Single Nucleotide Polymorphisms (SNPs) consist of single nucleotide substitutions at specific loci within the genome. SNPs may pinpoint susceptibility to disease as illustrated by the non-synonymous and non-conservative mutation found in the Sickle Cell trait. Most SNPs occur outside of coding sequences where there is reduced selective pressure, however these SNPs may also modify the expression of genes. While many SNPs do not correspond directly with traits in obvious ways, they are useful markers that are associated with inheritance through genetic linkage.
When SNPs occur within coding regions they are termed synonymous (resulting in same amino acid coded) or non-synonymous (resulting in a change in the coded amino acid). Nonsense mutations result in premature stop codons that terminate the coding sequence while missense mutations result in a different amino acid at the location. Missense mutations may be characterized as conservative if the variant amino acid shares biochemical characteristics with the original or non-conservative if the variant is dissimilar.
Amplified Polymorphic Sequences
PCR can be used to amplify polymorphic regions. The revelation of polymorphism in these amplified sequences can be illustrated as mini/microsatellites or VNTRs/STRs where variations in length demonstrate differences in repeated elements in what can be described as Amplified Fragment Length Polymorphisms (AFLPs). Cleaved Amplified Polymorphic Sequences (CAPS) represent PCR of loci known to contain polymorphic restriction sites. Different alleles using CAPS may be revealed by the presence or absence of RE digestion of amplified products that result in differential banding patterns. In these cases, SNPs may have historically introduced or ablated the presence of a specific restriction site and permits for the presentation of different alleles. A modification of CAPS specifically uses long primers that intentionally introduce a restriction site where one does not exist based on SNPs within the amplified region for SNPs not naturally creating a restriction site. The intentional creation or removal of restrictions sites for one allele versus the other in this case is referred to as a derived Cleaved Amplified Polymorphic Sequence (dCAPS).
dCAPS has the advantage of studying alleles using AFLPs technology through incorporation of a digestion site for genotyping purposes. A great disadvantage of this system is the mismatches in the primers lowers the PCR specificity. Design of dCAPS primers for SNP identification can be done at http://helix.wustl.edu/dcaps/dcaps.html
An example of dCAPS is the PTC lab exercise.