times more hypersensitivity due to HLA-B5701 allele reaction, whereas in an industry-sponsored study revealed that patients with the HLA-B5701 allele was associated with 24 times more likely to experience of hypersensitivity reaction [45]. Thus, one way to solve this issue is genetic testing which integrates pharmacogenetics into the clinical practice. The distribution of HLA-B5701 allele can be detected in many worldwide populations (**Table 4**).

#### **3.3 Statin therapy and polymorphic angiotensin-converting enzyme**

Statins (HMGCoA) reductase inhibitors most often used in management of hypercholesterolemia condition accompanying with elevation in risk to coronary heart disease [66, 67]. Due to increased number of cases of hypercholesterolemia along with volume of statins related prescriptions in US, it creates a significant interest in optimization of costs related to these therapies [31]. Recent investigations have told that polymorphism in I/D angiotensin converting enzyme (ACE) has correlation with risk of heart related syndromes in men when treated with statins [68–70]. Next 2 years of statin medication, in which males who are having DD genotype (equivalent to 27% of patients) shown to have no effect on the risk of coronary heart disease (with relative risk factor of 1.34), in comparison to males with ID (equivalent to 21% of patients) present a marked decreased in risk of coronary cardiovascular disease (with relative risk rate of 0.87), II genotype

**21**

compound [37, 75].

**Table 4.**

**Table 3.**

*Clinical performances of the test.*

*Pharmacogenomics: Overview, Applications, and Recent Developments*

**Clinical performances (%)** Percent responders 40.0 Sensitivity 75.0 Specificity 66.7 Frequency mutation 50.0 Positive predictive value (PPV) 60.0 Negative predictive value (PPV) 80.0

(equivalent to 22% of patients) having relative risk of 0.23, thus concluding that patients bearing DD genotype did not take advantages from statin treatment. Also, testing of I/D genotype might results in cost effective as few patients

**Population group HLA-B5701 carrier frequency range (%)**

Asian 00–6.5 Southwest Asian 4–19.5 Middle Eastern 0.5–6.2 African 0.0–3.5 European 1.5–10.5 Mexican 0.0–4.2 South American 1.2–3.2

These two conventional illustrations of pharmacogenetics involve the genetic variation along with enzymatic metabolism (enzymatic hydrolysis and acetylation). Both act as a monogenic trait and involved PK variations because of inheritance differences [71, 72]. It was observed that some patients with succinylcholine treatment experienced a serious and lethal adverse event i.e. prolonged muscle paralysis which is due to inherited "atypical" butyryl cholinesterase enzyme (BCHE). Later, it was established that BCHE allele which encodes the most usual atypical form of enzyme comprised with a nonsynonymous coding i.e. single nucleotide polymorphism (nSNP), G209 > A, results in Asp70 > Gly change in encoded amino acid which altered active sites of enzyme [73, 74]. But atypical BCHE has less ability to catalyze the succinylcholine hydrolysis and could resist to inhibition due to dibucaine

Tuberculosis is the most problematic disease of both developing as well as under-developed nations. The conformity to patients with tuberculosis is due to common lethal adverse reactions and supposed to have important aspect providing high prevalence [76, 77]. Many investigations showed that the polymorphisms of N-acetyl transferase 2 (NAT-2), CYP2E1 as well as glutathione S transferase (GST-1) would be able to influence concentration of liver toxic isoniazid metabolites in plasma. Some polymorphic genes contribute in the INH induced hepatotoxicity by

**3.4 Muscle relaxant succinylcholine and antitubercular drug, INH**

*DOI: http://dx.doi.org/10.5772/intechopen.93737*

presents the I/I or I/D genotype [70].

*Allele frequency of HLA-B5701 allele in various population groups.*

### *Pharmacogenomics: Overview, Applications, and Recent Developments DOI: http://dx.doi.org/10.5772/intechopen.93737*


#### **Table 3.**

*Drug Design - Novel Advances in the Omics Field and Applications*

In more concise way, patients having heterozygous gene variations are also at high risk in terms of toxicity and dosage reductions is prior in these cases up to their tolerate therapy. According to pharmacoeconomic studies, the determination of the TPMT genotype is cost-effective and it must be checked prior to the start of therapy. According to a review of the literature, it was found that TPMT testing with clinical performances for myelosuppression was estimated with specificity of 89%, sensitivity of 32%, 9% PPV and NPV of 97% (**Table 3**). The low estimated value represents low incidence of severity in myelosuppression especially in those patients who are carrier of not less than one defective allele. Researchers have estimated the net cost for avoidance of serious events of myelosuppression. Out of 1000 patients receiving azathioprine, only 3.2% (equivalent to 32 cases) have founded with severe

leukopenia and TPMT screening avoided as third of those trials [50, 58].

Iorio and co-workers have analyzed drug responses on various human cancer cell lines. The mapping was done for around 11K tumors obtained from different 29 different human tissues as per Cancer of Genome Atlas (TCGA) enlisted from 1000 cancer cell lines as per Genomics of Drug Sensitivity in Cancer resource. In another event, TCGA patient gene expression was studied for drug response. In this, more than 140 gene drug interactions were studied with specific somatic

Abacavir which is HIV-1 nucleoside with reverse transcriptase inhibition is employed for management of HIV/AIDS. It is well tolerated but sometimes shows common to more severe side-effects which include lactic acidosis, hypersensitivity [62]. In some studies, it was observed that a genetic testing/marker can help in predicting whether a HIV-infected patient is at high risk of abacavir induced severe hypersensitivity reactions (approx. 5% of patients) [63, 64]. This hypersensitivity reaction accompanies with lethal gastrointestinal symptoms, rashes, and fever. This reaction is life threatening, particularly if drug is restarted and discontinued. One study has shown about an occurrence of human leukocyte antigen (HLA) B05701 is main cause of hypersensitivity [45, 65]. Based on the Australian cohort, patients were 114 times more hypersensitivity due to HLA-B5701 allele reaction, whereas in an industry-sponsored study revealed that patients with the HLA-B5701 allele was associated with 24 times more likely to experience of hypersensitivity reaction [45]. Thus, one way to solve this issue is genetic testing which integrates pharmacogenetics into the clinical practice. The distribution of HLA-B5701 allele

**20**

biomarkers [59–61].

**3.2 Abacavir therapy and HLA testing**

can be detected in many worldwide populations (**Table 4**).

**3.3 Statin therapy and polymorphic angiotensin-converting enzyme**

Statins (HMGCoA) reductase inhibitors most often used in management of hypercholesterolemia condition accompanying with elevation in risk to coronary heart disease [66, 67]. Due to increased number of cases of hypercholesterolemia along with volume of statins related prescriptions in US, it creates a significant interest in optimization of costs related to these therapies [31]. Recent investigations have told that polymorphism in I/D angiotensin converting enzyme (ACE) has correlation with risk of heart related syndromes in men when treated with statins [68–70]. Next 2 years of statin medication, in which males who are having DD genotype (equivalent to 27% of patients) shown to have no effect on the risk of coronary heart disease (with relative risk factor of 1.34), in comparison to males with ID (equivalent to 21% of patients) present a marked decreased in risk of coronary cardiovascular disease (with relative risk rate of 0.87), II genotype

*Clinical performances of the test.*


#### **Table 4.**

*Allele frequency of HLA-B5701 allele in various population groups.*

(equivalent to 22% of patients) having relative risk of 0.23, thus concluding that patients bearing DD genotype did not take advantages from statin treatment. Also, testing of I/D genotype might results in cost effective as few patients presents the I/I or I/D genotype [70].
