**3. Association study**

By comparing the patterns with patterns obtained by analyzing the DNA from a group of individuals affected and unaffected by the disease is called as an 'association study'. This study demonstrates the linking between the polymorphism and diseases or drug respond.

#### **3.1. Minor allele frequency**

Minor allele frequency (MAF) refers to the frequency at which the less common allele occurs in a given population. MAF is widely employed in GWAS for complex traits [20]. SNPs with a minor allele frequency of 5% or greater were targeted by the HapMap project.

#### **3.2. Allele frequency and genotype frequency**

Allele frequency is the relative frequency of an allele at a particular locus in a population.

Genotype frequency in a population is the sum of the individuals with the same genotype divided by the total number of individual in that population. In addition, the genotype frequency, in population genetics, means the proportion or frequency of genotypes in a population (0 < *f* < 1). The genotype frequency may also be used in the genomic profiling to predict someone is having a disease [21] or even a birth [22] defect. It can also be used to determine ethnic diversity.

#### **3.3. Haplotypes**

Haplotypes are a combination of alleles at different markers along the same chromosome that is inherited as a unit. Each haplotype is a combination of major and minor alleles along the chromosomes, and each individual is represented twice to account for the maternal and paternal contributions [9]. The fundamental difference between haplotypes and individual genotypes at SNPs is that the alleles are assigned to a chromosome.

Haplotypes inform about the exchange of DNA during meiosis or recombination, which is useful for locating the mutation that are associate with diseases by using linkage method. It has an effect on linkage disequilibrium.

#### **3.4. Linkage disequilibrium (LD)**

of gene, or in the intergenic regions may affect gene splicing (SNPs at intron region), transcription factor binding (SNPs at 5′ untranslated region), messenger RNA degradation, or the sequence of non-coding RNA. The type of SNPs located upstream or downstream from the

By comparing the patterns with patterns obtained by analyzing the DNA from a group of individuals affected and unaffected by the disease is called as an 'association study'. This study demonstrates the linking between the polymorphism and diseases or drug respond.

Minor allele frequency (MAF) refers to the frequency at which the less common allele occurs in a given population. MAF is widely employed in GWAS for complex traits [20]. SNPs with a

Allele frequency is the relative frequency of an allele at a particular locus in a population.

Genotype frequency in a population is the sum of the individuals with the same genotype divided by the total number of individual in that population. In addition, the genotype frequency, in population genetics, means the proportion or frequency of genotypes in a population (0 < *f* < 1). The genotype frequency may also be used in the genomic profiling to predict someone is having a disease [21] or even a birth [22] defect. It can also be used to determine

Haplotypes are a combination of alleles at different markers along the same chromosome that is inherited as a unit. Each haplotype is a combination of major and minor alleles along

minor allele frequency of 5% or greater were targeted by the HapMap project.

gene that affect gene expression is referred to an expression SNP (eSNP).

**3. Association study**

**Figure 2.** SNP location.

6 Genetic Diversity and Disease Susceptibility

**3.1. Minor allele frequency**

ethnic diversity.

**3.3. Haplotypes**

**3.2. Allele frequency and genotype frequency**

In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population that may or may not be on the same chromosome. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is higher or lower than what would be expected if the loci were independent and associated randomly [23]. LD can detect differences between the SNP patterns of the two groups and reveal which pattern is most likely associated with the disease-causing gene or response to certain drugs.

LD is an important concept in genetic studies that aims to identify and localize genes related to disease susceptibility. LD is commonly used to indicate that two genes are physically linked. It is defined as the difference between the observed frequency of a particular combination of alleles at two loci and the frequency expected for random formation of haplotypes from alleles. The frequency of a particular allele at a given locus will be independent of alleles at other linked loci. LD plays a crucial role in the current methods for mapping complex disease or trait-associated genes or plays a key role in health and disease. The level of linkage disequilibrium is influenced by a number of factors such as genetic linkage, selection, the rate of recombination, the rate of mutation, genetic drift, non-random mating, and population structure.

#### **3.5. Genome-wide association studies (GWAS)**

GWAS identify the common disease-causing variants by using high throughput genotyping equipment to examine hundreds of thousands of common SNPs and compare these common genetic variants in large numbers of affected cases (patient) to those in unaffected controls (non-patient) to determine whether have an association with disease (**Figure 3**) [24, 25].

In most chromosome regions, there is strong association among SNP, therefore, only a few SNPs in each region are selected to be sequenced to predict the alleles of the remaining SNPs in that region. An accurate mapping of LD pattern among SNPs which differ across ancestral groups is required for selecting the best tag SNPs. The precise LD maps are needed to help genetic association studies and stimulated the developing of human haplotype map [26, 27]. GWAS pinpoint genes that may contribute to a risk of developing disease. The data derived from GWAS inform about disease etiology, therapeutic targets, and gene function [28].

of primer [31, 32]. The CPE approaches that use fluorescence-based detection involve SBE of primer with fluorescently labeled ddNTPs (**Figure 4b**). Specific primer extension (SPE) methods use two primers that have the same nucleotide sequences except specific allele/base at their 3′ end. The primers can extend if the nucleotide at their 3′ end of the primers perfectly binds with the SNP of complementary template, then allelic discrimination can be examined

Polymorphisms

9

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

**MassEXTEND™** procedure uses a mixture of dNTPs and ddNTPs for primer extension and discriminate the allele by mass detection. It provides medium-to-high-throughput genotyping

**Figure 4.** Primer extension approaches for SNP genotyping. (a) Mass spectrometry-based detection. This method uses a primer that anneals one base upstream of the SNP site followed by its extension with ddNTPs. Extension products are detected by mass spectrometry, and the difference between mass of extension product and primer identifies incorporated nucleotide(s) and therefore the SNP genotype. (b) Fluorescence detection using capillary electrophoresis. This technique uses a primer that anneals one base upstream of the SNP site after that its extension with ddNTPs that are labeled with different fluorescent tags. Products are detected by fluorescence after capillary electrophoresis and the color of dye indicates incorporated base(s). (c) Allele-specific primers with detection of PCR products. This method uses two allele-specific primers that anneal with their 3′ ends at the SNP site and a common reverse primer (not shown) for PCR reaction. The amplification occurs when the forward primer perfectly matches to the SNP at its 3′ end and the genotype

by mass different using gel electrophoresis (**Figure 4c**).

can be determined by gel electrophoresis of PCR product [29].

**Figure 3.** Genome-wide association studies (GWAS). (http://mmg-233-2014-genetics-genomics.wikia.com/wiki/File:GWAS. jpg).
