2p11 Duplicon architecture. (A) A schematic representation of the duplicon architecture (colored bars) is shown in reference to an ideogram of chromosome 2 and ∼700-kb BAC minimal tiling path. The black bar represents α-satellite sequence (∼175 kb), while light gray bars denote various pericentromeric-specific interspersed repeats (PIRs). Other enriched pericentromeric repeat sequences are indicated: C=CAAAAAG repeat, G=CAGGG, R=REP522, and T=TAR1 repeats (Smit 1996). Below the BAC tiling path are results of database searches using this entire sequence (represented by NT_034508) against the human genome (build34, July 2003). All pairwise alignments (>5 kb and >90%) to this segment are shown to other regions of the genome as indicated by the chromosome number and approximate position in megabases (ancestral loci are denoted by cytogenetic band position). A color scheme encodes the average percentage sequence identity for each alignment block (red, 99%; orange, 98–99%; yellow, 97–98%; green, 96–97%; blue, 95–96%; indigo, 94–95%; and violet, 90–94%). (B) Sequence overlaps were confirmed by Southern analysis between BAC clone and genomic DNA. An example of validation is shown for overlap D (between AC127391 [R11–389I13] and AC027612 [R11–165D20]). A PCR-generated probe (165D20–6n7) (Supplemental Table 2) was hybridized. The expected 2.2-kb band is observed in multiple overlapping BACs (389I13, 165D20, 34O12, and 1430E12) in addition to the chromosome 2 hybrid and genomic DNA samples. Note: An additional lower band is observed in the genomic DNA samples compared with the monochromosomal hybrid DNA samples, indicating that at least one additional copy of the GGT1 duplicon exists within the human genome. (C) Extended fiber FISH validating overlap (in yellow) of the three most proximal BACs in a chromosome 2 hybrid cell line (GM11712). Results in a second chromosome 2 hybrid line (GM11686) and total human cell lines showed similar results (data not shown).
