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Empirical testing of a 23-AIMs panel of SNPs for ancestry evaluations in four major US populations

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Abstract

Ancestry informative markers (AIMs) can be used to determine population affiliation of the donors of forensic samples. In order to examine ancestry evaluations of the four major populations in the USA, 23 highly informative AIMs were identified from the International HapMap project. However, the efficacy of these 23 AIMs could not be fully evaluated in silico. In this study, these 23 SNPs were multiplexed to test their actual performance in ancestry evaluations. Genotype data were obtained from 189 individuals collected from four American populations. One SNP (rs12149261) on chromosome 16 was removed from this panel because it was duplicated on chromosome 1. The resultant 22-AIMs panel was able to empirically resolve the four major populations as in the in silico study. Eight individuals were assigned to a different group than indicated on their samples. The assignments of the 22 AIMs for these samples were consistent with AIMs results from the ForenSeqTM panel. No departures from Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were detected for all 22 SNPs in four US populations (after removing the eight problematic samples). The principal component analysis (PCA) results indicated that 181 individuals from these populations were assigned to the expected groups. These 22 SNPs can contribute to the candidate AIMs pool for potential forensic identification purposes in major US populations.

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Authors and Affiliations

  1. Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas, 76107, USA

    Xiangpei Zeng, David H. Warshauer, Jonathan L. King, Jennifer D. Churchill, Ranajit Chakraborty & Bruce Budowle

  2. Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia

    Bruce Budowle

Authors
  1. Xiangpei Zeng
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  2. David H. Warshauer
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  3. Jonathan L. King
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  4. Jennifer D. Churchill
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  5. Ranajit Chakraborty
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  6. Bruce Budowle
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Corresponding author

Correspondence to Xiangpei Zeng.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplemental Table 1

The probe information of the 23 ancestry informative SNPs (XLSX 11.5 kb)

Supplemental Fig. 1

Average coverage of 22 SNPs in 189 individuals (TIFF 815 kb)

Supplemental Fig. 2

Example of sequence data for SNP rs12149261 shown in IGV. The three different individuals (005A, 011 and 35706) were Caucasian, Asian and Hispanic American, respectively (TIFF 2329 Kb)

Supplemental Fig. 3

BLAST results of 300 bp around SNP rs12149261. Supplemental Figure 3A is rs12149261 located in HYDIN gene on chromosome 16. Supplemental Figure 3B is the duplication of rs12149261 located in HYDIN2 gene on chromosome 1 (TIFF 1820 kb)

Supplementry Material 5(TIFF 2001 kb)

Supplemental Fig. 4

PCA plots of eight individuals using the ForenSeqTM panel. Eight samples (20882, 23169, 76194, 06498, 12574, 38859, 10916 and 61115) are labeled in red circles in Supplemental Figures 4A-4H, respectively (TIFF 2979 kb)

Supplementry Material 7 (TIFF 2980 kb)

Supplemental Figure 4C(TIFF 2965 kb)

Supplemental Figure 4D (TIFF 2987 kb)

Supplemental Figure 4E(TIFF 2950 kb)

Supplemental Figure 4F (TIFF 2949 kb)

Supplemental Figure 4G (TIFF 2979 kb)

Supplemental Figure 4H (TIFF 3021 kb)

Supplemental Fig. 5

The PCA plot of 181 individuals using 22-SNP AIMs panel (TIFF 1159 kb)

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Zeng, X., Warshauer, D.H., King, J.L. et al. Empirical testing of a 23-AIMs panel of SNPs for ancestry evaluations in four major US populations. Int J Legal Med 130, 891–896 (2016). https://doi.org/10.1007/s00414-016-1333-4

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  • DOI: https://doi.org/10.1007/s00414-016-1333-4

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