Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy

Abstract

Most studies of genomic disorders have focused on patients with cognitive disability and/or peripheral nervous system defects. In an effort to broaden the phenotypic spectrum of this disease model, we assessed 155 autopsy samples from fetuses with well-defined developmental pathologies in regions predisposed to recurrent rearrangement, by array-based comparative genomic hybridization. We found that 6% of fetal material showed evidence of microdeletion or microduplication, including three independent events that likely resulted from unequal crossing-over between segmental duplications. One of the microdeletions, identified in a fetus with multicystic dysplastic kidneys, encompasses the TCF2 gene on 17q12, previously shown to be mutated in maturity-onset diabetes, as well as in a subset of pediatric renal abnormalities. Fine-scale mapping of the breakpoints in different patient cohorts revealed a recurrent 1.5-Mb de novo deletion in individuals with phenotypes that ranged from congenital renal abnormalities to maturity-onset diabetes of the young type 5. We also identified the reciprocal duplication, which appears to be enriched in samples from patients with epilepsy. We describe the first example of a recurrent genomic disorder associated with diabetes.

Figure 1.

Recurrent microdeletion of 17q12. a, Kidney photographs from case FA-275, showing multiple cysts bilaterally with enlargement of the left kidney, hypoplastic bladder, and atresia of the left ureter. b, BAC array data for case FA-275, showing deletion of a chromosomal region represented by seven chromosome 17 BAC clones. c, Structural resolution of a 1.5-Mb microdeletion region of 17q12 by use of a high-density oligonucleotide microarray. Eight of the nine cases have proximal and distal breakpoints mapping to flanking segmental duplications. Plots show the log₂ ratio (Y-axis) for 48,256 probes (X-axis) in this region of 17q12 (hg17 coordinates chr17:31200000–33850000). For each individual, deviations of probe log₂ ratios from zero are depicted by gray and black lines, with those exceeding a threshold of 0.9 SDs (duplications) and 1.5 SDs (deletions) from the mean probe ratio colored green and red to represent relative gains and losses, respectively. Bars define regions of copy-number variation (shaded gray) in controls and common recurrent deletion (shaded pink).

Figure 2.

Structural resolution of additional rearrangements in the fetal autopsy series. a, A 157-kb duplication of chromosome 17q23 in FA-142, a fetus with multicystic dysplastic kidneys. Paired segmental duplications (seg dups) with >99% identity are indicated. Breakpoints of this duplication are in CLTC (proximal) and TMEM49 (distal). PTHR2 (BIT1) is entirely within the duplicated region. b, A 2.5-Mb microdeletion of chromosome 15q25.2 (hg17 coordinates chr15:81011700–83540700) in FA-602, a fetus with congenital diaphragmatic hernia and mild hydrocephalus. c, A 2-Mb deletion of 16p13.12-p12.3 in FA-180 (hg17 coordinates chr16:14200000–17200000). Regions of known copy-number polymorphism (CNP) in unaffected individuals are indicated (blue bars). Plots show the log₂ ratio (Y-axis) for probes (X-axis) in the region depicted. Deviations of probe log₂ ratios from zero are depicted as in figure 1c.

Figure 3.

Copy-number variation of the segmental duplications (Seg dups) at breakpoint regions. An expanded view of oligonucleotide array CGH within the segmental duplications located at the proximal (left) and distal (right) breakpoints of 17q12 rearrangements. Control set includes five unaffected individuals analyzed on same custom array as the patients with 17q12 deletion or duplication. For each individual, deviations of probe log₂ ratios from zero are depicted as in figure 1c. Control individuals show increased and decreased copy number in the segmental duplications, highlighting the difficulty in determining precise rearrangement breakpoints. Individuals shown are IMR379, 5812, 6498, FR12, FR92, FR09, FR37, C1, C2, C3, C4, and C5.

Figure 4.

Copy-number polymorphism of the segmental duplications at the breakpoint regions. An expanded view of figure 2, showing eight additional control individuals (controls C6–C13) analyzed on a custom oligonucleotide array targeted to segmental duplications (Seg dups) and five additional patients with 17q12 deletion. Controls C1–C5 are the same as in figure 2. For each individual, deviations of probe log₂ ratios from zero are depicted as in figures 1 and 2. The patients with 17q12 deletion shown are FR40, FR99, FR45, FR35, and FA-275.

Figure 5.

Reciprocal 17q12 duplication. a, Structural resolution of the reciprocal 1.5-Mb microduplication region of 17q12 by use of high-density oligonucleotide microarrays. Plots show the log₂ ratio (Y-axis) for 48,256 probes (X-axis) in this region of 17q12 (hg17 coordinates chr17:31200000–33850000). Three affected individuals with mental retardation and epilepsy and the unaffected mother of 6498 are shown. An expanded view of the LHX1 region (hg17 coordinates chr17:32325000–32345000) is also shown for individuals 6498 and 6840. The average log₂ ratio for the 765 probes in the 27-kb region (dotted lines) is 0.176 for individual 6498 and 0.030 for individual 6840 (the mother). c, Quantitative PCR results for exon 1 of LHX1 gene, confirming four patients with duplication (large dup) and patient FA-275 with deletion, when compared with five unaffected controls. Patient 6498 with epilepsy shows a duplication by quantitative PCR when compared with the mother (6840). d, Interphase FISH with LHX1 genomic probe (WIBR2-6022g13; see panel b for location). Of the lymphocyte nuclei from affected patient 6498, 98% show evidence of tandem duplication (three signals), compared with 28% of lymphoblast cells from the mother (6840). Two nuclei from 6840 show discordant results, with duplication present in only one of the two cells shown, suggesting that the mother is a mosaic for the duplication (see the slight signal-intensity increase observed in panel a).

Figure 6.

Pedigrees of three families with duplication in the 17q12 region. +dup = duplication is reciprocal to 17q12 deletion; +dup* = duplication of TCF2, mosaic duplication of LHX1; +dup** = duplication of TCF2 and LHX1 (see text); FCD = focal cortical dysplasia; MR = mental retardation. Only individuals 5812 and 6498 have had magnetic resonance imaging to evaluate for FCD.

Figure 7.

A 17q12 duplication identified in 1 of 960 unaffected control samples by use of the HumanHap300 Genotyping BeadChip (Illumina). Data show probe position (X-axis) against the log(R) intensity ratio (black) and the B-allele frequency (red) for probes on chromosome 17. Within the limits of resolution of these data, this duplication appears to be identical to that observed in patients IMR379 and 5812.