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. 2008 Dec 5;83(6):663–674. doi: 10.1016/j.ajhg.2008.10.006

Figure 2.

Figure 2

Examples of Copy-Number Determination at 4q13.2 by CNAT Analyses with Affymetrix Human Mapping 500K Array Data and Electrophoresis Analyses

A: CNV 4q13.2 calculated by CNAT analyses with the 350 unrelated control subjects used as the reference set.

AI: Three genotypes of the CNV 4q13.2: four copy numbers (a), three copy numbers (b), and two copy numbers (c). The x axis denotes genomic position. The y axis denotes the log2 ratio, which was calculated by comparison of the allele-intensity values of the test sample with those of the reference set.

AII: Electrophoresis analysis for PCR products (with deletion-specific primers) from the three genotypes at the CNV. Results for 4q13.2 inferred to have two copy numbers by CNAT analyses reveal no PCR products, indicating that this sample actually reflects a homozygous deletion.

B: CNV 4q13.2 calculated by CNAT with all of the subjects with nonhomozygous deletion used as the updated reference set.

BI: Three genotypes of CNV 4q13.2: two copy numbers (a), one copy number, (b) and zero copy numbers (c).

BII: On the basis of the UCSC Human Genome Brower, five genes are located in 4q13.2. The heavy arrow above “UGT2B17” means that the gene was found in CNV 4q13.2 with SNPs of rs4260611 and rs4860308 used as boundaries. When the boundaries were extended to SNPs of rs1730872 and rs293430 (the interval between these two SNPs was the maximal potential region for this CNV), four more protein-coding genes, named YTHDC1, TMPRSS11E, TMPRSS11E2, and UGT2B15, were found to be localized within this region (light arrows). CNV was only observed in UGT2B17.

BIII: Electrophoresis analysis for PCR products from gene-specific markers C (within exon 1 of UGT2B17), D (within 5′ upstream of UGT2B17), and E (within exon 6 of UGT2B17) and from deletion marker J of UGT2B17 . Subjects with two copy numbers of UGT2B17 had the ability to amplify markers C, D, and E but not marker J (a). Subjects with heterozygous deletion showed the ability to amplify markers C, D, E, and J simultaneously (b). Subjects with homozygous deletion had the ability to amplify only marker J (c). The results revealed that there was a deletion polymorphism in a 150 kb interval spanning the whole UGT2B17 gene.