Figure 2.

Characterization of der(21)ins(21;X)(q21.1;q28q28)dup(21)(q21.1q21.1) by oligonucleotide array CGH, linear amplification, and PCR. (A) 135k feature oligonucleotide microarray results showing a single-copy gain of 48 probes, ∼382 kb in size (chrX:152,676,843–153,058,941 based on the UCSC 2006 hg18 assembly), from Xq28 in proband 2. Probes are ordered on the x-axis with the most proximal Xq28 probes to the left and the most distal Xq28 probes to the right. Values along the y-axis represent log₂ ratios of patient:control signal intensities. (B) 2.1M feature oligonucleotide microarray results showing the same duplication as in A after linear amplification with primers XQR1 and XQR2. Successful amplification is evidenced by the elevated log ratios of probes in the proximal portion of the duplicated region. (C) 2.1M feature oligonucleotide microarray results showing a single-copy gain of 210 probes, ∼272 kb in size (chr21:22,347,877–22,623,043 based on the UCSC 2006 hg18 assembly), from 21q21.1 in proband 2. (D) 2.1 M feature oligonucleotide microarray results showing the same duplication as in C after linear amplification with the primers from B. The elevated log ratios in the proximal portion of the duplicated segment are indicative of the insertion of Xq22.2 sequence into 21q21.1, which allowed for continuous amplification across the breakpoint. The cluster of elevated probes that can be seen in the distal portion of the duplicated segment was also present in the unamplified sample and probably represents a CNV or artifact. (E) Gel electrophoresis of PCR amplicon produced with primers XQR1 and 21QR confirming the insertion site detected by linear amplification.