Panel-Based Population Next-Generation Sequencing for Inherited Retinal Degenerations

Abstract

Inherited retinopathies affect approximately two and a half million people globally, yet the majority of affected patients lack clear genetic diagnoses given the diverse range of genes and mutations implicated in these conditions. We present results from a next-generation sequencing study of a large inherited retinal disease patient population, with the goal of providing clear and actionable genetic diagnoses. Targeted sequencing was performed on 539 individuals from 309 inherited retinal disease pedigrees. Causative mutations were identified in the majority (57%, 176/309) of pedigrees. We report the association of many previously unreported variants with retinal disease, as well as new disease phenotypes associated with known genes, including the first association of the SLC24A1 gene with retinitis pigmentosa. Population statistics reporting the genes most commonly implicated in retinal disease in the cohort are presented, as are some diagnostic conundrums that can arise during such studies. Inherited retinal diseases represent an exemplar group of disorders for the application of panel-based next-generation sequencing as an effective tool for detection of causative mutations.

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

“…In agreement with previous reports on Target 5000 [15,27], ABCA4 c.5603A>T (p.Asn1868Ile) is a significant causal variant of a milder form of STGD1 in this IRD cohort. Of 110 STGD1 pedigrees with 2 positive candidate variants identified, this variant was observed 14 times.…”

“…A spectrum of IRDs were observed in this study, as can be seen in Figure 1. The positive candidate dectection rate has improved from previous reports [15,27], now reaching approximately 70% (495/710). Furthermore, a single candidate variant only has been identified in an additional 9% (64/710) of pedigrees diagnosed with an IRD that typically exhibits a recessive inheritance pattern ( Figure 2).…”

“…Variants in RHO (MIM: 180380) were the most common candidate variants for RP in this cohort, accounting for over 14% (26/178) of all sequenced RP pedigrees, and over 32% (26/81) of dominant pedigrees alone. It is important to note that there is likely an even higher prevalence of RHO-linked RP in the Irish IRD cohort, as many pedigrees involved in single-gene studies were excluded from this study due to the discovery of a causative variant previously [15,27]. Of these variants, namely c.533A>G (p.Tyr178Cys), c.541G>A (p.Glu181Lys), and c.620T>G (p.Met207Arg) collectively account for candidate RHO mutations across 13 different pedigrees to date.…”

Application of targeted exome and whole‐exome sequencing for Chinese families with Stargardt disease

“…Possible reasons for these results are as follows: (1) targeted exome sequencing and WES cannot detect gross deletions, gross insertions, or complex rearrangement variants (Broadgate, Yu, Downes, & Halford, 2017), which might have been present in these families; (2) the sequence depth and coverage in this study was insufficient to call all variants accurately; (3) novel STGD-associated genes may have been filtered out during our raw data analysis; (4) deep-intronic variants in ABCA4 that are potentially associated with autosomal recessive STGD could not be captured through targeted exome sequencing and WES (Albert et al, 2018;Bauwens et al, 2015Bauwens et al, , 2019Bax et al, 2015;Braun et al, 2013;Sangermano et al, 2014;Zernant et al, 2014); and (5) diseasecausing variants with high minor allele frequency, which had not been reported previously may have been filtered out, for example, c.5603A > T, p.(Asn1868Ile) (Cremers, Cornelis, Runhart, & Astuti, 2018;Runhart et al, 2018;Zernant et al, 2017). Whole-genome sequencing (WGS) may be a useful alternative strategy to resolve these problems (Carrigan et al, 2016). This study carefully investigated gene variants in a cohort of Chinese probands with STGD; however, there were some limitations.…”

Clinically-guided mutation screening of two families with hereditary retinal disease

“…In the HRD field, the molecular diagnosis of disease cases also benefits a lot from a variety of NGS-based methods, including whole exome sequencing and targeted capture sequencing. Correspondingly, the molecular diagnosis rate of HRD cases has been significantly improved [4][5][6][7][8][9][10][11][12][13] , and a series of novel HRD-associated genes have been identified [14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33] .…”