Perry et al. 10.1073/pnas.0602318103. |
Supporting Figure 4
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Supporting Table 4
Supporting Figure 6
Fig. 4. Chimpanzee array-based comparative genomic hybrdization (aCGH) self-self-hybridization experiment using the 1-Mb array. DNA from the reference chimpanzee (Clint; S006006) was hybridized as both the test and reference sample in a self-self-hybridization experiment using the 1-Mb aCGH platform. A single bacterial artificial chromosome (BAC) clone was determined to contain a copy number variant (CNV) (RP11-79L9 on human chromosome 3q22; this locus was not identified as a CNV in any of the 20 wild-born chimpanzees). This result is similar to results previously obtained from human self-self-hybridization experiments using the same aCGH platform (1). Together, these experiments suggest a false-positive error rate of ≤1 per aCGH experiment (2,632 clones). However, these estimates do not take into account an additional source of potential false positives, which is variability in DNA sample quality.
Fig 5.
Quantitative PCR (qPCR) validation of copy number variants. Chimpanzee and human CNVs were validated with qPCR, using the relative quantification method. The sample used as the standard curve (relative quantity = 1) is highlighted in yellow on the qPCR results. The CNV at locus RP11-81P11 for the human samples was confirmed as predicted based on the results of McCarroll et al. (2) and Conrad et al. (3) (vertical red bar; see Table 2). Error bars on qPCR results depict ±2 SD (95% confidence interval). Ref. = reference.Fig 6.
Comparison of 1-Mb array and segmental duplication-enriched aCGH results for a CNV on human chromosome 19 (chimpanzee chromosome 20). (a) Using the 1-Mb array, we identified a loss for chimpanzee #3339 relative to the reference chimpanzee Clint for BAC RP11-79F15. (b) With the segmental duplication array, the same region (BAC RP11-142H6) was determined to contain a genomic loss in the same chimpanzee individual. (c) The two BACs overlap approximately 100 kb, in a region that contains a cascade of segmental duplications that are shared by the human and chimpanzee genomes (4). This region was determined to also be copy number variable among phenotypically normal humans (1, 5, 6).1. Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W. & Lee, C. (2004) Nat Genet 36, 949-951.
2. McCarroll, S. A., Hadnot, T. N., Perry, G. H., Sabeti, P. C., Zody, M. C., Barrett, J. C., Dallaire, S., Gabriel, S. B., Lee, C., Daly, M. J., et al. (2006) Nat Genet 38, 86-92.
3. Conrad, D. F., Andrews, T. D., Carter, N. P., Hurles, M. E. & Pritchard, J. K. (2006) Nat Genet 38, 75-84.
4. Cheng, Z., Ventura, M., She, X., Khaitovich, P., Graves, T., Osoegawa, K., Church, D., DeJong, P., Wilson, R. K., Paabo, S., et al. (2005) Nature 437, 88-93.
5. Tuzun, E., Sharp, A. J., Bailey, J. A., Kaul, R., Morrison, V. A., Pertz, L. M., Haugen, E., Hayden, H., Albertson, D., Pinkel, D., et al. (2005) Nat Genet 37, 727-732.
6. Sharp, A. J., Locke, D. P., McGrath, S. D., Cheng, Z., Bailey, J. A., Vallente, R. U., Pertz, L. M., Clark, R. A., Schwartz, S., Segraves, R., et al. (2005) Am J Hum Genet 77, 78-88.