Single Nucleotide Polymorphism and its Application in Mapping Loci Involved in Developing Human Diseases and Traits

Single Nucleotide Polymorphism and its Application in Mapping Loci Involved in Developing Human Diseases and Traits

Rui-Ru Ji (Bristol-Myers Squibb, USA)
DOI: 10.4018/978-1-60960-491-2.ch005
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Abstract

Common diseases or traits in humans are often influenced by complex interactions among multiple genes as well as environmental and lifestyle factors rather than being attributable to a genetic variation within a single gene. Identification of genes that confer disease susceptibility can be facilitated by studying DNA markers such as single nucleotide polymorphism (SNP) associated with a disease trait. Genome-wide association approaches offers a systematic analysis of the association of hundreds of thousands of SNPs with a quantitative complex trait. This method has been successfully applied to a wide variety of common human diseases and traits, and has generated valuable findings that have improved the understanding of the genetic basis of many complex traits. This chapter outlines the general mapping process and methods, highlights the success stories, and describes some limitations and challenges that lie ahead.
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Introduction

SNP, or single nucleotide polymorphism, is a genetic variation in a person’s DNA sequence that occurs when a single nucleotide is replaced by one of the other three nucleotides. SNPs are very common in the human population, occurring in the genome more than one percent of the time (http://www.genome.gov/GWAStudies/).

Key Terms in this Chapter

Single Nucleotide Polymorphism (SNP): A variation in a person’s DNA, molecules inside cells that carry genetic information. It occurs when a single nucleotide is replaced with another. These changes may cause disease, and may affect how a person reacts to bacteria, viruses, drugs, and other substances.

Heritability: The proportion of phenotypic variation in a population that is attributable to genetic variation among individuals. It is estimated by the ratio of genetic variance to total trait variance, so that 0 indicates no genetic effect on trait variance and 1 indicates that all variance are under genetic control.

Quantitative Trait (QT): Trait that has measurable phenotypic variation.

Haplotype: In genetics, a haplotype is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype also refers to a set of single-nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated.

Linkage Disequilibrium (LD): Non-random association of alleles at two or more loci, not necessarily on the same chromosome. It describes a situation where some combinations of alleles or genetic markers occur more or less frequently in a population than would be expected from a random formation of haplotypes based on allelic frequencies.

Genome-Wide Association Study (GWAS): An examination of genetic variation across a given genome, designed to identify genetic associations with observable traits.

Quantitative Trait Locus (QTL): A genetic locus that affects a quantitative trait.

Complex Diseases and Traits: Diseases and traits that are influenced by more than one factor, which can be a gene or an environmental factor.

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