6-5.3(a).1.4 Single Nucleotide Polymorphisms (SNPs)

►  Polymorphisms resulting from point mutations are the most abundant polymorphism in organisms. They can give rise to different alleles comprising alternative bases at a given nucleotide position within a locus.

►  Advent of gene chip technology has improved the ability to genotype these single nucleotide polymorphisms (SNPs) in a large number of samples. These SNPs have emerged as a central point in the development of molecular markers.

►  SNPs marker development can be automated, and have the power to reveal hidden polymorphism not detected with other markers and methods.

►  There is very high number of SNPs in each genome which may help to generate RFLPs if there is any restriction site in the sequence.

►  At least 1.42 million SNPs are found in the human genome.

►  Considering SNP as a single alphabet spelling mistake (A, T, C, and G) in a word (stretch of DNA) theoretically, a SNP locus can have up to four variant alleles.

►  However in the real scenario, most SNPs are usually restricted to one of two alleles (most often either the two pyrimidines C/T or the two purines A/G) and thus consideredpredominantly as bi-allelic. They are getting inherited as co-dominant markers. Although the polymorphism information content (PIC), i.e. the measure of informativeness of a genetic marker to detect polymorphism, of SNPs is not as high as multi-allele microsatellites, this shortcoming is compensated by their remarkable abundance in the genome.

Methods available for SNP genotyping include:

1. Traditional methods as listed below suitable for small laboratories limited by budget and labor constraints

•  Direct sequencing,

•  Allele-specific oligonucleotide (aso) (Malmgren et al., 1996),

•  Single strand conformational polymorphism assays (sscp) (Suzuki et al., 1990),

•  Single base sequencing (Cotton, 1993),

•  Denaturing gradient gel electrophoresis (dgge) (Cariello et al., 1988) and

•  Ligation chain reaction (lcr), (Kalin et al., 1992).