Abstract

BackgroundEpigenetics is one of the factors shaping natural variability observed among human populations. A small proportion of heritable inter-population differences are observed in the context of both the genome-wide methylation level and the methylation status of individual CpG sites. It has been demonstrated that a limited number of carefully selected differentially methylated sites may allow discrimination between main human populations. However, most of the few published results have been performed exclusively on B-lymphocyte cell lines.ResultsThe goal of our study was to identify a set of CpG sites sufficient to discriminate between populations of European and Chinese ancestry based on the difference in the DNA methylation profile not only in cell lines but also in primary cell samples. The preliminary selection of CpG sites differentially methylated in these two populations (pop-CpGs) was based on the analysis of two groups of commercially available ethnically-specific B-lymphocyte cell lines, performed using Illumina Infinium Human Methylation 450 BeadChip Array. A subset of 10 pop-CpGs characterized by the best differentiating criteria (|Mdiff| > 1, q < 0.05; lack of the confounding genomic features), and 10 additional CpGs in their immediate vicinity, were further tested using pyrosequencing technology in both B-lymphocyte cell lines and in the primary samples of the peripheral blood representing two analyzed populations. To assess the population-discriminating potential of the selected set of CpGs (further referred to as “composite pop (CEU-CHB)-CpG marker”), three classification methods were applied. The predictive ability of the composite 8-site pop (CEU-CHB)-CpG marker was assessed using 10-fold cross-validation method on two independent sets of samples.ConclusionsOur results showed that less than 10 pop-CpG sites may distinguish populations of European and Chinese ancestry; importantly, this small composite pop-CpG marker performs well in both lymphoblastoid cell lines and in non-homogenous blood samples regardless of a gender.

Highlights

  • Epigenetics is one of the factors shaping natural variability observed among human populations

  • Our results showed that less than 10 pop-CpG sites may distinguish populations of European and Chinese ancestry; importantly, this small composite pop-CpG marker performs well in both lymphoblastoid cell lines and in non-homogenous blood samples regardless of a gender

  • The goal of our study was to identify a small set of differentially methylated CpG sites sufficient to discriminate between populations of European and Chinese ancestry, which could be used as an manageable, composite pop (CEU-Han Chinese in Beijing (CHB))-CpG marker for a forensic differentiation between samples based on their population origin

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Summary

Introduction

Epigenetics is one of the factors shaping natural variability observed among human populations. It has been demonstrated that a limited number of carefully selected differentially methylated sites may allow discrimination between main human populations. The differences between human populations are shaped by the genomic DNA variation and by transcriptomic and DNA methylation variation [13,14,15,16,17,18,19,20,21,22]. Besides the most frequently used genomic DNA markers, some “non-classical markers”, representing inter-population differences in the expression and in the DNA methylation level, can potentially be used to discriminate between populations. A number of population-specific mRNA markers have been identified and tested in both B-cell lines and in a primary biological material, e.g. blood see [23]

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