Nucleotide sequence variation

Clark AG, Weiss KM, Nickerson DA, Taylor SL, Buchanan A, Stengard J et al. Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am J Hum Genet 1998 63 595— 612. 

Studies of the Impact of Nucleotide Sequence Variation on Drug Effects... 

Clark, A. G., Weiss, K. M., Nickerson, D. A., Taylor, S. L., Buchanan, A., Stengard, J., Salomaa, V., Virtianen, E., Perola, M., Boerwinkle, E., and Sing, C. F. (1998). Haplo-type structure and population genetic inferences from Nucleotide-sequence variation in human lipoprotein lipase. Am. J. Hum. Genet. 63, 595-612. 

Suomalainen A, Syvanen AC. Analysis of nucleotide sequence variations by solid-phase minisequencing. Methods Mol Biol 2003 226 361-366. 

More importantly, it is sometimes more informative. A very long nucleotide sequence may be required to provide more information than a restriction site survey. For example, a phylogenetic analysis of 22 taxa from the sunflower family used both restriction site variation in chloroplast DNA and nucleotide sequence variation in the chloroplast-encoded gene rbcL.5 The restriction site survey identified 583 variable sites of which 169 were shared between two or more taxa, whereas the sequence survey found only 109 shared variable positions. Even though the restriction site survey included only 11 enzymes, nearly 3500 nucleotides are included in the variable sequences surveyed, whereas rbcL is only 1428 base pairs (bp) in length. 

Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation. URL http //www.ncbi.nlm. nih.gov/SNP/index.html. Uses SNP in the much looser sense of minor genetic variations and includes microsatellite repeats and small insertion/deletion polymorphisms. 

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. 

The study of the genome supports the fundamental unity of human beings throughout the world. We all share at least 99.9% of the letters of code (nucleotide sequence) in our genome [1, 77]. And yet, it is remarkable that the extraordinary diversity of human beings at the genetic level is encoded by less than 0.1% variation in our DNA. In a sense, this is the variation that is the basis for pharma-cogenomics. In any physician s practice, patients are predisposed to different con-... 

Polymorphism A common (i.e., at least 1% prevalence of the minor allele in the population) sequence variation observed in an individual at a polymorphic site. Polymorphisms include nucleotide substitutions, insertions, deletions and microsatellites. They may be functional or silent, i.e., they do not result in detectable differences in gene expression or protein function. 

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

Mutations, polymorphism, and variations in the sequence that are often given separate entries in the nucleotide sequence databases. 

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