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. 2002 Apr 29;70(6):1520–1531. doi: 10.1086/340849

Figure 2.

Figure 2

Large ABCD1 deletions that extend into the coding region of DXS1357E, in Pt1, Pt2, and Pt3. A, ABCD1, which spans ∼24 kb and has 10 exons (Sarde et al. 1994). Genomic DNA BamHI digestion was predicted to yield three ABCD1 fragments from Xq28. B, Results of Southern blot validation studies and analyses of patients. Validation studies were conducted to identify genomic fragments containing DNA from autosomal homologs (Eichler et al. 1997; Smith et al. 1999) that might cross-react with the full-length ABCD1 cDNA probe. DNA from wild-type mouse, from a mouse cell line harboring one human X chromosome (AHA11a [Dorman et al. 1978]), and from a human control subject (Ctl) were analyzed simultaneously. Four bands appeared for the AHA11a DNA, one corresponding to the band from wild-type mouse and three matching the predicted sizes (i.e., 10, 8.3, and 5.6 kb) of fragments for ABCD1 on Xq28 and aligning with bands in Ctl. The two additional bands in Ctl correspond to autosomal homologs that cross-react with the cDNA probe, since they did not appear in the mouse hybrid cell line harboring the human X chromosome. Pt1 and Pt3 lack the three ABCD1 bands corresponding to all 10 exons. In contrast, Pt2 lacks bands corresponding to exons 1–6 but retains the 8.3-kb band representing exons 6–10. Ex = exons. C, DNA map for Xq28, showing the location of four STS markers (gels A, B, D, and G), in relation to ABCD1 and surrounding genes (se the Entrez Nucleotide Web site of the National Center for Biotechnology Information [accession number U52111]). In addition, the location of ABCD1 exons 2 and 10 (gels E and F, respectively), the boundary between ABCD1 intron 5 and exon 6 (denoted by the asterisk [*]), and DXS1357E exon 5 (gel C) are shown. DXS1357E shares a CpG island and is in a head-to-head orientation with ABCD1 (Mosser et al. 1994). D, PCR primers for the markers shown were used for analysis in Pt1, Pt2, and Pt3 and in a male control subject (Ctl). These results are summarized in figure 3. E, Amplification of template for Xq28 and 16P11. Because of sequence homology between Xq28 and 16p11, the primers for reaction C (DXS1357E exon 5) amplify both templates. Compared with DNA from the control subject and Pt2, that from Pt1 and Pt3 yielded a small amount of product. When the amplicon from Pt1 and Pt3 was sequenced by use of primer CDM-1S (see the “Material and Methods” section), a 16p11-specific sequence was revealed, whereas the products from Pt2 and the control subject had DNA sequence specific to Xq28. Sequence specific to 16p11 was detectable only in the absence of the corresponding Xq28 region.