Clinical and molecular delineation of the 17q21.31 microdeletion syndrome

Abstract

Background: The chromosome 17q21.31 microdeletion syndrome is a novel genomic disorder that has originally been identified using high resolution genome analyses in patients with unexplained mental retardation.

Aim: We report the molecular and/or clinical characterisation of 22 individuals with the 17q21.31 microdeletion syndrome.

Results: We estimate the prevalence of the syndrome to be 1 in 16,000 and show that it is highly underdiagnosed. Extensive clinical examination reveals that developmental delay, hypotonia, facial dysmorphisms including a long face, a tubular or pear-shaped nose and a bulbous nasal tip, and a friendly/amiable behaviour are the most characteristic features. Other clinically important features include epilepsy, heart defects and kidney/urologic anomalies. Using high resolution oligonucleotide arrays we narrow the 17q21.31 critical region to a 424 kb genomic segment (chr17: 41046729-41470954, hg17) encompassing at least six genes, among which is the gene encoding microtubule associated protein tau (MAPT). Mutation screening of MAPT in 122 individuals with a phenotype suggestive of 17q21.31 deletion carriers, but who do not carry the recurrent deletion, failed to identify any disease associated variants. In five deletion carriers we identify a <500 bp rearrangement hotspot at the proximal breakpoint contained within an L2 LINE motif and show that in every case examined the parent originating the deletion carries a common 900 kb 17q21.31 inversion polymorphism, indicating that this inversion is a necessary factor for deletion to occur (p<10(-5)).

Conclusion: Our data establish the 17q21.31 microdeletion syndrome as a clinically and molecularly well recognisable genomic disorder.

Figure 1

Identification of the 17q21.31 deletions. (A) Chromosome 17 plot of case 1 obtained by whole genome oligonucleotide array (Agilent Human Genome CGH Microarray Kit 244A, Agilent Technologies). Chromosome 17 is represented by 5881 coding and non-coding human sequences (indicated by circles representing the log₂-transformed and normalised test: reference intensity ratios ((log₂(T/R)), ordered from pter to qter for chromosome 17, in hg17 (NCBI build 35, May 2004). The arrow indicates the presence of a copy number loss at 17q21.31. (B) FISH analysis on metaphase spreads of case 7, using the BAC clones CTD-2324N3 (red) and RP11-413P22 (green) which are both located within the deleted 17q21.31 region. The patient shows only one signal for CTD-2324N3 and RP11-413P22, indicating an aberrant chromosome 17 (arrow). (C) Detection of a heterozygous MAPT deletion in case 4 using the microdeletion/microduplication QMPSF assay. The electropherogram of the patient (in red) was superimposed on that of a normal female control (in blue) by adjusting to the same level the peaks obtained for the control amplicon. The Y axis displays fluorescence intensity, and the X axis indicates the genes tested. The heterozygous deletion is detected by a 50% reduction of the MAPT peak compared to the normal control (arrow). (D) MLPA results for case 19 (triangles) and two healthy controls (rectangles), showing a deletion of all 13 probes in the CRHR1, IMP5, MAPT, and STH genes within the 17q21.31 genomic interval.

Figure 2

Ultra high resolution oligonucleotide array analysis. Results of ultra high resolution oligonucleotide array analysis of the 17q21.31 microdeletion proximal breakpoint (mean probe density 1 probe/5.2 bp). (A) Data from a 50 kb region (chr17:41025000–41075000, hg17) in five unrelated 17q21.31 deletion patients and one control. In each deletion, the proximal breakpoint occurred in a segmental duplication of length, 34.2 kb, identity 98.7% (chr17:41026709–41060948). (B) Zoomed view showing a 5 kb region (chr17:41044500–41049500). All five patients have breakpoints which are indistinguishable, mapping to within an interval of <500 bp contained within an L2 LINE motif. The highly variable dynamic response of certain probes in this region to report the deletion is likely a result of their different sequence properties (38). For each individual, deviations of probe log₂ ratios from zero are depicted by grey/black bars, with those exceeding a threshold of 1.5 standard deviations from the mean probe ratio coloured green and red to represent relative gains and losses, respectively. Tracks above each plot indicate segmental duplications (grey/yellow bars represent duplicons with 90–98%/98–99% sequence identity, respectively).

Figure 3

Genotyping H1 and H2 on 17q21.31 and parent-of-origin analysis. Genotyping results in the family of case 4. (A) PCR results of a 238 bp deletion in intron 9 of MAPT indicative for the H2 lineage. Both parents are H1/H2 heterozygotes. Far left and far right: 100 bp marker lanes. (B) PCR results of a VNTR (chr17: 41,224,986–41,225,022) within the deleted 17q21.31 region excluding a paternal origin. (C) Reconstruction of genomic markers located within and outside the deleted 17q21.31 segment shows the maternal origin of the deletion. Dinucleotide marker DG17S142 is indicative for the H2 lineage (11).

Figure 4

Faces of individuals with a 17q21.31 deletion. Facial photographs of case 1, at age 10 months; case 2, at age 1 year; case 3, at age 2 years; case 4, at age 3 years; case 5, at age 3 years; case 6, at age 3 years 5 months; case 7, at age 3 years 8 months; case 8, at age 3 years; case 9, at age 5 years 8 months; case 10 at age 5 years; case 11, at age 3 years 9 months; case 12, at age 8 years 6 months; case 14, at age 13 years; case 15, at age 14 years; case 16, at 14 years; case 18, at 16 years; case 19, at 13 years; case 20, at age 18 years; case 21, at 17 years and case 22, at age 26 years.

Figure 5

Facial photographs at different ages (<1, 1–4, 5–6, 7–12, and >12 years of age). Note that the facial characteristics of the patients change with age. With increasing age there is elongation of the face and broadening of the chin and also the “tubular” or “pear” shape form of the nose becomes more pronounced.