Figure 3

Nucleotide-level mapping of the recurrent 8q13.2-13.3 deletions. A Schematic figure of mapping primers used in long-range and nested PCR. The numbers are the coordinate of chromosome 8 (gnome build hg18). HERVH are presented as two red rectangles (HERVH-int1 and HERVH-int2). The black lines represent the genomic size of the 8q13 region. The green and blue lines represent the size of the amplicons produced by the long-range and nested PCR, respectively. The small brown and blue dots in the red rectangles represent the primers 2F and 2R, and the larger black dots represent the primers 1F and 1R. While primer 1F and 1R, 2R are unique sequences in the human genome, the 2F is scattered sequence in the human genome but is unique for the amplicon produced by the nested PCR. The 800 bp fragment produced in the nested PCR was also amplified in the control due to two identical sequences of the 2F primer in HERVH-int1 and HERVH-int2 (two brown dots in two HERVH blocks). B Gel electrophoresis images (0.8% agarose) of PCR products from the two cases and a control. P1: case 1, P2: case 2, C: mixed DNA from 10 controls. Lane 1–2: DNA marker ladder (M); Lane 3–5: long-range PCR products using genomic DNA with primer 1F and 1R; Lane 7–9: general PCR products using genomic DNA with primer 2F and 2R; Lane 11–12: nested PCR products using the amplicon in lanes 3 (P1-1) and 4 (P2-1) as template with primers 2F and 2R; Lane 6 and 10: blanks.