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Non-STR DNA Markers: SNPs, Y-STRs, LCN and mtDNA

Single Nucleotide Polymorphisms (SNPs)

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The most common form of genetic variation in the human genome (approximately 90%) is a class of genetic marker known as a single nucleotide polymorphism (SNP).  As its name suggests, this class of variant is characterized by alternative deoxyribonucleotides at specific chromosomal sites. 

For example, a particular SNP could be represented as ATTGCG[C/T]GATTCG in which the SNP is characterized by a C and a T allele embedded in non-variant flanking sequence. SNPs can be present in coding, regulatory, and intronic sequences within genes or in intergenic regions.

Example SNP represented as ATTGCG[C/T]GATTCG in which the SNP is characterized by a C and a T allele embedded in non-variant flanking sequence
National Institute of Justice (NIJ) (see reuse policy).

Population studies from various populations indicate that SNP sites (defined as sites of variation present in at least 1% of individuals) occur every 300-500 base pairs along the genome.01   It has been estimated that approximately seven million SNPs, exist, with a minimum allele frequency (MAF) of 5% across the genome, and an additional approximately four million occurring with a MAF of 1%.01   There are also innumerable single base variants that exist within a single individual.  A number of studies indicate that the amount of variation present in the human genome is somewhat reduced due to substantial linkage disequilibrium between closely linked SNP markers, in effect creating haplotype blocks separated from one another by recombination hotspots.02

Read more about linkage disequilibrium in course: Population Genetics & Statistics.

SNPs initially arise via rare spontaneous mutations (approximately 10-8 per base pair per generation) and attain an appreciable population frequency by genetic drift and other evolutionary forces, such as selection. The spontaneous mutation rate is so low that the chances of a further mutation at the same site on the same individual chromosome (either reversal to the original base or conversion to any of the other two) are negligible. Thus, most SNPs are de facto unique event polymorphisms (UEP) and are biallelic in nature with modest levels of heterozygosity in the population (50% maximum).

Read more about selection in course: Population Genetics & Statistics.

Approximately 50-100 SNPs with a MAF between 20-50% would be required to provide a similar discriminating power to that afforded by the standard 13 CODIS STR loci, which have greater than 5 alleles per locus.03  

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