Physical mapping of APBA2 and PCR-RFLP analysis of APBA2 duplications. A. An expanded view of the 15q12-q14 region containing distal duplication breakpoints is shown. Breakpoints BP3 and BP5 are depicted as jagged, hatched structures; BP4 is not thus shown but its position is indicated by an arrow over the map. STS marker positions are indicated on the map by closed circles, and arrows over the map indicate transcriptional orientation for genes in this region. YAC and BAC clone locations are shown below the map; YAC 764C6 is located in contig WC-153 and 962D11 is in WC-699. Closed circles within clones reflects the inclusion and position of specific STS markers shown above. B. PCR amplification of an APBA2-specific STS using genomic, YAC and BAC templates is shown. Position of clone pairs relative to cytogenetic banding and public sequence assemblies is indicated. Product consistent with genomic template is present only in clones from the region just telomeric to BP3. C. PCR from genomic or BAC clone template, followed by restriction with either Hinf l or Ava ll is shown. Unique banding patterns, corresponding to single nucleotide differences between copies, may be observed for the intact locus and each of the two duplication copies. RT-PCR using adult or fetal cDNA reveals the pattern corresponding to the intact locus only.