Copy-number variations measured by single-nucleotide-polymorphism oligonucleotide arrays in patients with mental retardation

Abstract

Whole-genome analysis using high-density single-nucleotide-polymorphism oligonucleotide arrays allows identification of microdeletions, microduplications, and uniparental disomies. We studied 67 children with unexplained mental retardation with normal karyotypes, as assessed by G-banded chromosome analyses. Their DNAs were analyzed with Affymetrix 100K arrays. We detected 11 copy-number variations that most likely are causative of mental retardation, because they either arose de novo (9 cases) and/or overlapped with known microdeletions (2 cases). The eight deletions and three duplications varied in size from 200 kb to 7.5 Mb. Of the 11 copy-number variations, 5 were flanked by low-copy repeats. Two of those, on chromosomes 15q25.2 and Xp22.31, have not been described before and have a high probability of being causative of new deletion and duplication syndromes, respectively. In one patient, we found a deletion affecting only a single gene, MBD5, which codes for the methyl-CpG-binding domain protein 5. In addition to the 67 children, we investigated 4 mentally retarded children with apparent balanced translocations and detected four deletions at breakpoint regions ranging in size from 1.1 to 14 Mb.

Figure 1.

Heat map of the median normalized intensity values of 169 HindIII arrays. The log₂ intensity values of 1,000 SNPs are displayed after hierarchical clustering. The sum of the intensity values of alleles A and B was used for this calculation. The columns contain the different arrays; the rows contain the different SNPs. The banner across the top of the heat map shows a color code for the four different time points at which the arrays were hybridized. Although the copy-number profile should be almost the same for each chip, it shows at least four clearly separated groups.

Figure 2.

Genomic profiles showing the log₂ intensity ratios of CNVs and of the surrounding genomic regions detected in patients with MR. The length of the CNVs is indicated on the X-axis. log₂ Intensity ratios are calculated as described in the “Material and Methods” section. Displayed are the log₂ intensity ratios after median smoothing with a window of 9. The dosage values of homozygous and heterozygous SNPs are depicted in black and gray, respectively. The gray horizontal lines are drawn at log₂(0.75) and log₂(1.25).

Figure 3.

Facial features of patients. A, Patient 27737, with a common 17p11.2 duplication, at age 10 mo, showing a telecanthus, triangular face, and broad forehead. B, Patient 29195, with an MBD5 deletion, at age 15 mo, showing a normal facies without dysmorphic features.

Figure 4.

Schematic representation of the regions affected in patients 29836 and 29195. A, Duplication in Xp22.31 in patient 29836. Genes are indicated by white boxes. The arrows denote the direction of transcription. The primers used for qPCR are shown above the genomic representation as numbered black bars. Primers 9060 and 9821 showed a single dosage; primers 9822 and 9820, a double dosage. The nonallelic homologous recombination must have occurred within the homologous regions flanked by primers 9060 and 9820 and primers 9822 and 9821. B, Deletion of part of the MBD5 gene in patient 29195. Exons are indicated by numbered black boxes (untranslated sequence) or gray boxes (translated sequence). The extent of the deletion is shown by a black bar below the gene scheme. Exons 1A–1E of MBD5 denote the 5′ untranslated exons established in this study.