Evaluation of the classification method using ancestry SNP markers for ethnic group

Hyo Jung Lee, Sun Pyo Hong, Soong Deok Lee, Hwan seok Rhee, Ji Hyun Lee, Su Jin Jeong, Jae Won Lee

Research output: Contribution to journalArticle

Abstract

Various probabilistic methods have been proposed for using interpopulation allele frequency differences to infer the ethnic group of a DNA specimen. The selection of the statistical method is critical because the accuracy of the statistical classification results vary. For the ancestry classification, we proposed a new ancestry evaluation method that estimate the combined ethnicity index as well as compared its performance with various classical classification methods using two real data sets. We selected 13 SNPs that are useful for the inference of ethnic origin. These single nucleotide polymorphisms (SNPs) were analyzed by restriction fragment mass polymorphism assay and followed by classification among ethnic groups. We genotyped 400 individuals from four ethnic groups (100 African-American, 100 Caucasian, 100 Korean, and 100 Mexican-American) for 13 SNPs and allele frequencies that differed among the four ethnic groups. Additionally, we applied our new method to HapMap SNP genotypes for 1,011 samples from 4 populations (African, European, East Asian, and Central- South Asian). Our proposed method yielded the highest accuracy among statistical classification methods. Our ethnic group classification system based on the analysis of ancestry informative SNP markers can provide a useful statistical tool to identify ethnic groups.

Original languageEnglish
Pages (from-to)1-9
Number of pages9
JournalCommunications for Statistical Applications and Methods
Volume26
Issue number1
DOIs
StatePublished - 1 Jan 2019

Keywords

  • Allele
  • Classification
  • Ethnic group
  • Korean population
  • Single nucleotide polymorphisms (SNP)

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