ATR-16 syndrome: mechanisms linking monosomy to phenotype

Abstract

Background: Deletions removing 100s-1000s kb of DNA, and variable numbers of poorly characterised genes, are often found in patients with a wide range of developmental abnormalities. In such cases, understanding the contribution of the deletion to an individual's clinical phenotype is challenging.

Methods: Here, as an example of this common phenomenon, we analysed 41 patients with simple deletions of ~177 to ~2000 kb affecting one allele of the well-characterised, gene dense, distal region of chromosome 16 (16p13.3), referred to as ATR-16 syndrome. We characterised deletion extents and screened for genetic background effects, telomere position effect and compensatory upregulation of hemizygous genes.

Results: We find the risk of developmental and neurological abnormalities arises from much smaller distal chromosome 16 deletions (~400 kb) than previously reported. Beyond this, the severity of ATR-16 syndrome increases with deletion size, but there is no evidence that critical regions determine the developmental abnormalities associated with this disorder. Surprisingly, we find no evidence of telomere position effect or compensatory upregulation of hemizygous genes; however, genetic background effects substantially modify phenotypic abnormalities.

Conclusions: Using ATR-16 as a general model of disorders caused by CNVs, we show the degree to which individuals with contiguous gene syndromes are affected is not simply related to the number of genes deleted but depends on their genetic background. We also show there is no critical region defining the degree of phenotypic abnormalities in ATR-16 syndrome and this has important implications for genetic counselling.

Keywords: ATR16; CNV; developmental delay; thalassemia.

Figure 1

Chromosome 16 breakpoint sequences. DNA sequences at ATR-16 breakpoints. Patient codes are given in the upper left of each panel. For each case, alignment of the two normal sequences is shown with sequence from the derivative chromosome (upper) with chromatogram traces traversing each breakpoint (lower). Areas of ambiguity are highlighted with grey boxes and the location of the last unambiguous base pair(s) are denoted by arrowheads and red boxes. Chr16, normal chromosome 16 sequence; Bpt, breakpoint sequence; Tel, telomere repeat sequence; SubTel, subtelomere repeat sequence; Prox, proximal chromosome 16 sequence; Dist, distal chromosome 16 sequence; AluY, AluY repetitive element. Asterisks indicate informative polymorphisms allowing sequence origins to be identified. For patients MY and OY, a telomere primer with a mismatched G nucleotide was used.

Figure 2

Summary of ATR-16 deletions. Upper: HiC interaction map showing interactions across the terminal 2 Mb of chromosome 16 at a 5 kb resolution in K562 cells (data from Rao et al 40). This shows how the ATR-16 deletions detailed in the lower section may impact the genome organisation. Middle: the positions of the α-globin cluster and other genes within this region are indicated. The α-globin genes and genes that, when mutated, are associated with tuberous sclerosis and adult polycystic kidney disease are shown in shaded boxes. Lower: the extent of each deletion is shown with the patient code (left). Deletions shown in green cause no other abnormalities apart from α-thalassaemia and those in red cause at least one other abnormality present in ATR-16. Solid bars indicate regions known to be deleted and fine lines show regions of uncertainty. Asterisks indicate individuals whose deletion breakpoints have been cloned or refined in this work.

Figure 3

Effect of breakpoints and deletions on gene expression. (A) Schematic view of breakpoint positions in three patients with nearby expressed polymorphic genes. Genes are represented by black bars and transcription direction is indicated by an arrow. Polymorphic bases are shown by red letters indicating variant alleles and the distance of the promoter of each measured gene from the breakpoint is shown. On the right of each panel chromatograms show the quantity of the allele present in genomic DNA and cDNA from patient lymphoblastoid cells. (B) Expression of 12 genes within 500 kb of the tip of the short arm of chromosome 16 in lymphoblastoid cells from 20 normal individuals, shown as reference (red column) and from 11 ATR-16 individuals hemizygous for each gene. Measurements in control cells are normalised to 1 (red column), relative expression in ATR-16 patient cells is shown in blue. Error bars show SD. Gene expression was measured in triplicate and data combined.