Genetics and Genomics of Core Short Tandem Repeat Loci Used in Human Identity Testing

Abstract

Over the past decade, the human identity testing community has settled on a set of core short tandem repeat (STR) loci that are widely used for DNA typing applications. A variety of commercial kits enable robust amplification of these core STR loci. A brief history is presented regarding the selection of core autosomal and Y-chromosomal STR markers. The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing. Internet resources for additional information on core STR loci are reviewed. Additional topics are also discussed, including potential linkage of STR loci to genetic disease-causing genes, probabilistic predictions of sample ethnicity, and desirable characteristics for additional STR loci that may be added in the future to the current core loci. These core STR loci, which form the basis for DNA databases worldwide, will continue to play an important role in forensic science for many years to come.

Variations in short tandem repeats deduced on the basis of the number of repeats and the relationship of these variations with longevity

“…STRs are named according to the number of repeats; different STR alleles can occur in a single STR locus, thereby resulting in STR polymorphism. Generally, an STR polymorphism is considered the result of gene mutation (Butler 2006;Eckert and Hile 2009;Laghi et al 2008). Accordingly, an STR with the highest frequency distribution in a certain population is considered a conservative STR, and an STR with relatively low or very low frequency distribution is considered a result of gene mutation and natural selection.…”

A new set of markers for human identification based on 32 polymorphic Alu insertions

“…These data are encouraging; however, validation of the 32 Alu set on larger human sample panel before wide use is needed. The calculated mean match probability 5.53Â10 À14 indicates that the discrimination power of the proposed set is comparable with that of existing genetic identification systems, 3,4,6,7 and is sufficient for kinship determination or genetic 'passportization.' The probability of paternity exclusion, when the maternal genotype is known, was calculated at 99.784% that is comparable with existing SNP-based genetic tests (98.9% for 22 SNPs and 99.91-99.98% for 52 SNPs).…”

“…3,7,8 The use of fluorescence-based approaches allows performing large-scale human genetic tests and significantly reduces contamination because of keeping laboratory microtubes closed after PCR amplification. Accordingly, we checked the possibility of polymorphic Alu allelic discrimination by means of real-time PCR with Sybr Green dye and dissociation curves analysis using two primer pairs from our set.…”

“…Many human identification genetic systems based on STRs and SNPs have been developed and used since human genome structure was published and information on human genome diversity accumulated. 3,[5][6][7] Initially, the most commonly used human genotypic systems were based on STRs, each of them having multiple alleles with different population frequencies. These markers possess a very strong discrimination power but have a higher mutation rate as compared with SNP or RE 3,27 and laborious and expensive allele identification.…”

“…STR-based human identification systems have been widely used for many years and became common in forensic studies. 3 SNP-based MGMs are mostly biallelic and have therefore less discriminative power compared to STRs. An increasing number of well-characterized SNPs and some unique characteristics of this MGM type made them a useful tool for human identification [4][5][6][7] Both SNP and STR assays include two steps: (i) PCR amplification of multiple loci containing MGM and (ii) identification of the number of tandem repeats or SNP allele in each amplified locus.…”