**5. Application of SNPs**

#### **5.1. SNPs as biological markers of human diseases**

Most SNPs are not responsible for a disease state. They serve as biological markers for pinpointing a disease on the human genome map. SNPs occur on average once every 200 base pairs [18, 51–53] in the human genome. Common SNPs (a minor allele frequency range from 5% to *>*20%) can explain a proportion of common human disease. Most SNPs do not occur in the coding region of genes or even in genes [4]. Nonsynonymous SNPs that suspect in causing a human disease do not account for all SNPs that can cause disease or susceptibility to disease. Other functional SNPs associated with human disease or susceptibility to disease includes SNPs located in promoters [54, 55], introns [56], splice sites [57], and intragenic region [56, 58]. Even synonymous SNPs have been involved in functional consequences via unknown mechanism [59].

#### **5.2. SNPs and drug development**

**Figure 10.** High resolution melting (HRM) analysis (https://www.dna.utah.edu/Image/Hi\_Res%20Melting\_Normalized.

This method, the fragment cover SNP is amplified by real-time PCR and followed by HRM. The HRM is a technique for the detection mutations and SNPs, which based on analysis of melting curve when double-strand DNA (dsDNA) separate into single-strand DNA (ssDNA) during increased temperature from around 50°C up to around 95°C. At some point during this process, the melting temperature of the amplicon is reached and the two strands of DNA separate. This can visualize the melting behavior of the product through a fluorescent dye [50]. The fluorescent dye binds to double-strand DNA during the amplification resulting in an increase of fluorescence (**Figure 10**). This method is simple, cost-effective, fast and able to accurately genotype many samples rapidly. It also reduces the need to design multiple

It is a method for screening DNA samples for SNPs and inherited mutations. The analysis begins with a PCR amplification, followed by a step of denaturation-renaturation to create hetero-and homoduplexes from the two populations in the PCR. The heteroduplexes with mismatch pairing and homoduplex can be detected on reversed-phase chromatography of denaturing high performance liquid chromatography (DHPLC). The heteroduplexes thermally that less stable than their corresponding homoduplexes will be resolved by chromatography when subjected to a sufficiently high temperature. This mismatch will decrease the interaction with

the column and a reduced retention time compared to the homoduplexes (**Figure 11**).

JPG).

*4.3.2. High resolution melting analysis (HRM)*

16 Genetic Diversity and Disease Susceptibility

pairs of primers or purchase expensive probes.

*4.3.3. Denaturing high performance liquid chromatography (DHPLC)*

Variants of genes encoding drug metabolizing enzymes or drug targets have been studied in association with personal drug responses. SNPs are popular molecular markers in such pharmacogenomics studies. Using SNPs to study the genetics of drug response will help in the creation of personalized medicine or the most appropriate drug for an individual and could be determined in advance of treatment by analyzing a patient's SNP profile. SNPs may be associated with the absorbance and clearance of therapeutic agents. The association of different SNPs with a wide range of human diseases such as cancer, infectious diseases autoimmune, neuropsychiatric and others can be used as targets for drug therapy [60].

association between an intronic SNP (rs1784519) and the risk of schizophrenia in a Thai pop-

Polymorphisms

19

http://dx.doi.org/10.5772/intechopen.76728

Dyslipidemia is an abnormal of lipid and/or lipoproteins in the blood. It is a major risk factor of coronary heart disease and atherosclerosis. A genome-wide association study (GWAS) examined the concentrations of HDL-C and triglyceride in European ethic and identified the SNP at 15 loci which associated with HDL-C levels (such as, APOA1/C3/A4/A5 gene cluster) and SNPs at 12 loci associated with triglycerides (such as APOB, APOE gene) [68]. Thongket et al. examined SNP in apolipoprotein E receptor 2 gene using real-time PCR and HRM analysis and found that the rs2297660 showed strong association with risk of dyslipidemia in Thai

Diabetes mellitus (DM) is a group of metabolic disorders. Untreated diabetes patient can cause many complications. Acute complications can include diabetic ketoacidosis, hyperosmolar hyperglycemic state, or death [70]. SNPs in the gene encoding aldose reductase (*AKR1B1*) were studied for their association with diabetic nephropathy by Wolford et al. They genotyped eight SNPs of *AKR1B1* gene in two different case control sets by Pyrosequencing™ method and found that common *AKR1B1* SNPs were unlikely to be major determinants of diabetic nephropathy [71]. Altshuler et al. genotyped SNPs from 3000 individuals to investigated the association of two polymorphisms, a missense variant in *PPARG* (Pro12Ala) and a silent C/T polymorphism in exon 22 of *ABCC8*, with type 2 diabetes using FRET and FP methods. It was found that only

Pro12Ala showed a significant association with decreased risk of type 2 diabetes [72].

MS, GeneChip® array, pyrosequencing, DHPLC, HRM, RFLP, and so on.

Polymorphism is a variation in DNA sequence that may affect individual phenotypes. It occurs more often in the general population than mutations (frequency ≥ 1%). The majority of variation is single nucleotide polymorphism (SNP) which is a single base change in a DNA sequence that occurs at a specific position in the genome. SNP may locate within coding, or non-coding, or intergenic regions of genes. Most of SNPs have two alleles, for an individual SNP, one is major allele and the other is the minor allele based on their observed frequency in the general population. Genome-wide association studies (GWAS) search for SNPs that occur more frequently in person with a particular disease than in person without the disease and pinpoint genes that may contribute to risk of disease. Linkage disequilibrium (LD) is commonly used to indicate that two or more genes are physically linked. It plays an important role in health and disease. Most SNPs are not responsible for a disease state but serve as biological markers for various complex diseases such as cancer, diabetes, dyslipidemia, schizophrenia, and so on. There are several methods for analyzing SNPs such as MALDI-TOF

ulation [*p* = 0.00036, odds ratio for the minor A allele: 2.11(1.57–2.84)] [67].

**6.3. Dyslipidemia**

population [69].

**7. Conclusion**

**6.4. Diabetes mellitus**
