The publisher would like to apologise for an error in the printing of the above article. On page R171 only Figure 3 was printed and the legend and article text was omitted. The complete page R171 including the omitted text is printed on the following page. This error only affected the print issue, the online version of the article is correct.
Figure 3. Direct comparison of two CNV surveys using the same SNP array platform and CNV calling algorithms. (A) Venn-diagram illustrating the degree of overlap in CNVRs discovered in different HapMap populations. CNVs were derived from 269 HapMap samples (3) using Affymetrix 500 K SNP array sets and any of three CNV calling algorithms, dChip (26), CNAG (27) and GEMCA (28). Variants spanning centromeres were split if the number of consecutive SNP probes in either flank was >3 and the derived variants were >1 kb. Immunoglobulin loci were masked before calling CNVs and calls were filtered for cell line-specific artifacts, as described in Redon et al. (18). Overlapping CNVs detected within each of the three HapMap continental populations (CEU: European, JPT + CHB: Asian, YRI: African) were merged into a non-redundant set of distinct CNVRs as described in Figure 2. Numbers in brackets correspond to the stringent CNVR dataset for each population group (Fig. 2). Full and Stringent CNVR datasets were used for subsequent analyses. CEU- 90 Utah residents with ancestry from Northern and Western Europe, including 30 trios; YRI-90 Yoruba from Ibadan, Nigeria, including 30 trios; CHB + JPT-89 Han Chinese from Beijing, China and Japanese from Tokyo, Japan. (B) Triangle plot of inferred population structure for PopGen controls. PopGen individuals were clustered without regard to their geographical origin using STRUCTURE (23,24) and 780 unlinked SNPs, assuming three ancestral populations (Red). Genotypes from the 209 unrelated HapMap individuals were used as reference in the same clustering, and colored according to their continental origin: Green, European (60 unrelated CEU); Blue, African (60 unrelated YRI); Yellow, Asian (89 unrelated CHB+JPT). The three PopGen individuals outside the HapMap clusters (coefficient of ancestry <0.90) were removed from further analyses. (C) Venn-diagram of CNVR overlap between HapMap populations and PopGen controls. Non-redundant and stringent CNVR datasets were calculated as in (A).
theory (33) of modern human origin, higher levels of genetic variation should exist in the more ancient African populations and less diversity in the younger, non-African populations, which is supported by SNP diversity studies (34). Accordingly, a higher number of distinct CNVs/ CNVRs within samples of African ancestry would also be expected. It is currently unclear whether the absence of such difference is due to the limited sample size or related to the distribution of CNVRs among populations. These observations further underscore the need to genotype large samples to determine CNV and CNVR frequencies and distribution across different populations.
FUTURE CONSIDERATIONS
Next-Generation Platforms
The next generation of SNP arrays (e.g. the commercial Affymetrix 5.0 and 6.0, and Illumina 1 M) has been designed to offer the potential to simultaneously interrogate SNPs and
