Next-generation sequencing applied to a large French cone and cone-rod dystrophy cohort: mutation spectrum and new genotype-phenotype correlation

Boulanger-Scemama et al. Orphanet Journal of Rare Diseases (2015) 10:85 DOI 10.1186/s13023-015-0300-3 RESEARCH Open Access Next-generation sequencing applied to a large French cone and cone-rod dystrophy cohort: mutation spectrum and new genotype-phenotype correlation Elise Boulanger-Scemama1,2,3, Said El Shamieh1,2,3, Vanessa Démontant1,2,3, Christel Condroyer1,2,3, Aline Antonio1,2,3,6, Christelle Michiels1,2,3, Fiona Boyard1,2,3, Jean-Paul Saraiva4, Mélanie Letexier4, Eric Souied5, Saddek Mohand-Saïd1,2,3,6, José-Alain Sahel1,2,3,6,7,8,9, Christina Zeitz1,2,3*† and Isabelle Audo1,2,3,6,9*† Abstract Background: Cone and cone-rod dystrophies are clinically and genetically heterogeneous inherited retinal disorders with predominant cone impairment. They should be distinguished from the more common group of rod-cone dystrophies (retinitis pigmentosa) due to their more severe visual prognosis with early central vision loss. The purpose of our study was to document mutation spectrum of a large French cohort of cone and cone-rod dystrophies. Methods: We applied Next-Generation Sequencing targeting a panel of 123 genes implicated in retinal diseases to 96 patients. A systematic filtering approach was used to identify likely disease causing variants, subsequently confirmed by Sanger sequencing and co-segregation analysis when possible. Results: Overall, the likely causative mutations were detected in 62.1 % of cases, revealing 33 known and 35 novel mutations. This rate was higher for autosomal dominant (100 %) than autosomal recessive cases (53.8 %). Mutations in ABCA4 and GUCY2D were responsible for 19.2 % and 29.4 % of resolved cases with recessive and dominant inheritance, respectively. Furthermore, unexpected genotype-phenotype correlations were identified, confirming the complexity of inherited retinal disorders with phenotypic overlap between cone-rod dystrophies and other retinal diseases. Conclusions: In summary, this time-efficient approach allowed mutation detection in the most important cohort of cone-rod dystrophies investigated so far covering the largest number of genes. Association of known gene defects with novel phenotypes and mode of inheritance were established. Keywords: Inherited retinal disorders, Cone-rod dystrophy, Next-generation sequencing, Genotype-phenotype correlation * Correspondence: ; † Equal contributors 1 INSERM, U968, Paris F-75012, France Full list of author information is available at the end of the article © 2015 Boulanger-Scemama et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Boulanger-Scemama et al. Orphanet Journal of Rare Diseases (2015) 10:85 Background Cone and cone-rod dystrophy (CCRD) refer to a heterogeneous group of inherited retinal disorders (IRDs), characterized by predominant cone impairment. They are the most common cause of hereditary cone dysfunction, with a prevalence of 1:40000 [1]. Patients typically complain of progressive central visual loss associated with photophobia and colour vision abnormalities in childhood or early adult life. In case of associated rod system involvement, patients may also experience dim light vision disturbances and peripheral visual field constriction, leading to severe visual loss and complete blindness in some cases [1]. On fundoscopy, the macular appearance ranges from normal to bull’s eye maculopathy or more severe macular atrophy with possible pigmentary changes in the periphery in case of rod photoreceptor involvement [2]. Full-field electroretinogram (ERG) is the key examination for diagnosis and reveals predominant cone dysfunction with rod responses initially normal or minimally impaired. Advanced stages are characterized by both cone and rod impairment making the differential diagnosis with rod-cone dystrophy (or Retinitis Pigmentosa, RP) difficult. Progressive CCRD need to be distinguished from cone dysfunction syndromes, which are typically stationary, congenital with normal rod function [3]. However, these two entities have some phenotypic overlaps with difficulties for differential diagnosis when the congenital onset is not clearly documented. In addition CCRD often presents as an isolated disease, but can also be part of a syndrome as in Bardet-Biedl, Jalili syndrome or Spinocerebellar ataxia 7 [1, 5–7]. The genetic basis of CCRD is highly heterogeneous. Inheritance of CCRD can be either autosomal recessive (ar), autosomal dominant (ad) or X-linked (xl). Simplex CCRD are also frequent for which inheritance pattern is difficult to determine. A recent review estimated that ar (including isolated cases), ad and xl inheritance were found in 77 %, 22 %, and 1 % of CCRD, respectively [8]. To date, mutations in 30 genes have been implicated in CCRD (https://sph.uth.edu/retnet/ March 2015). Mutations in ABCA4 (ATP-binding cassette, sub-family A, member 4) [8, 9], GUCY2D (Guanylate Cyclase 2D) [10, 11] and RPGR (Retinitis Pigmentosa GTPase regulator) [12, 13] are major causes of ar, ad, and xl CCRD respectively. Novel gene defects still need to be identified since recent comprehensive studies genetically resolved less than 25 % of ar CCRD [2, 8]. Furthermore, clinical and genetic overlaps exist between CCRD and other IRDs. Distinct mutations in a same gene can cause distinct phenotypes, thereby leading to new phenotype-genotype correlations. For example, mutations in ABCA4, CRX, CERKL, PROM1, SEMA4A, GUCY2D can cause either CCRD, but also RP or Leber congenital amaurosis Page 2 of 20 (LCA). In this context, Next Generation Sequencing (NGS) targeting not only genes known to underlie CCRD but also more comprehensively other genes mutated in IRDs provides the method of choice, compared to Sanger sequencing, to encompass clinical and genetic heterogeneity of this disease group [14]. Targeted NGS has been successfully applied for investigating IRD: studies covering from 45 to 254 known genes implicated in IRDs were able to genetically resolve from 25 % to 57 % of cases [14–20]. In contrast, only one study so far applied NGS, targeting 25 genes, to CRD [21]. The purpose of our study was to conduct a more comprehensive analysis of CCRD by applying a NGS panel covering 123 genes, improved from a previous report [14], to a French cohort of 96 clinically well characterized patients (95 index patients) who had never been genetically investigated and therefore assess the distribution and prevalence of mutations and genes involved in CCRD. Methods Clinical diagnosis of CCRD Ninety-six patients, from 95 unrelated families (2 siblings) with a presumed diagnosis of non-syndromi (...truncated)