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. 2009 Nov 23;4(11):e7958.
doi: 10.1371/journal.pone.0007958.

Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations

Affiliations

Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations

Jian Li et al. PLoS One. .

Abstract

Although copy number variation (CNV) has recently received much attention as a form of structure variation within the human genome, knowledge is still inadequate on fundamental CNV characteristics such as occurrence rate, genomic distribution and ethnic differentiation. In the present study, we used the Affymetrix GeneChip(R) Mapping 500K Array to discover and characterize CNVs in the human genome and to study ethnic differences of CNVs between Caucasians and Asians. Three thousand and nineteen CNVs, including 2381 CNVs in autosomes and 638 CNVs in X chromosome, from 985 Caucasian and 692 Asian individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1% in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p<0.01). After merging overlapping CNVs, 1135 copy number variation regions (CNVRs), covering approximately 439 Mb (14.3%) of the human genome, were obtained. Our findings of ethnic differentiation of CNVs, along with the newly constructed CNV genomic map, extend our knowledge on the structural variation in the human genome and may furnish a basis for understanding the genomic differentiation of complex traits across ethnic groups.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Characteristics of CNVs on autosomes.
(A) Distribution of CNV numbers per individual. (B) Distribution of CNV sizes.
Figure 2
Figure 2. CNVR chromosomal coverage in CAU and in CHI.
The vertical axis is the proportion of a specific chromosome covered by CNVRs. The proportion ranges from ∼3% to ∼15% in CHI and from ∼5% to ∼11% in CAU on autosomes and an extensive difference on X chromosome.
Figure 3
Figure 3. Genomic map for CNVs found in CAU and in CHI.
The figure was drawn by IdeogramBrowser . Individual chromosomes are shown by the karyograms, with dots on the left and right sides of the karyograms indicating chromosomal locations of copy number losses and gains, respectively. For dots in the two columns on the same side of the karyograms, those closer to the karyograms represent CNVs detected in CAU, and those further away indicate CNVs detected in CHI. Blue bars with white space on the right side of the karyograms indicate locations of known genes, based on the database available when the analyses were performed.
Figure 4
Figure 4. Distribution of CNV genes in 1677 individuals.

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