%0 Journal Article %J Invest Ophthalmol Vis Sci %D 2017 %T The Genetic Causes of Nonsyndromic Congenital Retinal Detachment: A Genetic and Phenotypic Study of Pakistani Families. %A Keser, Vafa %A Khan, Ayesha %A Siddiqui, Sorath %A Lopez, Irma %A Ren, Huanan %A Qamar, Raheel %A Nadaf, Javad %A Majewski, Jacek %A Chen, Rui %A Koenekoop, Robert K %K Basic Helix-Loop-Helix Transcription Factors %K Child %K Child, Preschool %K DNA Mutational Analysis %K Female %K Genotype %K Helix-Loop-Helix Motifs %K Humans %K Incidence %K Infant %K Male %K Mutation %K Pakistan %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Retina %K Retinal Diseases %X

PURPOSE: To evaluate consanguineous pedigrees from Pakistan with a clinical diagnosis of nonsyndromic congenital retinal nonattachment (NCRNA) and identify genes responsible for the disease as currently only one NCRNA gene is known (atonal basic helix-loop-helix transcription factor 7: ATOH7).

METHODS: We implemented a three-step genotyping platform: single nucleotide polymorphism genotyping to identify loss of heterozygosity regions in patients, Retinal Information Network panel screening for mutations in currently known retinal genes. Negative patients were then subjected to whole exome sequencing.

RESULTS: We evaluated 21 consanguineous NCRNA pedigrees and identified the causal mutations in known retinal genes in 13 out of our 21 families. We found mutations in ATOH7 in three families. Surprisingly, we then found mutations in familial exudative vitreoretinopathy (FEVR) genes; low-density lipoprotein receptor-related protein 5 mutations (six families), tetraspanin 12 mutations (two families), and NDP mutations (two families). Thus, 62% of the patients were successfully genotyped in our study with seven novel and six previously reported mutations in known retinal genes.

CONCLUSIONS: Although the clinical diagnosis of all children was NCRNA with severe congenital fibrotic retinal detachments, the molecular diagnosis determined that the disease process was in fact a very severe form of FEVR in 10 families. Because severe congenital retinal detachment has not been previously associated with all the FEVR genes, we have thus expanded the phenotypic spectrum of FEVR, a highly variable retinal detachment phenotype that has clinical overlap with NCRNA. We identified seven novel mutations. We also established for the first time genetic overlap between the Iranian and Pakistani populations. We identified eight NCRNA families that do not harbor mutations in any known retinal genes, suggesting novel causal genes in these families.

%B Invest Ophthalmol Vis Sci %V 58 %P 1028-1036 %8 2017 Feb 01 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/28192794?dopt=Abstract %R 10.1167/iovs.16-20281 %0 Journal Article %J Genet Med %D 2015 %T Comprehensive analysis of patients with Stargardt macular dystrophy reveals new genotype-phenotype correlations and unexpected diagnostic revisions. %A Zaneveld, Jacques %A Siddiqui, Sorath %A Li, Huajin %A Wang, Xia %A Wang, Hui %A Wang, Keqing %A Li, Hui %A Ren, Huanan %A Lopez, Irma %A Dorfman, Allison %A Khan, Ayesha %A Wang, Feng %A Salvo, Jason %A Gelowani, Violet %A Li, Yumei %A Sui, Ruifang %A Koenekoop, Robert %A Chen, Rui %K Adult %K ATP-Binding Cassette Transporters %K DNA Copy Number Variations %K DNA Mutational Analysis %K Female %K Genetic Association Studies %K High-Throughput Nucleotide Sequencing %K Humans %K Macular Degeneration %K Male %K Middle Aged %K Sequence Deletion %K Stargardt Disease %X

PURPOSE: Stargardt macular dystrophy (STGD) results in early central vision loss. We sought to explain the genetic cause of STGD in a cohort of 88 patients from three different cultural backgrounds.

METHODS: Next-generation sequencing using a novel capture panel was used to search for disease-causing mutations. Patients with undetermined causes were clinically reexamined and tested for copy-number variations as well as intronic mutations.

RESULTS: We determined the cause of disease in 67% of our patients. Our analysis identified 35 novel ABCA4 alleles. Eleven patients had mutations in genes not previously reported to cause STGD. Finally, 45% of our patients with unsolved causes had single deleterious mutations in ABCA4, a recessive disease gene. No likely pathogenic copy-number variations were identified.

CONCLUSION: This study expands our knowledge of STGD by identifying dozens of novel alleles that cause the disease. The frequency of single mutations in ABCA4 among STGD patients is higher than that among controls, indicating that these mutations contribute to disease. Disease in 11 patients was explained by mutations outside ABCA4, underlining the need to genotype all retinal disease genes to maximize genetic diagnostic rates. Few ABCA4 mutations were observed in our French Canadian patients. This population may contain an unidentified founder mutation. Our results indicate that copy-number variations are unlikely to be a major cause of STGD.

%B Genet Med %V 17 %P 262-70 %8 2015 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/25474345?dopt=Abstract %R 10.1038/gim.2014.174 %0 Journal Article %J Hum Genet %D 2014 %T Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. %A Wang, Feng %A Wang, Hui %A Tuan, Han-Fang %A Nguyen, Duy H %A Sun, Vincent %A Keser, Vafa %A Bowne, Sara J %A Sullivan, Lori S %A Luo, Hongrong %A Zhao, Ling %A Wang, Xia %A Zaneveld, Jacques E %A Salvo, Jason S %A Siddiqui, Sorath %A Mao, Louise %A Wheaton, Dianna K %A Birch, David G %A Branham, Kari E %A Heckenlively, John R %A Wen, Cindy %A Flagg, Ken %A Ferreyra, Henry %A Pei, Jacqueline %A Khan, Ayesha %A Ren, Huanan %A Wang, Keqing %A Lopez, Irma %A Qamar, Raheel %A Zenteno, Juan C %A Ayala-Ramirez, Raul %A Buentello-Volante, Beatriz %A Fu, Qing %A Simpson, David A %A Li, Yumei %A Sui, Ruifang %A Silvestri, Giuliana %A Daiger, Stephen P %A Koenekoop, Robert K %A Zhang, Kang %A Chen, Rui %K Alleles %K Computational Biology %K Exons %K Genes, Recessive %K Genetic Association Studies %K Genetic Testing %K Genotype %K High-Throughput Nucleotide Sequencing %K Humans %K Membrane Glycoproteins %K Molecular Chaperones %K Mutation %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Reproducibility of Results %K Retinitis Pigmentosa %K Sequence Analysis, DNA %X

Retinitis pigmentosa (RP) is a devastating form of retinal degeneration, with significant social and professional consequences. Molecular genetic information is invaluable for an accurate clinical diagnosis of RP due to its high genetic and clinical heterogeneity. Using a gene capture panel that covers 163 of the currently known retinal disease genes, including 48 RP genes, we performed a comprehensive molecular screening in a collection of 123 RP unsettled probands from a wide variety of ethnic backgrounds, including 113 unrelated simplex and 10 autosomal recessive RP (arRP) cases. As a result, 61 mutations were identified in 45 probands, including 38 novel pathogenic alleles. Interestingly, we observed that phenotype and genotype were not in full agreement in 21 probands. Among them, eight probands were clinically reassessed, resulting in refinement of clinical diagnoses for six of these patients. Finally, recessive mutations in CLN3 were identified in five retinal degeneration patients, including four RP probands and one cone-rod dystrophy patient, suggesting that CLN3 is a novel non-syndromic retinal disease gene. Collectively, our results underscore that, due to the high molecular and clinical heterogeneity of RP, comprehensive screening of all retinal disease genes is effective in identifying novel pathogenic mutations and provides an opportunity to discover new genotype-phenotype correlations. Information gained from this genetic screening will directly aid in patient diagnosis, prognosis, and treatment, as well as allowing appropriate family planning and counseling.

%B Hum Genet %V 133 %P 331-45 %8 2014 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/24154662?dopt=Abstract %R 10.1007/s00439-013-1381-5 %0 Journal Article %J J Med Genet %D 2013 %T Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing. %A Wang, Xia %A Wang, Hui %A Sun, Vincent %A Tuan, Han-Fang %A Keser, Vafa %A Wang, Keqing %A Ren, Huanan %A Lopez, Irma %A Zaneveld, Jacques E %A Siddiqui, Sorath %A Bowles, Stephanie %A Khan, Ayesha %A Salvo, Jason %A Jacobson, Samuel G %A Iannaccone, Alessandro %A Wang, Feng %A Birch, David %A Heckenlively, John R %A Fishman, Gerald A %A Traboulsi, Elias I %A Li, Yumei %A Wheaton, Dianna %A Koenekoop, Robert K %A Chen, Rui %K Alleles %K Amino Acid Sequence %K Base Sequence %K Exome %K Female %K Genotype %K High-Throughput Nucleotide Sequencing %K Humans %K Leber Congenital Amaurosis %K Mutation %K Pedigree %K Polymorphism, Single Nucleotide %K Reproducibility of Results %K Retinitis Pigmentosa %K Sensitivity and Specificity %X

BACKGROUND: Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP) are inherited retinal diseases that cause early onset severe visual impairment. An accurate molecular diagnosis can refine the clinical diagnosis and allow gene specific treatments.

METHODS: We developed a capture panel that enriches the exonic DNA of 163 known retinal disease genes. Using this panel, we performed targeted next generation sequencing (NGS) for a large cohort of 179 unrelated and prescreened patients with the clinical diagnosis of LCA or juvenile RP. Systematic NGS data analysis, Sanger sequencing validation, and segregation analysis were utilised to identify the pathogenic mutations. Patients were revisited to examine the potential phenotypic ambiguity at the time of initial diagnosis.

RESULTS: Pathogenic mutations for 72 patients (40%) were identified, including 45 novel mutations. Of these 72 patients, 58 carried mutations in known LCA or juvenile RP genes and exhibited corresponding phenotypes, while 14 carried mutations in retinal disease genes that were not consistent with their initial clinical diagnosis. We revisited patients in the latter case and found that homozygous mutations in PRPH2 can cause LCA/juvenile RP. Guided by the molecular diagnosis, we reclassified the clinical diagnosis in two patients.

CONCLUSIONS: We have identified a novel gene and a large number of novel mutations that are associated with LCA/juvenile RP. Our results highlight the importance of molecular diagnosis as an integral part of clinical diagnosis.

%B J Med Genet %V 50 %P 674-88 %8 2013 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/23847139?dopt=Abstract %R 10.1136/jmedgenet-2013-101558