Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing

Abstract

Copy number variants (CNVs) account for the majority of human genomic diversity in terms of base coverage. Here, we have developed and applied a new method to combine high-resolution array comparative genomic hybridization (CGH) data with whole-genome DNA sequencing data to obtain a comprehensive catalog of common CNVs in Asian individuals. The genomes of 30 individuals from three Asian populations (Korean, Chinese and Japanese) were interrogated with an ultra-high-resolution array CGH platform containing 24 million probes. Whole-genome sequencing data from a reference genome (NA10851, with 28.3x coverage) and two Asian genomes (AK1, with 27.8x coverage and AK2, with 32.0x coverage) were used to transform the relative copy number information obtained from array CGH experiments into absolute copy number values. We discovered 5,177 CNVs, of which 3,547 were putative Asian-specific CNVs. These common CNVs in Asian populations will be a useful resource for subsequent genetic studies in these populations, and the new method of calling absolute CNVs will be essential for applying CNV data to personalized medicine.

Figure 1

Overview of the CNV discovery project for Asian populations. The genomic DNA from ten Altaic Korean individuals, ten CHB HapMap individuals of Chinese ancestry, ten JPT HapMap individuals with Japanese ancestry and three platform-control comparison resource individuals (AK1, NA12878 and NA19240) were used for aCGH experiments. Genome sequence data from three subjects (AK1, AK2 and NA10851) were used to filter out false positive CNV calls and to obtain absolute CNV calls.

Figure 2

Original approach for calling absolute copy number status. (a) Right: The top, panel shows aCGH data for a genomic region on chromosome 3 in AK1 as compared to the reference sample, NA10851. The second panel down shows read-depth information for the same genomic region, derived from whole-genome sequencing data of NA10851. The third panel down is a ‘corrected’ absolute copy number result for this genomic region in AK1 using the absolute copy number algorithm analysis method described in this study. The bottom panel displays the same genomic region for AK1 using read-depth information derived from whole-genome sequencing data. (b) Comparison between relative copy number states and absolute copy number values for CNV segments, before and after corrections for NA10851 copy number states. Out of the total 21,905 CNVs identified in the 30 Asian individuals by aCGH (that is, by relative copy number states), the relative copy number values of 10,925 were not affected by CNVs in the NA10851 reference. Among 10,980 ‘obscure’ CNVs, 4,970 were determined to be non-CNVs by absolute calls and were removed from the final list of CNVs. An additional 3,164 CNVs, which were considered ‘covert’ CNVs and were initially missed by the aCGH experiments, were also identified by the absolute copy number state calling algorithm.

Figure 3

Frequency of copy number gains and losses among 33 individuals. (a) Distribution of absolute copy number gains (copy number >2) and losses (copy number <2) in 33 individuals. (b) Distribution of relative and absolute copy number gains and losses by CNV size. The x and y axes represent size and number of CNV segments, respectively.

Figure 4

Putative Asian population–specific copy number variants. (a) Venn diagram showing validated putative Asian-specific CNVEs. The lower part of the figure (blue) indicates the ethnic distribution of 4,959 CNVEs that were discovered by a 42M NimbleGen aCGH platform and validated with a genotyping microarray in the same study. The upper part of the figure indicates that 3,547 out of 5,177 CNVEs found among the 30 Asian individuals in this study do not reach a 1-bp overlap with CNVEs recently found by the Genome Structural Variation Consortium. The Genome Structural Variation Consortium reported that they found 4,978 validated CNVEs, but we show only 4,959 of them in this Venn diagram because 19 were nonpolymorphic. (b) Distribution of gene ontology categories for genes in which coding sequences overlap with common copy number– gain regions (outer circle) and copy number–loss regions (inner circle) identified from 30 Asian subjects. (c) CNVE location and number of Asian individuals involved (bar graph, right). Red, copy number gain; green, copy number loss. Selected genes and miRNAs are also shown on the left.

Figure 5

Effect of aCGH platforms in the CNV discovery. Absolute CNVs found from two HapMap individuals (NA12878 and NA19240) in this study using the Agilent 24M aCGH array were compared with CNVs found by genotyping microarray in the Genomic Structural Variation Consortium data. We also compared CNVs from AK1 obtained by Agilent 24M and Nimblegen 42M microarrays.