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Enhancing resolution and statistical power by utilizing mass spectrometry for detection of SNPs within the short tandem repeats

NCJ Number
Forensic Science International Genetics Supplement Series Volume: 2 Issue: 1 Dated: December 2009 Pages: 529-531
John V. Planz ; Bruce Budowle ; Thomas Hall ; Arthur J. Eisenberg ; Kristin A. Sannes-Lowery; Steven A. Hofstadler
Date Published
December 2009
3 pages

Using an electrospray ionization mass spectrometry (ESI-MS) system developed by Ibis Biosciences Inc., this project generated population databases for the 13 core CODIS STRs from African Americans, Caucasians, and Hispanics, capturing both the length of the allele, as well as SNP variation contained within repeat motifs.


Short tandem repeats (STRs) are used routinely for the analysis of DNA samples from evidentiary items, convicted offenders, relationship testing and other identity testing disciplines. The discriminatory power of the STRs is sufficient in most human identity testing comparisons to render an identification. However, STRs have some limitations in evaluations, such as parentage testing, identification of human remains, or pairwise evaluations of putative relatives by familial searching. A major assumption is that shared alleles in these associations stem from common ancestry, i.e., are Identical by Descent (IBD). However, STR alleles by definition are Identical by State (IBS). In the current project, SNPs were identified in 10 of the loci and some common alleles were subdivided with SNP typing. Inclusion of SNPs increases discrimination power significantly, whereby the seven most polymorphic SNP-containing STR loci have the discriminatory power of 10 traditionally typed loci. A system of nomenclature has been developed that facilitates the databasing, searching and analyses of these combined data forms. (Published abstract provided.)