A comprehensive analysis of common copy-number variations in the human genome

Abstract

Segmental copy-number variations (CNVs) in the human genome are associated with developmental disorders and susceptibility to diseases. More importantly, CNVs may represent a major genetic component of our phenotypic diversity. In this study, using a whole-genome array comparative genomic hybridization assay, we identified 3,654 autosomal segmental CNVs, 800 of which appeared at a frequency of at least 3%. Of these frequent CNVs, 77% are novel. In the 95 individuals analyzed, the two most diverse genomes differed by at least 9 Mb in size or varied by at least 266 loci in content. Approximately 68% of the 800 polymorphic regions overlap with genes, which may reflect human diversity in senses (smell, hearing, taste, and sight), rhesus phenotype, metabolism, and disease susceptibility. Intriguingly, 14 polymorphic regions harbor 21 of the known human microRNAs, raising the possibility of the contribution of microRNAs to phenotypic diversity in humans. This in-depth survey of CNVs across the human genome provides a valuable baseline for studies involving human genetics.

Figure A1.

Flowchart for calculations. A, Determination of false-positive and false-negative rates in this study by use of six repeat experiments of single female DNA vs male reference DNA, analyzed using our CNV algorithm. B, Calculation for CNV overlaps in replicate experiments.

Figure 1.

Example of a karyogram from a hybridization experiment in this study. Custom SeeGH software was used to visualize normalized data as log₂ ratio plots. The figure illustrates an example of a hybridization of a female sample versus the male reference. The log₂ ratios of the data are shown as dots; the left and right vertical lines represent threshold lines for this experiment at log₂ ratios of −0.18 and 0.18, respectively.

Figure 2.

Detection of CNVs. The upper part illustrates a region of CNV at 19p13.2 among four individuals. Each short line represents the average fluorescent intensity ratio between sample and reference DNA for an individual BAC clone spotted on the array. The left and right vertical lines represent the average threshold for the hybridizations shown, at log₂ ratios of −0.25 and 0.25. A ratio to the right of the positive threshold line represents a copy-number gain, whereas a ratio to the left of the negative threshold represents a copy-number loss. Equal, greater, and fewer copies relative to the reference DNA are shown. The lower part illustrates a single BAC clone CNV at 7q32.1 among the four individuals; the clone (RP11-636E12) overlaps with the IMPDH1 gene, a mutation in which was shown to cause retinitis pigmentosa.

Figure 3.

Distribution of overlapped CNVs at different recurrence levels. The percentage of our CNV loci that overlapped with previously reported CNVs were plotted against minimum recurrence levels of CNVs from 1 to 50 within our sample set of 95.

Figure 4.

Overlap of CNVs with segmental duplications (SD). The percentage of BACs that contain segmental duplications (>10 kb) is graphed against the frequency of the CNV (0 = no variation) for two measures of human segmental duplication (WSSD and WGAC; see the “Material and Methods” section). Segmental duplications unique to human or chimpanzee are further distinguished.

Figure 5.

Cluster analysis by use of a CEPH pedigree. Clustering of 105 individuals was based on the high-frequency CNV clones. The 14 CEPH pedigree members are indicated by triangles.

Figure 6.

Distribution of CNV clones. High-frequency CNV clones are shown as dots to the right of each chromosome; red, green, and black dots represent presence in three, four or five, and six or more individuals, respectively. Dots to the left of the chromosomes represent locations of CNVs that overlap microRNAs (red dots) and select cancer genes (black dots).

Figure 7.

Detection of immunoglobulin variations. The three parts illustrate expected CNVs associated with the immunoglobulin loci at 2p11.2, 14q32.33, and 22q11.22 (top, middle, and bottom, respectively). The left and right vertical lines represent the average threshold for the hybridizations shown, at log₂ ratios of −0.2 and 0.2. An equal intensity ratio falls on the middle line (log₂ ratio of 0), a ratio to the right of the positive threshold line represents a copy-number gain, and a ratio to the left of the negative threshold represents a copy-number loss. chr = Chromosome.

Figure 8.

Inheritance of CNVs at five olfactory receptor loci in 14 members of a CEPH pedigree. The five loci (and clones), in the order shown, are OR2A1 (RP11-466J6), OR2Z1 (RP11-367L15 and RP11-282G19), OR4K1 (RP11-449I24 and CTD-2024K23), OR4M1 (RP11-597A11), and OR4Q3 (RP11-490A23). − = Copy-number loss; + = copy-number gain; 0 = no copy-number change; UI = uninformative. Male and female family members are shown as squares and circles, respectively.