Molecular Screening of 43 Brazilian Families Diagnosed with Leber Congenital Amaurosis or Early-Onset Severe Retinal Dystrophy

G C A T T A C G G C A T genes Article Molecular Screening of 43 Brazilian Families Diagnosed with Leber Congenital Amaurosis or Early-Onset Severe Retinal Dystrophy Fernanda B. O. Porto 1,2 ID , Evan M. Jones 3,4, Justin Branch 4, Zachry T. Soens 3,4, Igor Mendes Maia 5, Isadora F. G. Sena 5, Shirley A. M. Sampaio 1, Renata T. Simões 5 and Rui Chen 3,4,6,* 1 2 3 4 5 6 * INRET Clínica e Centro de Pesquisa, Belo Horizonte, 30150290 Minas Gerais, Brazil; (F.B.O.P.); (S.A.M.S.) Centro Oftalmológico de Minas Gerais, COMG, Belo Horizonte, 30150290 Minas Gerais, Brazil Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (E.M.J.); (Z.T.S.) Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Instituto de Ensino e Pesquisa da Santa Casa de Belo Horizonte, IEP/SCBH, Belo Horizonte, 30150290 Minas Gerais, Brazil; (I.M.M.); (I.F.G.S.); (R.T.S.) Structural and Computational Biology & Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA Correspondence: ; Tel.: +1-713-798-5194 Received: 29 August 2017; Accepted: 21 November 2017; Published: 29 November 2017 Abstract: Leber congenital amaurosis (LCA) is a severe disease that leads to complete blindness in children, typically before the first year of life. Due to the clinical and genetic heterogeneity among LCA and other retinal diseases, providing patients with a molecular diagnosis is essential to assigning an accurate clinical diagnosis. Using our gene panel that targets 300 genes that are known to cause retinal disease, including 24 genes reported to cause LCA, we sequenced 43 unrelated probands with Brazilian ancestry. We identified 42 unique variants and were able to assign a molecular diagnosis to 30/43 (70%) Brazilian patients. Among these, 30 patients were initially diagnosed with LCA or a form of early-onset retinal dystrophy, 17 patients harbored mutations in LCA-associated genes, while 13 patients had mutations in genes that were reported to cause other diseases involving the retina. Keywords: retina; genetics; ophthalmology; Leber congenital amaurosis; early-onset retinal dystrophy; next-generation sequencing 1. Introduction Inherited retinal dystrophies are a large heterogeneous group of diseases that are characterized by a degeneration of the light sensitive photoreceptor cells that are found in the retina. Some disorders lead to damage in both the rod and cone photoreceptor cells, leading to a complete loss of vision while others cause the specific loss of central or peripheral vision. Among this group of dystrophies is Leber congenital amaurosis (LCA), a primarily autosomal recessive disease, which is considered to be the most common cause of childhood blindness that affects both rod and cone photoreceptors [1]. LCA is estimated to affect 1 in 50,000 individuals and accounts for 5% of all retinal dystrophies and 20% of blindness in school-age children. The disease typically manifests within the first year of life and is characterized by minimal if any vision beyond infancy, congenital nystagmus, normal fundus appearance initially or various fundus changes, and a minimal or non-detectable signal on an Genes 2017, 8, 355; doi:10.3390/genes8120355 www.mdpi.com/journal/genes Genes 2017, 8, 355 2 of 18 electroretinogram (ERG) [2]. Despite these defined features, the clinical phenotype and genetic cause of LCA largely overlaps with that of other retinal dystrophies, which creates challenges in providing patients with a definitive clinical and molecular diagnosis [1,3]. For example, the clinical features of early-onset severe retinal dystrophies (EOSRD), such as juvenile retinitis pigmentosa (RP), can be similar to those of LCA. In 1869 Theodor Leber, the first to describe a child with LCA, initially diagnosed the disease as a congenital form of RP [4]. An abnormal recording on an ERG was later used to be an essential classifier of LCA [5]. In a later publication in 1916, Leber described a milder form of the same disease that manifests in the 6th and 7th years of life and led to blindness by 30 years of age, which he considered to be on the same spectrum as LCA. The disease has since been referred to as EOSRD [6]. Some patients fulfill the criteria for LCA but retain relatively good vision and better fit the definition of EOSRD. Therefore, the classification of these patients is not always clear. Moreover, juvenile RP and cone-rod dystrophy (CORD) tend to possess a milder phenotype than LCA in that vision loss is progressive [7]. The genetic overlap among retinal dystrophies can also complicate the diagnostic process in that variants in a particular set of genes may be associated with multiple retinal phenotypes [1]. Variants in several LCA-associated genes (CRX, CRB1, IMPDH1, RDH12, RPE65, TULP1, SPATA7) have been implicated to cause juvenile RP and CORD [2,3]. Furthermore, retinal dystrophies can be syndromic, in which non-retinal features are reported. Such syndromic dystrophies that cause LCA or an LCA like phenotype include Alström syndrome [8,9], Bardet-Biedl syndrome [10], and Senior-Loken syndrome [9,11]. Due to the genetic heterogeneity of LCA, a molecular diagnosis is essential for providing a patient with an accurate prognosis of disease, genetic counseling, and access to genetic therapies. While there exists no effective cure for retinal dystrophies, currently growing gene therapy clinical trials will potentially offer a remedy for inherited retinal disease patients [12,13]. To date, there are 24 genes that have been associated with LCA, in which next-generation sequencing (NGS) of the protein coding regions has led to a molecular diagnostic rate of about 75% [2]. In addition, previous studies have shown that the mutation spectrum differs among different populations [14–16]. The goal of this study was to perform a molecular screening of 43 unrelated probands of Brazilian ancestry initially diagnosed with LCA or EOSRD, which so far has been understudied. To evaluate the variant spectrum, a NGS capture panel that targets and sequences the exons of all known retinal disease genes has been developed. Using this targeted approach, we have previously sequenced multiple patient cohorts with retinal disease, including a Chinese cohort of 145 families that were diagnosed with LCA, leading to a solving rate of 76.6% [2]. In the study reported herein, our capture panel approach was able to achieve a solving rate of 70%, in which we identified variants in a total of 30 Brazilian probands. Among these 30 probands, 17 were solved by variants found in genes that have been reported to cause LCA while the remaining 13 probands were solved by variants in genes that were reported to cause other retinal diseases. Based upon our molecular diagnosis of these 13 probands, we were able to refine the clinical diagnosis of four patients, which reveals the importance of combining genetic and clinical information to provide r (...truncated)