Duplication events downstream of IRX1 cause North Carolina macular dystrophy at the MCDR3 locus

Abstract

Autosomal dominant North Carolina macular dystrophy (NCMD) is believed to represent a failure of macular development. The disorder has been linked to two loci, MCDR1 (chromosome 6q16) and MCDR3 (chromosome 5p15-p13). Recently, non-coding variants upstream of PRDM13 (MCDR1) and a duplication including IRX1 (MCDR3) have been identified. However, the underlying disease-causing mechanism remains uncertain. Through a combination of sequencing studies on eighteen NCMD families, we report two novel overlapping duplications at the MCDR3 locus, in a gene desert downstream of IRX1 and upstream of ADAMTS16. One duplication of 43 kb was identified in nine families (with evidence for a shared ancestral haplotype), and another one of 45 kb was found in a single family. Three families carry the previously reported V2 variant (MCDR1), while five remain unsolved. The MCDR3 locus is thus refined to a shared region of 39 kb that contains DNAse hypersensitive sites active at a restricted time window during retinal development. Publicly available data confirmed expression of IRX1 and ADAMTS16 in human fetal retina, with IRX1 preferentially expressed in fetal macula. These findings represent a major advance in our understanding of the molecular genetics of NCMD and provide insights into the genetic pathways involved in human macular development.

Unique noncoding variants upstream of PRDM13 are associated with a spectrum of developmental retinal dystrophies including progressive bifocal chorioretinal atrophy

“…Given the phenotypic similarity observed in Family 3 to both NCMD and PBCRA, it was hypothesised that the disease‐associated genetic variant may be located within the associated loci. Using the WGS SNV and structural variant (SV) call data and manual interrogation of the paired‐end reads using the Integrative Genomics Viewer (IGV; Thorvaldsdóttir, Robinson, & Mesirov, ),) all known NCMD‐associated variants were excluded at both the chr5 and chr6 loci (Bowne et al, ; Cipriani, Silva et al, ; Manes et al, ; Small et al, ). At the PBCRA/MCDR1 locus, 75 SNV variants with MAF < 0.01 (and allele count <3 from NIHR data set), were shared, of which 18 were absent from gnomAD (Table S3).…”

“…Given the rarity of the phenotype and the discovery of the same variant in two not knowingly related families, we sought to determine whether a common ancestral haplotype could account for the disease. Haplotype sharing analysis (Cipriani, Kalhoro et al, ; Cipriani, Silva et al, ) of SNP‐array data showed that the families had a different chromosomal background at the 6q linkage region (Figure S1). Furthermore, WGS enables the characterisation of every SNV (common or rare) in the linkage region in both families.…”

“…Genomic DNA was purified from peripheral blood mononuclear cells of eight affected individuals from three unrelated families (Figures a and e) for whole‐genome sequencing (WGS). WGS was performed independently or as part of the National Institute for Health Research BioResource‐Rare Disease study (NIHR BR‐RD) as previously described (Carss et al, ; Cipriani, Silva et al, ), generating minimum coverage of 15× for 95% of the genome. Reads were aligned to the hg19 human reference sequence (build GRCh37) with Novoalign (version 3.02.08).…”

“…Six affected individuals (two from Family 1 and four from Family 2) were selected for SNP‐array genotyping using the Illumina HumanOmniExpress‐24 v1.0 beadchip (Illumina, Inc., San Diego, CA). Genotypes were determined using the Genotyping Module in the Illumina GenomeStudio v2011.1 software and used for haplotype sharing analysis as previously described (Cipriani, Kalhoro et al, ; Cipriani, Silva et al, ).…”

“…In addition, three distinct tandem duplications encompassing PRDM13 and its upstream region were also reported (Bowne et al, ; Manes et al, ; Small et al, ). Tandem duplications were also identified on a second locus at 5p21 (MCDR3, MIM# 608850), where the critical region for phenotype was narrowed down to a 39 kb noncoding region (Cipriani, Silva et al, ; Small et al, ). The disease mechanism at both loci is undetermined.…”