Figure 5.

A chimpanzee genomic disorder. (A) A genome browser snapshot of the 17p11.2 Smith-Magenis syndrome (SMS) critical region with a copy number heat map of the Western chimpanzee Susie-A and the Nigerian–Cameroon chimpanzee Koto. Susie-A has a 1.7-Mb deletion of this locus, which encompasses RAI1, the critical gene associated with the SMS phenotype. We confirm this deletion by array CGH. (B) Copy number of great apes assessed in this study over the Susie-A deletion breakpoint 2 H-duplicon. (C) Organization of the 17p11.2 SMS locus and 17p12 in humans with four blocks of segmental duplication. The typical human SMS deletion spans ∼3.7 Mb with different breakpoints from the Susie-A deletion (Elsea and Girirajan 2008). (D) Segmental duplication architecture of the 17p11.2 locus as represented in the human reference genome and constructed in chimpanzees from high-quality sequencing of 22 BAC clones. We were able to assemble and anchor 11 of these clones into seven contigs. The remaining 11 contigs were placed at their most likely locations and orientations based on their underlying duplication architecture and read-depth analysis of Susie-A compared to normal chimpanzees. We hypothesize that a nonallelic homologous recombination event between the directly oriented chimpanzee G duplicons resulted in Susie-A's deletion.