SNPS are particular nucleotide sequences that are repeated within a region of a DNA strand (called an STR locus). STR loci occur frequently in the human genome, and the number of repeated sequences within an STR locus varies highly from person to person. For example, one individual’s DNA may have eleven ATT repeats at a given STR locus, while another individual may have 14 at the same locus. These variations are referred to as alleles (see above) or markers, of the particular locus. Alleles are responsible for “polymorphisms” or genetic differences between individuals. No one allele varies enough to differentiate one person from another to a statistically significant degree. A particular set of alleles at multiple loci within an individual’s DNA, however, can be used to create a DNA “finger-print” unique to that individual. This mehthod of identificaiton is called “STR profiling” and is useful in many fields, including forensic science.  

SNPs or single nucleotide polymorphisms are points in the genome at which one base can differ between individuals. SNPs are single base positions in DNA at which different alleles, or alternative nucleotides, exist in a population. An individual may be homozygous or heterozygous for an allele at each SNP position. The genomes of all organisms undergo spontaneous mutation in the course of their continuing evolution, generating variant forms of progenitor genetic sequences. A variant form may confer an evolutionary advantage or disadvantage relative to a progenitor form or may be neutral. In some instances, a variant form confers an evolutionary advantage to the species and is eventually incorporated into the DNA of many or most members of the species and effectively becomes the progenitor form. Additionally, the effects of a variant form may be both beneficial and detrimental, depending on the cirucmstances. For example, a heterozygous sickle cell mutation confers resistance to malaria, but a homozygous sicle cecell is usually lethal. About 90% of all polymorphisms in the human genome are SNPs.

Causative SNPs: 

 SNP can, in some instances, be referred to as a “cSNP” to denote that the nucloetide sequence containing the SNP is an amino acid coding sequence. Causative SNPs produce alterations in gene expression or in the expression, structure, and/or function of a gene product. Causative SNPs do not necessarily have to occur in coding regions; causative SNPs can occur in, for example, any genetic region that can ultimately affect the expression, structure, and/or activity of the protein encoded by a nucleic acid.

SNPs and Disease: 

An association study of a SNP and a specific disorder invovles determing the presence or frequency of the SNP allele in biological samples from individuals with the disorder of itnerest. A SNP may be screened in diseased tissue samples and compared to control smaples, and selected for its increased (or decreased) occurrence in a specific pathological condition, such as pathologies related to myocardial infaction. If a particular SNP is inherited with a disease, it is also a strong indication that a gene that confers susceptibility lies somewhere nearby. There are thought to be some ten million common SNPs scattered throughout the human genome. Once a statistically significant association is established between one or more SNP(s) and a pathological condition of interest, then the region around the SNP can optionally be thoroughly screened to identify the causative genetic locus/sequenc(s) (e.g., causative SNP/mutation, gene, regulatory region, etc) that influences the pathological condition or phenotype. SNPs can thus be used to identify patients most suited to therapy with particular pharmaceutical agents (this term is often termed “pharmacogenomics”). Similarly, SNPs can be used to exclude patients from certain treatment due to the patient’s increased likelihood of developing toxic side effects or their liklihood of not responding to the treatment.