1
|
Félix TM, Fischinger Moura de Souza C, Oliveira JB, Rico-Restrepo M, Zanoteli E, Zatz M, Giugliani R. Challenges and recommendations to increasing the use of exome sequencing and whole genome sequencing for diagnosing rare diseases in Brazil: an expert perspective. Int J Equity Health 2023; 22:11. [PMID: 36639662 PMCID: PMC9837951 DOI: 10.1186/s12939-022-01809-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023] Open
Abstract
Early diagnosis of genetic rare diseases is an unmet need in Brazil, where an estimated 10-13 million people live with these conditions. Increased use of chromosome microarray assays, exome sequencing, and whole genome sequencing as first-tier testing techniques in suitable indications can shorten the diagnostic odyssey, eliminate unnecessary tests, procedures, and treatments, and lower healthcare expenditures. A selected panel of Brazilian experts in fields related to rare diseases was provided with a series of relevant questions to address before a multi-day conference. Within this conference, each narrative was discussed and edited through numerous rounds of discussion until agreement was achieved. The widespread adoption of exome sequencing and whole genome sequencing in Brazil is limited by various factors: cost and lack of funding, reimbursement, awareness and education, specialist shortages, and policy issues. To reduce the burden of rare diseases and increase early diagnosis, the Brazilian healthcare authorities/government must address the barriers to equitable access to early diagnostic methods for these conditions. Recommendations are provided, including broadening approved testing indications, increasing awareness and education efforts, increasing specialist training opportunities, and ensuring sufficient funding for genetic testing.
Collapse
Affiliation(s)
- Têmis Maria Félix
- grid.414449.80000 0001 0125 3761Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos, 2350, Porto Alegre, 90,035–903 Brazil
| | - Carolina Fischinger Moura de Souza
- grid.414449.80000 0001 0125 3761Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos, 2350, Porto Alegre, 90,035–903 Brazil
| | - João Bosco Oliveira
- grid.413562.70000 0001 0385 1941Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Edmar Zanoteli
- grid.11899.380000 0004 1937 0722Faculdade de Medicina, Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Mayana Zatz
- grid.11899.380000 0004 1937 0722Human Genome and Stem-cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Roberto Giugliani
- grid.414449.80000 0001 0125 3761Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos, 2350, Porto Alegre, 90,035–903 Brazil ,House of Rares, Porto Alegre, Rio Grande do Sul Brazil
| |
Collapse
|
2
|
Wang J, Xiao X, Li S, Jiang H, Sun W, Wang P, Zhang Q. Landscape of pathogenic variants in six pre-mRNA processing factor genes for retinitis pigmentosa based on large in-house data sets and database comparisons. Acta Ophthalmol 2022; 100:e1412-e1425. [PMID: 35138024 DOI: 10.1111/aos.15104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/31/2021] [Accepted: 01/20/2022] [Indexed: 12/29/2022]
Abstract
PURPOSE Variants in six genes encoding pre-mRNA processing factors (PRPFs) are a common cause of autosomal dominant retinitis pigmentosa (ADRP). This study aims to determine the characteristics of potential pathogenic variants (PPVs) in the six genes. METHODS Variants in six PRPF genes were identified from in-house exome sequencing data. PPVs were identified based on comparative bioinformatics analysis, clinical phenotypes and the ACMG/AMP guidelines. The features of PPVs were revealed by comparative analysis of in-house data set, gnomAD and previously published literature. RESULTS Totally, 36 heterozygous PPVs, including 19 novels, were detected from 45 families, which contributed to 4.4% (45/1019) of RP cases. These PPVs were distributed in PRPF31 (17/45, 37.8%), SNRNP200 (12/45, 26.7%), PRPF8 (10/45, 22.2%) and PRPF3 (6/45, 13.3%) but not in PRPF6 or PRPF4. Different types of PPVs were predominant in different PRPF genes, such as loss-of-function variants in PRPF31 and missense variants in the five remaining genes. The clustering of PPVs in specific regions was observed in SNRNP200, PRPF8 and PRPF3. The pathogenicity for certain classes of variants in these genes, such as loss-of-function variants in PRPF6 and missense variants in PRPF31 and PRPF4, requires careful consideration and further validation. The predominant fundus changes were early macular involvement, widespread RPE atrophy and pigmentation in the mid- and far-peripheral retina. CONCLUSION Systemic comparative analysis may shed light on the characterization of PPVs in these genes. Our findings provide a brief landscape of PPVs in PRPF genes and the associated phenotypes and emphasize the careful classification of pathogenicity for certain types of variants that warrant further characterization.
Collapse
Affiliation(s)
- Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Hongmei Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
3
|
Bhardwaj A, Yadav A, Yadav M, Tanwar M. Genetic dissection of non-syndromic retinitis pigmentosa. Indian J Ophthalmol 2022; 70:2355-2385. [PMID: 35791117 PMCID: PMC9426071 DOI: 10.4103/ijo.ijo_46_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Retinitis pigmentosa (RP) belongs to a group of pigmentary retinopathies. It is the most common form of inherited retinal dystrophy, characterized by progressive degradation of photoreceptors that leads to nyctalopia, and ultimately, complete vision loss. RP is distinguished by the continuous retinal degeneration that progresses from the mid-periphery to the central and peripheral retina. RP was first described and named by Franciscus Cornelius Donders in the year 1857. It is one of the leading causes of bilateral blindness in adults, with an incidence of 1 in 3000 people worldwide. In this review, we are going to focus on the genetic heterogeneity of this disease, which is provided by various inheritance patterns, numerosity of variations and inter-/intra-familial variations based upon penetrance and expressivity. Although over 90 genes have been identified in RP patients, the genetic cause of approximately 50% of RP cases remains unknown. Heterogeneity of RP makes it an extremely complicated ocular impairment. It is so complicated that it is known as “fever of unknown origin”. For prognosis and proper management of the disease, it is necessary to understand its genetic heterogeneity so that each phenotype related to the various genetic variations could be treated.
Collapse
Affiliation(s)
- Aarti Bhardwaj
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Anshu Yadav
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Manoj Yadav
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Mukesh Tanwar
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| |
Collapse
|
4
|
Clinical and Genetic Re-Evaluation of Inherited Retinal Degeneration Pedigrees following Initial Negative Findings on Panel-Based Next Generation Sequencing. Int J Mol Sci 2022; 23:ijms23020995. [PMID: 35055178 PMCID: PMC8780304 DOI: 10.3390/ijms23020995] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
Although rare, inherited retinal degenerations (IRDs) are the most common reason for blind registration in the working age population. They are highly genetically heterogeneous (>300 known genetic loci), and confirmation of a molecular diagnosis is a prerequisite for many therapeutic clinical trials and approved treatments. First-tier genetic testing of IRDs with panel-based next-generation sequencing (pNGS) has a diagnostic yield of ≈70-80%, leaving the remaining more challenging cases to be resolved by second-tier testing methods. This study describes the phenotypic reassessment of patients with a negative result from first-tier pNGS and the rationale, outcomes, and cost of second-tier genetic testing approaches. Removing non-IRD cases from consideration and utilizing case-appropriate second-tier genetic testing techniques, we genetically resolved 56% of previously unresolved pedigrees, bringing the overall resolve rate to 92% (388/423). At present, pNGS remains the most cost-effective first-tier approach for the molecular assessment of diverse IRD populations Second-tier genetic testing should be guided by clinical (i.e., reassessment, multimodal imaging, electrophysiology), and genetic (i.e., single alleles in autosomal recessive disease) indications to achieve a genetic diagnosis in the most cost-effective manner.
Collapse
|
5
|
Lee IH, Lin Y, Alvarez WJ, Hernandez-Ferrer C, Mandl KD, Kong SW. WEScover: selection between clinical whole exome sequencing and gene panel testing. BMC Bioinformatics 2021; 22:259. [PMID: 34016036 PMCID: PMC8139020 DOI: 10.1186/s12859-021-04178-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/09/2021] [Indexed: 11/18/2022] Open
Abstract
Background Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted gene panel testing may be a dependable option to ascertain true negatives for genomic variants in known disease-associated genes. We developed a web-based tool to quickly gauge whether all genes of interest would be reliably covered by WES or whether targeted gene panel testing should be considered instead to minimize false negatives in candidate genes. Results WEScover is a novel web application that provides an intuitive user interface for discovering breadth and depth of coverage across population-scale WES datasets, searching either by phenotype, by targeted gene panel(s) or by gene(s). Moreover, the application shows metrics from the Genome Aggregation Database to provide gene-centric view on breadth of coverage. Conclusions WEScover allows users to efficiently query genes and phenotypes for the coverage of associated exons by WES and recommends use of panel tests for the genes with potential incomplete coverage by WES. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04178-5.
Collapse
Affiliation(s)
- In-Hee Lee
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA
| | - Yufei Lin
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA
| | - William Jefferson Alvarez
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA.,Agios Pharmaceuticals, Boston, MA, USA
| | - Carles Hernandez-Ferrer
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA.,Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Barcelona, Spain
| | - Kenneth D Mandl
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
6
|
Cunningham ET, Pichi F, Mahajan VB, Rosenbaum JT, Zierhut M. Genetics of Uveitis. Ocul Immunol Inflamm 2021; 29:215-218. [PMID: 33950774 DOI: 10.1080/09273948.2021.1910430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Emmett T Cunningham
- The Department of Ophthalmology, California Pacific Medical Center, San Francisco, California, USA.,The Department of Ophthalmology, Stanford University School of Medicine, Stanford, California, USA.,The Francis I. Proctor Foundation, UCSF School of Medicine, San Francisco, California, USA
| | - Francesco Pichi
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates.,Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Vinit B Mahajan
- Omics Laboratory, Stanford University, Palo Alto, California, USA.,The Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, USA.,Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
| | - James T Rosenbaum
- The Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, USA.,The Department of Medicine, Oregon Health and Science University, Portland, Oregon, USA.,Legacy Devers Eye Institute, Portland, Oregon, USA
| | - Manfred Zierhut
- Centre for Ophthalmology, University Tuebingen, Tuebingen, Germany
| |
Collapse
|
7
|
Heydari K, Levi SR, Tsang SH. Commentary on "Exome sequencing and electro-clinical features in pediatric patients with very early-onset retinal dystrophies: A cohort study". Eur J Paediatr Neurol 2021; 31:106-107. [PMID: 33736886 DOI: 10.1016/j.ejpn.2021.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Kimia Heydari
- Jonas Children's Vision Care, Department of Ophthalmology, New York-Presbyterian Hospital, New York, NY, USA
| | - Sarah R Levi
- Jonas Children's Vision Care, Department of Ophthalmology, New York-Presbyterian Hospital, New York, NY, USA
| | - Stephen H Tsang
- Jonas Children's Vision Care, Department of Ophthalmology, New York-Presbyterian Hospital, New York, NY, USA; Department of Pathology & Cell Biology, Institute of Human Nutrition, and Columbia Stem Cell Initiative, New York, NY, USA.
| |
Collapse
|
8
|
Grudzinska Pechhacker MK, Di Scipio M, Vig A, Tumber A, Roslin N, Tavares E, Vincent A, Hèon E. CRB1-related retinopathy overlapping the ocular phenotype of S-adenosylhomocysteine hydrolase deficiency. Ophthalmic Genet 2020; 41:457-464. [PMID: 32689861 DOI: 10.1080/13816810.2020.1790013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND S-adenosylhomocysteine hydrolase deficiency due to pathologic variants in AHCY gene is a rare neurometabolic disease for which no eye phenotype has been documented. Pathologic variants in CRB1 gene are known to cause a wide spectrum of autosomal recessive retinal diseases with Leber's congenital amaurosis as a most common. The aim of this study is to report co-inheritance of neurometabolic disease and eye disease in a pedigree. MATERIALS AND METHODS Comprehensive eye examination was performed in available family members together with color vision test, visual fields, fundus images, OCT, electroretinogram and visual evoked potentials. Genetic testing included whole-exome sequencing (WES), retinal dystrophy gene panel and segregation analysis. RESULTS Two children from a family not known to be consanguineous were affected with neurometabolic disease and one of them presented with reduced vision due to maculopathy. The mother had symptoms of retinal degeneration of unspecified cause. Clinical WES revealed homozygous missense pathologic variants in AHCY gene c.148G>A, p.(Ala50Thr) as a cause of S-adenosylhomocysteine hydrolase deficiency. Retinal dystrophy gene panel sequencing revealed two heterozygous missense pathologic variants in CRB1 gene c.1831T>C, p.(Ser611Pro) and c.3955T>C, p.(Phe1319Leu) in the proband and her mother. These variants segregated with disease phenotype in family members. CONCLUSIONS Establishing an ocular genetic diagnosis may be challenging with the co-existence of a rare systemic genetic disease with previously unknown eye involvement. Extensive phenotyping and genotyping of available family members showed that the proband and her mother shared a CRB1-related retinopathy at different stages while the brother did not.
Collapse
Affiliation(s)
- Monika K Grudzinska Pechhacker
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children , Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto , Toronto, Canada
| | - Matteo Di Scipio
- Genetics and Genome Biology, The Hospital for Sick Children , Toronto, Canada
| | - Anjali Vig
- Genetics and Genome Biology, The Hospital for Sick Children , Toronto, Canada
| | - Anupreet Tumber
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children , Toronto, Canada
| | - Nicole Roslin
- Genetics and Genome Biology, The Hospital for Sick Children , Toronto, Canada
| | - Erika Tavares
- Genetics and Genome Biology, The Hospital for Sick Children , Toronto, Canada
| | - Ajoy Vincent
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children , Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto , Toronto, Canada.,Genetics and Genome Biology, The Hospital for Sick Children , Toronto, Canada
| | - Elise Hèon
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children , Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto , Toronto, Canada.,Genetics and Genome Biology, The Hospital for Sick Children , Toronto, Canada
| |
Collapse
|