Figure 1
Figure 1. aCGH identifies deletions in FANCA, FANCC, and FANCD2 and duplication in FANCB. (A) Deletion in FANCC. The CGH data for the FANCC gene region in FA10 DNA are displayed in the top panel, genomic coordinates are above, and exons are below. The display was generated using SignalMap (Nimblegen). The y-axis shows the intensity ratio (log value) between the test sample and the reference DNA. A “0” represents 2 copies and thus no change in copy number, but the region of decreased ratio (blue shading) indicates a deletion. The red line connects the individual data points (black dots displaying a 500-bp moving average) with a similar intensity ratio. The arrow indicating FANCC points in the direction of transcription of the gene, right to left. This deletion removes exon 1 and 5 kb upstream. The CGH data were generated from the maternal DNA. The Sanger sequencing trace shows the paternal mutation (*) in the genomic DNA. RT-PCR using FA10 RNA for the region of paternal mutation is shown along with that of a control RNA. The normal-size product present in the control lane is absent in the FA10 RNA lane. The 2 lower-size bands in FA10 lane (indicated by • and ••) represent the alternatively spliced products caused by the paternal mutation in intron 5 skipping either the entire or a portion (39 bases) of exon 6. The maternal allele that carries the deletion is not expressed. (B) Deletion in FANCD2. The CGH data for the FANCD2 gene region in FA18 DNA are displayed, along with genomic coordinates above, and the exons below. The FANCD2 gene transcription is from left to right (arrow). The 4.7-kb deletion (blue shading) highlighted by the reduced intensity ratio indicates the loss of exon 18. (C) Duplication in FANCB. The CGH data displayed for the FANCB region in FA11 are shown. The reference DNA is from a male, and thus the intensity ratio for FANCB on the X chromosome is still “0”. The arrow (right to left) points to the direction of transcription of FANCB. The blue shading indicates an increased ratio and represents a duplication that includes exons 2 and 3. (D) Deletion in FANCA. The CGH data for the FANCA region in FA1 are displayed. The intensity ratios, shaded blue, indicate that the deletion in FA1 removes exons 16 to 17. The arrow (right to left) points in the direction of transcription of FANCA.

aCGH identifies deletions in FANCA, FANCC, and FANCD2 and duplication in FANCB. (A) Deletion in FANCC. The CGH data for the FANCC gene region in FA10 DNA are displayed in the top panel, genomic coordinates are above, and exons are below. The display was generated using SignalMap (Nimblegen). The y-axis shows the intensity ratio (log value) between the test sample and the reference DNA. A “0” represents 2 copies and thus no change in copy number, but the region of decreased ratio (blue shading) indicates a deletion. The red line connects the individual data points (black dots displaying a 500-bp moving average) with a similar intensity ratio. The arrow indicating FANCC points in the direction of transcription of the gene, right to left. This deletion removes exon 1 and 5 kb upstream. The CGH data were generated from the maternal DNA. The Sanger sequencing trace shows the paternal mutation (*) in the genomic DNA. RT-PCR using FA10 RNA for the region of paternal mutation is shown along with that of a control RNA. The normal-size product present in the control lane is absent in the FA10 RNA lane. The 2 lower-size bands in FA10 lane (indicated by • and ••) represent the alternatively spliced products caused by the paternal mutation in intron 5 skipping either the entire or a portion (39 bases) of exon 6. The maternal allele that carries the deletion is not expressed. (B) Deletion in FANCD2. The CGH data for the FANCD2 gene region in FA18 DNA are displayed, along with genomic coordinates above, and the exons below. The FANCD2 gene transcription is from left to right (arrow). The 4.7-kb deletion (blue shading) highlighted by the reduced intensity ratio indicates the loss of exon 18. (C) Duplication in FANCB. The CGH data displayed for the FANCB region in FA11 are shown. The reference DNA is from a male, and thus the intensity ratio for FANCB on the X chromosome is still “0”. The arrow (right to left) points to the direction of transcription of FANCB. The blue shading indicates an increased ratio and represents a duplication that includes exons 2 and 3. (D) Deletion in FANCA. The CGH data for the FANCA region in FA1 are displayed. The intensity ratios, shaded blue, indicate that the deletion in FA1 removes exons 16 to 17. The arrow (right to left) points in the direction of transcription of FANCA.

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