Genetic spectrum of retinal dystrophies in Tunisia

www.nature.com/scientificreports OPEN Genetic spectrum of retinal dystrophies in Tunisia Imen Habibi 1*, Yosra Falfoul2, Ahmed Turki2, Asma Hassairi2, Khaled El Matri Ahmed Chebil2, Daniel F. Schorderet 1,3,4 & Leila El Matri2 2 , We report the molecular basis of the largest Tunisian cohort with inherited retinal dystrophies (IRD) reported to date, identify disease-causing pathogenic variants and describe genotype–phenotype correlations. A subset of 26 families from a cohort of 73 families with clinical diagnosis of autosomal recessive IRD (AR-IRD) excluding Usher syndrome was analyzed by whole exome sequencing and autozygosity mapping. Causative pathogenic variants were identified in 50 families (68.4%), 42% of which were novel. The most prevalent pathogenic variants were observed in ABCA4 (14%) and RPE65, CRB1 and CERKL (8% each). 26 variants (8 novel and 18 known) in 19 genes were identified in 26 families (14 missense substitutions, 5 deletions, 4 nonsense pathogenic variants and 3 splice site variants), with further allelic heterogeneity arising from different pathogenic variants in the same gene. The most common phenotype in our cohort is retinitis pigmentosa (23%) and cone rod dystrophy (23%) followed by Leber congenital amaurosis (19.2%). We report the association of new disease phenotypes. This research was carried out in Tunisian patients with IRD in order to delineate the genetic population architecture. Inherited retinal dystrophies (IRD) are a large group of inherited eye disorders which affect photoreceptors and lead to visual impairment. The prevalence of IRD has been estimated in one case for each 2,500–7,000 persons among the general p opulation1. IRDs are further classified into as retinitis pigmentosa (RP), cone rod dystrophy (CRD), and cone dystrophy (CD). Initial symptoms include night blindness, photophobia and/or progressive loss of the peripheral vision2. Clinical symptoms vary across different IRD subtypes and different disease genes. Genetically, different IRD can be caused by pathogenic variants in more than 300 genes, over 100 of these have been linked to syndromic IRD (https: //sph.uth.edu/retnet /), displaying three form of inheritance: autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL). Occasionally, mitochondrial variants and digenic inheritance have been identified3. Molecular genetics is essential for gene-based treatment, clarify diagnoses and to direct appropriate counseling. However, it is currently unknown how many genes are involved in IRDs, and even by using the latest next generation sequencing (NGS) techniques, pathogenic and likely pathogenic variants are identified only in 50% to 75% of p atients4. Due to the relatively high frequency of consanguinity in Tunisia, ranging from 20 to 40%, this population could contribute to the identification of new genes responsible for AR-IRD5. To identify causative pathogenic variants in a large cohort of families diagnosed with nonsyndromic (24/26) or syndromic (2/26) AR-IRD, homozygosity mapping of known IRD loci was carried out. Pathogenic variant screening of the identified genes in all 74 families gave an overall idea about the most frequent genes and variants in patients with IRD in Tunisia. We believe it is essential to combine molecular and clinical data to diagnose IRD patients, especially with the emergence of therapeutic options. Results Clinical diagnosis and pathogenic and likely pathogenic (P/LP) variants identified. 50 affected and 48 unaffected relatives belonging to 26 families with suspected recessive inheritance were included. Pathogenic variants are listed in Table 1. A total of 26 causative P/LP variants in 19 genes were identified in 26 families, including 14 missense substitutions (53.9%), 5 deletions (19.2%), 4 nonsense P/LP variants (15.4%) and 3 splice site pathogenic variants (11.5%). 8 (30.8%) P/LP variants were novel, while the remaining 18 (69.2%) were reported previously. 96.2% of all P/LP variants were homozygous, only one family carried a heterozygous patho- 1 IRO-Institute for Research in Ophthalmology, Av du Grand‑Champsec 64, 1950 Sion, Switzerland. 2Oculogenetic Laboratory LR14SP01, Hedi Rais Institute of Ophthalmology (Department B), Tunis, Tunisia. 3Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland. 4Faculty of Life Sciences, Ecole Polytechnique fédérale de Lausanne, Lausanne, Switzerland. *email: Scientific Reports | (2020) 10:11199 | https://doi.org/10.1038/s41598-020-67792-y 1 Vol.:(0123456789) www.nature.com/scientificreports/ Family ID Disease Genotyping Method Size of homozygous region, in Mb Chr Gene DNA pathogenic variant Predicted protein variant Reference sequence Previously reported SIFT PolyPhen F1 LCA WES – 14q11.2 RPGRIP1 c.[3113-3114delCT];[3113-3114delCT] p.[T1038Rfs*8]; T1038Rfs*8] NM_020366 This study – – F2 LCA IROme – 17p31.1 GUCY2D c.[2660 T > G];[2660 T > G] p.[V887G];[V887G] NM_000180 This study and6 0 0.999 F3 LCA Asper – 1p31.3 RPE65 c.[700C > T];[700C > T] p.[R234*];[R234*] NM_000329 29 – – F4 LCA WES – 3q13.33 IQCB1 c.[994C > T];[994C > T] p.[R332*];[R332*] NM_001023570 30 – – F5 LCA WES – 1q31.3 CRB1 c.[3542 + 1G > A];[3542 + 1G > A] – NM_201253.2 This study – – F6 CRD WES 40 1q31.3 CRB1 c.[2506C > A];[2506C > A] p.[P836T];[P836T] NM_201253.2 31 0.04 0.999 F7 CRD WES 124 1q31.3 CRB1 c.[ 2105A > G];[ 2105A > G] p.[Y702C];[Y702C] NM_201253.2 32 0 0.89 F8 CRD WES – 10q23.1 CDHR1 c.[863-2_863-1delAG];[863-2_863-1delAG] – NM_033100 This study – – – F9 CRD WES – 8q22.1 C8ORF37 c.[470 + 1G > T];[470 + 1G > T] – NM_177965 This study – F10 CRD WES – 2p23.2 C2ORF71 c.[2756_2768del13];[ 2756_2768del13] p.[K919Tfs*2];[ K919Tfs*2] NM_001029883 33 – – F11 CRD WES 35 1p22.1 ABCA4 c.[1916A > G];[1916A > G] p.[Y639C];[Y639C] NM_000350.2 This study 0.01 1 F12 RP WES 77 1p22.1 ABCA4 c.[4139C > T];[4139C > T] p.[P1380L];[P1380L] NM_000350.2 34 0 0.716 F13 STGD WES – 1p22.1 ABCA4 c.[1140 T > A];[1140 T > A] p.[N380K];[N380K] NM_000350.2 35 0.01 0.05 F14 STGD WES – 1p22.1 ABCA4 c.[3259G > A];[3259G > A] p.[E1087K]; [E1087K] NM_000350.2 36 0 0.999 F15 CRD/STGD WES – 1p22.1 ABCA4 c.[3259G > A];[3259G > A] p.[E1087K]; [E1087K] NM_000350.2 36 0 0.999 F16 RP WES – 1p36.22 NMNAT1 c.[37G > A];[37G > A] p.[A13T];[A13T] NM_001297778.1 8 0 1 F17 RP WES – 6p21.1 PRPH2 c.[133C > T];[ =] p.[L45F];[ =] NM_000322 37 0 0.991 F18 RP WES – 2p15 FAM161A c.[685C > T];[685C > T] p.[R229*];[R229*] NM_001201543 38 – – F19 RP WES – 16q21 CNGB1 c.[2293C > T];[2293C > T] p.[R765C];[R765C] NM_001297 This study and 6 0 0.999 F20 RP WES – 6q12 EYS c.(1766 + 1_1767-1)_(2023 + 1_2024-1)del – NM_001292009 39 – – F21 RP WES – 6q12 EYS c.[5928-2A > G];[5928-2A > G (...truncated)