Figure 2

Homozygous deletion and characterization of the breakpoint in patient FAP15. A: Agarose gel of multiplex PCR performed for MUTYH exons 1 to 16 (E1-E16) and control genes GAPDH or HPRT1. The patient (FAP15) exhibited absence of amplification for MUTYH exons 3 to 16, whereas a healthy individual (Control) presented all expected fragments. B: The blue line on the profile of chromosome 1 (bottom panel) indicates the mapping at 1p34.1 of the two intragenic probes with log₂ ratio values compatible with a homozygous deletion (green circles, upper panel); probes flanking this deletion (at 5' of MUTYH, and downstream of its 3' end) exhibited normal values. The red arrow indicates the position of probe A_14_P118536 where novel reverse primers were designed. C: Schematic drawing of the normal gene with genomic and cDNA (NM_001128425.1) positions of the breakpoints. D: Schematic drawing of the deleted gene and primer locations (2F primer: chr1: 45800257-45800276; 16R1 primer: chr1: 45794388-45794407). E: Agarose gel showing the amplification of the deletion junction in the patient and amplicon absence in the control DNA pool. F: Partial chromatogram of the junction sequencing showing in highlight the two inserted nucleotides (TA). G: Nucleotide sequence around the deletion breakpoints and the deletion junction. Red larger nucleotides are the non-template insertion (filler DNA). Light gray nucleotides indicate the deleted sequence. Shaded nucleotides represent shared sequences between the breakpoints. Rearrangement-promoting elements GAG/GCS* are shown underlined. The gray arrow beneath the intergenic deleted sequence shows the location of the AluJr element. *S denotes the ambiguity code symbol for G/C. Coordinates at chromosome 1 are given according UCSC Feb. 2009 (GRCh37/hg19) assembly.