Single-nucleotide polymorphisms genomics

Introduction to Genomics and Single Nucleotide Polymorphisms Genomics... 

Taillon-Miller, P., Gu, Y., Li, Q., Hillier, L., and Kwok, P. Y. (1998). Overlapping genomic sequences a treasure trove of single-nucleotide polymorphisms. Genome Res. 8, 748-784. 

Ranade K, et al. High-throughput genotyping with single nucleotide polymorphisms. Genome Res 2001 11(7) 1262—1268. 

Single Nucleotide Polymorphisms (SNPs) are single base pair positions in genomic DNA at which normal individuals in a given population show different sequence alternatives (alleles) with the least frequent allele having an abundance of 1% or greater. SNPs occur once every 100-300 bases and are hence the most common genetic variations. 

SNP Single nucleotide polymorphism. Refers to the fact that single nucleotide genetic variation in genome sequence exists at discrete loci throughout the chromosomes. Measurement of allelic SNP differences is useful for gene mapping studies. 

Rapid sequencing and single nucleotide polymorphisms (SNPs) will play a major role in associating sequence variations with heritable clinical phenotypes of drug or xenobiotic response. SNPs occur approximately once every 300-3,000 base pairs if one compares the genomes of two unrelated individuals [13, 14]. Any two individuals thus differ by approximately 1-10 million base pairs, i.e., in < 1% of the approximately 3.2 billion base pairs of the haploid genome (23 chromosomes). 

The International SNP Map Working Group 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 2001 409 928-933. 

Seki T, Tanaka T, Nakamura Y. Genomic stmcture and multiple single-nucleotide polymorphisms (SNPs) of the thio-purine S-methyltransferase (TPMT) gene. J Hum Genet 2000 45 299-302. 

Wang DG, Fan JB, Siao CJ et al. Large-scale identification, mapping, and geno-typing of single-nucleotide polymorphisms in the human genome. Science 1998 280 1077-1082. 

Lai E et al. A 4-Mb high-density single nucleotide polymorphism-based map around human APOE. Genomics 1998 54(1) 31—38. 

Clifford, R., et al., "Expression-Based Genetic/Physical Maps of Single Nucleotide Polymorphisms Identified by the Cancer Genome Anatomy Project," Genome Res., 10, 1259-1265 (2000). 

Sachidanandam, R., et al., "A Map of Human Genome Sequence Variation Containing 1. Million Single Nucleotide Polymorphisms," Nature, 409, 928-933 (2001). 

Wang, D.G., et al., "Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome," Science 280, 1077-1082 (1998). 

---