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

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

Research output: Contribution to journalArticle

5 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)891-896
Number of pages6
JournalInternational journal of legal medicine
Volume130
Issue number4
DOIs
StatePublished - 1 Jul 2016

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Single Nucleotide Polymorphism
Population
Computer Simulation
HapMap Project
Chromosomes, Human, Pair 16
Chromosomes, Human, Pair 1
Linkage Disequilibrium
Principal Component Analysis
Genotype

Keywords

  • Ancestry informative markers (AIMs)
  • Custom oligonucleotide probe
  • Population differentiation
  • Principal component analysis (PCA)
  • Single nucleotide polymorphisms (SNPs)

Cite this

Zeng, Xiangpei ; Warshauer, David H. ; King, Jonathan L. ; Cihlar, Jennifer Churchill ; Chakraborty, Ranajit ; Budowle, Bruce. / Empirical testing of a 23-AIMs panel of SNPs for ancestry evaluations in four major US populations. In: International journal of legal medicine. 2016 ; Vol. 130, No. 4. pp. 891-896.
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Empirical testing of a 23-AIMs panel of SNPs for ancestry evaluations in four major US populations. / Zeng, Xiangpei; Warshauer, David H.; King, Jonathan L.; Cihlar, Jennifer Churchill; Chakraborty, Ranajit; Budowle, Bruce.

In: International journal of legal medicine, Vol. 130, No. 4, 01.07.2016, p. 891-896.

Research output: Contribution to journalArticle

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