Target 5000: Target Capture Sequencing for Inherited Retinal Degenerations

Abstract

There are an estimated 5000 people in Ireland who currently have an inherited retinal degeneration (IRD). It is the goal of this study, through genetic diagnosis, to better enable these 5000 individuals to obtain a clearer understanding of their condition and improved access to potentially applicable therapies. Here we show the current findings of a target capture next-generation sequencing study of over 750 patients from over 520 pedigrees currently situated in Ireland. We also demonstrate how processes can be implemented to retrospectively analyse patient datasets for the detection of structural variants in previously obtained sequencing reads. Pathogenic or likely pathogenic mutations were detected in 68% of pedigrees tested. We report nearly 30 novel mutations including three large structural variants. The population statistics related to our findings are presented by condition and credited to their respective candidate gene mutations. Rediagnosis rates of clinical phenotypes after genotyping are discussed. Possible causes of failure to detect a candidate mutation are evaluated. Future elements of this project, with a specific emphasis on structural variants and non-coding pathogenic variants, are expected to increase detection rates further and thereby produce an even more comprehensive representation of the genetic landscape of IRDs in Ireland.

A nationwide genetic analysis of inherited retinal diseases in Israel as assessed by the Israeli inherited retinal disease consortium (IIRDC)

“…The two most frequently mutated genes in the Israeli IRD cohort are ABCA4 (14%) and USH2A (7%). These findings are similar to those found in large IRD cohorts from other populations (Carss et al, ; Dockery et al, ; Haer‐Wigman et al, ; Stone et al, ). However, some of our findings are unique.…”

“…Overall, we succeeded to identify the genetic basis of disease in 56% of the recruited families (64% among families recruited up to December 2015). This percentage is within the range of diagnostic rates reported recently in other large cohorts of IRD patients (Carss et al, ; Dockery et al, ; Haer‐Wigman et al, ; Stone et al, ). It should be noted that of the unsolved families, only 17% have undergone WES and only 0.5% have undergone WGS.…”

“…Here, we describe a cohort of 3,413 Israeli IRD patients recruited since the year 1999. Though genetic analyses in large cohorts of IRD patients have been previously reported (ranging from 722 to 1000 patients; Carss et al, ; Dockery et al, ; Stone et al, ), to the best of our knowledge this is by far the largest IRD cohort reported to date. In 2017, Dockery et al reported partial results of genetic analysis among 750 individuals, as part of the Target 5000 project, a national effort aimed to genetically characterize IRDs in the Irish population.…”

Findings from a Genotyping Study of over 1000 People with Inherited Retinal Disorders in Ireland

“…DNA was isolated from either blood (DNA Blood Maxi Kit, Qiagen, Hilden, Germany) or saliva (Oragene-DNA, DNA Genotek, ON, Canada) samples from participants. Sample preparation was carried out using a hybridisation-based target capture sequencing method previously described [15]. The average read coverage achieved was 125× per captured region.…”

“…Raw sequencing data were demultiplexed and mapped to the IRD-relevant regions of the human genome (Hg38) as previously described [15]. The American College of Medical Genetics and Genomics (ACMG) criteria for classifying pathogenic variants was utilised to interpret variants [21].…”