Analysis of syntenic human and chimpanzee LR-PCR products for deletions and insertions. (A) The lengths of syntenic human (H) and chimpanzee (C) LR-PCR products are compared by gel electrophoresis. Syntenic LR-PCR products are the same length (lane 6) indicating that no rearrangement is present, longer in humans than in the chimpanzees (lanes 1–4), indicating that the chimpanzee sequence is deleted with respect to the human sequence, or longer in the chimpanzee than in human (lane 7), indicating that the chimpanzee sequence contains an insertion relative to the human sequence. LR-PCR product #1 corresponds to the rearrangement in Segment 32 at 320 kb as given in Suppl. Table 1, #2 = Segment 36 at 28 kb, #3 = Segment 71 at 234 kb, #4 = Segment 77 at 125 kb, and #7 = Segment 2 at 292 kb. (B) The human and chimpanzee LCR-PCR products shown in (A) were hybridized to the 21q arrays, and their percent conformance (vertical axis), which is a measure of their similarity (Frazer et al. 2001), was plotted relative to their position in the human reference sequence (horizontal axis). Each tick mark in the scale represents a 1-kb interval. The sequence positions of the PCR products in (A) and (C) are indicated by horizontal lines. The overlap of the LR-PCR products in (A) with neighboring chromosome 21 LR-PCR products is shown. The sharp drop in conformance values (yellow circles) indicates the positions of the sequences deleted in the chimpanzee LR-PCR products 1–5 in (A). Sequences with absent conformance information, such as those indicated by black arrows, correspond to interspersed repeats, which were not tiled on the 21q arrays (see Methods). LR-PCR product #1 is the only fragment in which two localized deletions account for a size difference between chimpanzees and humans. For LR-PCR product #5, the variation in the sizes of the human and chimpanzee bands is not detectable on the gel but the deletion is evident in the comparative 21q array data. (C) Paired PCR primers designed to the sequences flanking the deletions in LR-PCR products 1–5 in (A) as shown in (B) were used to amplify human and chimpanzee DNA. The lengths of the human vs. chimpanzee PCR products provide more precise information about the deletion sizes (in bp).