US Population Data for 94 Identity-Informative SNP Loci
The US National Institute of Standards and Technology (NIST) analyzed a set of 1036 samples representing four major US population groups (African American, Asian American, Caucasian, and Hispanic) with 94 single nucleotide polymorphisms (SNPs) used for individual identification (iiSNPs). The compact...
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MDPI AG
2023-05-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/5/1071 |
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| author | Kevin M. Kiesler Lisa A. Borsuk Carolyn R. Steffen Peter M. Vallone Katherine B. Gettings |
| author_facet | Kevin M. Kiesler Lisa A. Borsuk Carolyn R. Steffen Peter M. Vallone Katherine B. Gettings |
| author_sort | Kevin M. Kiesler |
| collection | DOAJ |
| description | The US National Institute of Standards and Technology (NIST) analyzed a set of 1036 samples representing four major US population groups (African American, Asian American, Caucasian, and Hispanic) with 94 single nucleotide polymorphisms (SNPs) used for individual identification (iiSNPs). The compact size of iiSNP amplicons compared to short tandem repeat (STR) markers increases the likelihood of successful amplification with degraded DNA samples. Allele frequencies and relevant forensic statistics were calculated for each population group as well as the aggregate population sample. Examination of sequence data in the regions flanking the targeted SNPs identified additional variants, which can be combined with the target SNPs to form microhaplotypes (multiple phased SNPs within a short-read sequence). Comparison of iiSNP performance with and without flanking SNP variation identified four amplicons containing microhaplotypes with observed heterozygosity increases of greater than 15% over the targeted SNP alone. For this set of 1036 samples, comparison of average match probabilities from iiSNPs with the 20 CODIS core STR markers yielded an estimate of 1.7 × 10<sup>−38</sup> for iiSNPs (assuming independence between all 94 SNPs), which was four orders of magnitude lower (more discriminating) than STRs where internal sequence variation was considered, and 10 orders of magnitude lower than STRs using established capillary electrophoresis length-based genotypes. |
| first_indexed | 2024-03-11T03:42:28Z |
| format | Article |
| id | doaj.art-3dd8568a83404864842f71b212def0c4 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T03:42:28Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-3dd8568a83404864842f71b212def0c42023-11-18T01:30:04ZengMDPI AGGenes2073-44252023-05-01145107110.3390/genes14051071US Population Data for 94 Identity-Informative SNP LociKevin M. Kiesler0Lisa A. Borsuk1Carolyn R. Steffen2Peter M. Vallone3Katherine B. Gettings4National Institute of Standards and Technology, 100 Bureau Drive, Mailstop 8314, Gaithersburg, MD 20899, USANational Institute of Standards and Technology, 100 Bureau Drive, Mailstop 8314, Gaithersburg, MD 20899, USANational Institute of Standards and Technology, 100 Bureau Drive, Mailstop 8314, Gaithersburg, MD 20899, USANational Institute of Standards and Technology, 100 Bureau Drive, Mailstop 8314, Gaithersburg, MD 20899, USANational Institute of Standards and Technology, 100 Bureau Drive, Mailstop 8314, Gaithersburg, MD 20899, USAThe US National Institute of Standards and Technology (NIST) analyzed a set of 1036 samples representing four major US population groups (African American, Asian American, Caucasian, and Hispanic) with 94 single nucleotide polymorphisms (SNPs) used for individual identification (iiSNPs). The compact size of iiSNP amplicons compared to short tandem repeat (STR) markers increases the likelihood of successful amplification with degraded DNA samples. Allele frequencies and relevant forensic statistics were calculated for each population group as well as the aggregate population sample. Examination of sequence data in the regions flanking the targeted SNPs identified additional variants, which can be combined with the target SNPs to form microhaplotypes (multiple phased SNPs within a short-read sequence). Comparison of iiSNP performance with and without flanking SNP variation identified four amplicons containing microhaplotypes with observed heterozygosity increases of greater than 15% over the targeted SNP alone. For this set of 1036 samples, comparison of average match probabilities from iiSNPs with the 20 CODIS core STR markers yielded an estimate of 1.7 × 10<sup>−38</sup> for iiSNPs (assuming independence between all 94 SNPs), which was four orders of magnitude lower (more discriminating) than STRs where internal sequence variation was considered, and 10 orders of magnitude lower than STRs using established capillary electrophoresis length-based genotypes.https://www.mdpi.com/2073-4425/14/5/1071single nucleotide polymorphismhuman identificationmicrohaplotypenext generation sequencing |
| spellingShingle | Kevin M. Kiesler Lisa A. Borsuk Carolyn R. Steffen Peter M. Vallone Katherine B. Gettings US Population Data for 94 Identity-Informative SNP Loci Genes single nucleotide polymorphism human identification microhaplotype next generation sequencing |
| title | US Population Data for 94 Identity-Informative SNP Loci |
| title_full | US Population Data for 94 Identity-Informative SNP Loci |
| title_fullStr | US Population Data for 94 Identity-Informative SNP Loci |
| title_full_unstemmed | US Population Data for 94 Identity-Informative SNP Loci |
| title_short | US Population Data for 94 Identity-Informative SNP Loci |
| title_sort | us population data for 94 identity informative snp loci |
| topic | single nucleotide polymorphism human identification microhaplotype next generation sequencing |
| url | https://www.mdpi.com/2073-4425/14/5/1071 |
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