Allele frequencies for 40 autosomal SNP loci typed for US population samples using electrospray ionization mass spectrometry

Published

May 20, 2013

Author(s)

Kevin M. Kiesler, Peter M. Vallone

Abstract

Aim -- To type a set of 194 US African American, Caucasian,and Hispanic samples (self-declared ancestry) for 40 autosomal single nucleotide polymorphism (SNP) markers intended for human identification purposes. Methods -- Genotyping was performed on an automated commercial electrospray ionization time-of-flight mass spectrometer, the PLEX-ID. The 40 SNP markers were amplified in eight unique 5plex PCRs, desalted, and resolved based on amplicon mass. For each of the three US sample groups statistical analyses were performed on the resulting genotypes. Results -- The assay was found to be robust and capable of genotyping the 40 SNP markers consuming approximately= 4 nanograms of template per sample. The combined random match probabilities for the 40 SNP assay ranged from 10−16 to 10−21. Conclusion -- The multiplex PLEX-ID SNP-40 assay is the first fully automated genotyping method capable of typing a panel of 40 forensically relevant autosomal SNP markers on a mass spectrometry platform. The data produced provided the first allele frequencies estimates for these 40 SNPs in a National Institute of Standards and Technology US population sample set. No population bias was detected although one locus deviated from its expected level of heterozygosity.

Citation

Croatian Medical Journal

Volume

54

Issue

3

Pub Type

Journals

Download Paper

https://doi.org/10.3325/cmj.2013.54.225

Keywords

single nucleotide polymorphism, PCR, mass spectrometry, allele frequencies

Citation

Kiesler, K. and Vallone, P. (2013), Allele frequencies for 40 autosomal SNP loci typed for US population samples using electrospray ionization mass spectrometry, Croatian Medical Journal, [online], https://doi.org/10.3325/cmj.2013.54.225 (Accessed October 14, 2025)