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

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-...

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Autores principales: Kiesler, Kevin M., Vallone, Peter M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Croatian Medical Schools 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692330/
https://www.ncbi.nlm.nih.gov/pubmed/23771752
http://dx.doi.org/10.3325/cmj.2013.54.225
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author Kiesler, Kevin M.
Vallone, Peter M.
author_facet Kiesler, Kevin M.
Vallone, Peter M.
author_sort Kiesler, Kevin M.
collection PubMed
description 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.
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spelling pubmed-36923302013-06-27 Allele frequencies for 40 autosomal SNP loci typed for US population samples using electrospray ionization mass spectrometry Kiesler, Kevin M. Vallone, Peter M. Croat Med J Forensic Science 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. Croatian Medical Schools 2013-06 /pmc/articles/PMC3692330/ /pubmed/23771752 http://dx.doi.org/10.3325/cmj.2013.54.225 Text en Copyright © 2013 by the Croatian Medical Journal. All rights reserved. http://creativecommons.org/licenses/by/2.5/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Forensic Science
Kiesler, Kevin M.
Vallone, Peter M.
Allele frequencies for 40 autosomal SNP loci typed for US population samples using electrospray ionization mass spectrometry
title Allele frequencies for 40 autosomal SNP loci typed for US population samples using electrospray ionization mass spectrometry
title_full Allele frequencies for 40 autosomal SNP loci typed for US population samples using electrospray ionization mass spectrometry
title_fullStr Allele frequencies for 40 autosomal SNP loci typed for US population samples using electrospray ionization mass spectrometry
title_full_unstemmed Allele frequencies for 40 autosomal SNP loci typed for US population samples using electrospray ionization mass spectrometry
title_short Allele frequencies for 40 autosomal SNP loci typed for US population samples using electrospray ionization mass spectrometry
title_sort allele frequencies for 40 autosomal snp loci typed for us population samples using electrospray ionization mass spectrometry
topic Forensic Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692330/
https://www.ncbi.nlm.nih.gov/pubmed/23771752
http://dx.doi.org/10.3325/cmj.2013.54.225
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