Recurrent deletions and reciprocal duplications of 10q11.21q11.23 including CHAT and SLC18A3 are likely mediated by complex low-copy repeats

Abstract

We report 24 unrelated individuals with deletions and 17 additional cases with duplications at 10q11.21q21.1 identified by chromosomal microarray analysis. The rearrangements range in size from 0.3 to 12 Mb. Nineteen of the deletions and eight duplications are flanked by large, directly oriented segmental duplications of >98% sequence identity, suggesting that nonallelic homologous recombination (NAHR) caused these genomic rearrangements. Nine individuals with deletions and five with duplications have additional copy number changes. Detailed clinical evaluation of 20 patients with deletions revealed variable clinical features, with developmental delay (DD) and/or intellectual disability (ID) as the only features common to a majority of individuals. We suggest that some of the other features present in more than one patient with deletion, including hypotonia, sleep apnea, chronic constipation, gastroesophageal and vesicoureteral refluxes, epilepsy, ataxia, dysphagia, nystagmus, and ptosis may result from deletion of the CHAT gene, encoding choline acetyltransferase, and the SLC18A3 gene, mapping in the first intron of CHAT and encoding vesicular acetylcholine transporter. The phenotypic diversity and presence of the deletion in apparently normal carrier parents suggest that subjects carrying 10q11.21q11.23 deletions may exhibit variable phenotypic expressivity and incomplete penetrance influenced by additional genetic and nongenetic modifiers.

Figure 1

Chromosomal microarray results for eight samples analyzed by BCM, using RocheNimbleGen oligonucleotide-based microarrays. At the top is a schematic of the genomic architecture of the region. Black boxes represent sequence gaps. Colored boxes represent segmental duplications. For each plot, probes are arranged on the X-axis according to physical mapping positions, with the most proximal 10q11.21 probes to the left and the most distal 10q11.23 probes to the right. Values along the Y-axis represent log₂ ratios of patient:control signal intensities. Deletion intervals are represented by a dotted bracket (patients 1–5) or vertical, solid black lines (patients 6, 19–20).

Figure 2

Chromosomal microarray results for patient samples analyzed by SignatureChip oligonucleotide-based microarray. At the top is a schematic of the genomic architecture of the region. Black boxes represent sequence gaps. Colored boxes represent segmental duplications. For each plot, probes are arranged on the X-axis according to physical mapping positions, with the most proximal 10q11.22 probes to the left and the most distal 10q11.23 probes to the right. Values along the Y-axis represent log₂ ratios of patient:control signal intensities.

Figure 3

Summary of chromosomal microarray analysis of individuals with deletions and duplications 10q11.21q21.1. At the top of the figure is a partial idiogram showing chromosome bands 10q11.21q21.1 with genomic coordinates corresponding to the hg18 build of the human genome. Green bars represent the deletions and the orange bars the duplications. Red bars represent segmental duplications. Only the directly oriented paralogous LCR subunits (18) between LCR10q11.2s A–C and D–F, that have a potential for NAHR, are shown for illustrative purposes as the colored arrows. Each of the 18 paralogous pairs is shown in different color (Supp. Table S1). Note that NAHR might have mediated rearrangements in patients 2, 4–12, 15, 17–18, 20, 23, 24, 26, 28, 33, 40, and 41 (between LCR10q11.2A and LCR10q11.2E), 16 and 21 (between LCR10q11.2C and LCR10q11.2D), 22, 29, and 32 (between LCR10q11.2A–B and LCR10q11.2D–E), and 35 (between LCR10q11.2B and LCR10q11.2E). Dark blue bars depict seven genomic gaps. Semitransparent light blue shading represents the collapsed LCR clusters A–F. Semitransparent yellow shading represents the smallest region of unique sequence shared by all deletion patients.

Figure 4

DNA sequence homology between the proximal (chr10: 45,300,000–49,200,000) and distal (chr10: 49,300,000–53,200,000) LCR10q11.2 clusters for the paralogous subunits larger than 1 kb in size (hg18) using Miropeats program analysis. The upper and bottom panels depict the UCSC segmental duplication track.