SNP and Haplotype Analyses

SECTION 1 SNP ANALYSIS 108 Part I Introduction 108 1. What Is SNP? 108 2. SNP Discovery and Assay 108 3. SNP and Human Disease 112 4. SNP Databases 113 Part II Step-By-Step Tutorial 114 1. Search for SNP Information of PBEF 1 Gene from dbSNP 114 2. Search for SNP Information of IL-10 Gene from SeattleSNPs 116 Part III Sample Data 117 SECTION 2 HAPLOTYPE ANALYSIS 117 Part I Introduction 117 1. What Is a Haplotype? 117 2. Methods of Haplotype Analysis 118 3. Linkage Disequilibrium, Haplotype Block, and Haplotype Tagging 119 4. Medical Applications of Haplotyping 122 Part II Step-By-Step Tutorial 123 1. Find All SNPs in the Human PBEF1 Gene 124 2. Select tagSNP 124 3. Download PBEF1 SNP Genotype Data from HapMap to the Haploview Program to Perform LD Select and Haplotype Analysis 126 Part III Sample Data 126 SECTION 1 SNP ANALYSIS Part I Introduction 1. What Is SNP? SNP, pronounced “snip,” stands for single-nucleotide polymorphism, which represents a substitution of one base for another, e.g., C to T or A to G. SNP is the most common variation in the human genome and occurs approximately once every 100 to 300 bases. SNP is terminologically distinguished from mutation based on an arbitrary population frequency cutoff value: 1%, with SNP > 1% and mutation < 1%. A key aspect of research in genetics is associating sequence variations with heritable phenotypes. Because SNPs are expected to facilitate large-scale association genetics studies, there has been an increasing interest in SNP discovery and detection.