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Zolotareva O, Kleine M. A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. J Integr Bioinform 2019; 16:/j/jib.ahead-of-print/jib-2018-0069/jib-2018-0069.xml. [PMID: 31494632 PMCID: PMC7074139 DOI: 10.1515/jib-2018-0069] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 07/12/2019] [Indexed: 12/16/2022] Open
Abstract
Modern high-throughput experiments provide us with numerous potential associations between genes and diseases. Experimental validation of all the discovered associations, let alone all the possible interactions between them, is time-consuming and expensive. To facilitate the discovery of causative genes, various approaches for prioritization of genes according to their relevance for a given disease have been developed. In this article, we explain the gene prioritization problem and provide an overview of computational tools for gene prioritization. Among about a hundred of published gene prioritization tools, we select and briefly describe 14 most up-to-date and user-friendly. Also, we discuss the advantages and disadvantages of existing tools, challenges of their validation, and the directions for future research.
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Affiliation(s)
- Olga Zolotareva
- Bielefeld University, Faculty of Technology and Center for Biotechnology, International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes" and Genome Informatics, Universitätsstraße 25, Bielefeld, Germany
| | - Maren Kleine
- Bielefeld University, Faculty of Technology, Bioinformatics/Medical Informatics Department, Universitätsstraße 25, Bielefeld, Germany
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Simpson A, Avdic A, Roos BR, DeLuca A, Miller K, Schnieders MJ, Scheetz TE, Alward WL, Fingert JH. LADD syndrome with glaucoma is caused by a novel gene. Mol Vis 2017; 23:179-184. [PMID: 28400699 PMCID: PMC5373035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/28/2017] [Indexed: 10/30/2022] Open
Abstract
PURPOSE Lacrimo-auriculo-dento-digital (LADD) syndrome is an autosomal dominant disorder displaying variable expression of multiple congenital anomalies including hypoplasia or aplasia of the lacrimal and salivary systems causing abnormal tearing and dry mouth. Mutations in the FGF10, FGFR2, and FGFR3 genes were found to cause some cases of LADD syndrome in prior genetic studies. The goal of this study is to identify the genetic basis of a case of LADD syndrome with glaucoma and thin central corneal thickness (CCT). METHODS Whole exome sequencing was performed, and previously described disease-causing genes (FGF10, FGFR2, and FGFR3) were first evaluated for mutations. Fifty-eight additional prioritized candidate genes were identified by searching gene annotations for features of LADD syndrome. The potential pathogenicity of the identified mutations was assessed by determining their frequency in large public exome databases; through sequence analysis using the Blosum62 matrix, PolyPhen2, and SIFT algorithms; and through homology analyses. A structural analysis of the effects of the top candidate mutation in tumor protein 63 (TP63) was also conducted by superimposing the mutation over the solved crystal structure. RESULTS No mutations were detected in FGF10, FGFR2, or FGFR3. The LADD syndrome patient's exome data was searched for mutations in the 58 candidate genes and only one mutation was detected, an Arg343Trp mutation in the tumor protein 63 (TP63) gene. This TP63 mutation is absent from the gnomAD sequence database. Analysis of the Arg343Trp mutation with Blosum62, PolyPhen2, and SIFT all suggest it is pathogenic. This arginine residue is highly conserved in orthologous genes. Finally, crystal structure analysis showed that the Arg343Trp mutation causes a significant alteration in the structure of TP63's DNA binding domain. CONCLUSIONS We report a patient with no mutations in known LADD syndrome genes (FGF10, FGFR2, and FGFR3). Our analysis provides strong evidence that the Arg343Trp mutation in TP63 caused LADD syndrome in our patient and that TP63 is a fourth gene contributing to this condition. TP63 encodes a transcription factor involved in the development and differentiation of tissues affected by LADD syndrome. These data suggest that TP63 is a novel LADD syndrome gene and may also influence corneal thickness and risk for open-angle glaucoma.
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Affiliation(s)
- Allie Simpson
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
| | - Armin Avdic
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Ben R. Roos
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
| | - Adam DeLuca
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
| | - Kathy Miller
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
| | - Michael J. Schnieders
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA,Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Todd E. Scheetz
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
| | - Wallace L.M. Alward
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
| | - John H. Fingert
- Department of Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, IA,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA
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Wolf A, Aslanidis A, Langmann T. Retinal expression and localization of Mef2c support its important role in photoreceptor gene expression. Biochem Biophys Res Commun 2016; 483:346-351. [PMID: 28017720 DOI: 10.1016/j.bbrc.2016.12.141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 11/17/2022]
Abstract
Photoreceptor-specific gene expression is controlled by a hierarchical network of transcription factors, including the master regulators cone-rod homeobox (Crx) and neural retina leucine zipper (Nrl). Myocyte-enhancer factor 2c (Mef2c) is an ubiquitously expressed transcription factor with important functions in the cardiovascular system. Here, we performed a detailed analysis of Mef2c expression, localization and function in the retina to further elucidate its potential role for photoreceptor gene regulation. We showed that murine retinal Mef2c mRNA expression was high at birth and peaked at late postnatal developmental stages. Using immunohistochemistry and Western blot, Mef2c protein was detected in the outer nuclear layer of adult mouse and human retinas and localized to the nucleus of 661W photoreceptor-like cells. Mef2c knock-down in 661W cells reduced the expression of arrestin 3 (Arr3) and medium-wave-sensitive cone opsin (Opn1mw) but increased transcript levels of mitogen-activated protein kinase 15 (Mapk15) and phosphodiesterase 6h (Pde6h). In conclusion, Mef2c is highly expressed in the retina where it modulates photoreceptor-specific gene expression.
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Affiliation(s)
- Anne Wolf
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Cologne, Germany
| | - Alexander Aslanidis
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Cologne, Germany
| | - Thomas Langmann
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Cologne, Germany.
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DeLuca AP, Whitmore SS, Barnes J, Sharma TP, Westfall TA, Scott CA, Weed MC, Wiley JS, Wiley LA, Johnston RM, Schnieders MJ, Lentz SR, Tucker BA, Mullins RF, Scheetz TE, Stone EM, Slusarski DC. Hypomorphic mutations in TRNT1 cause retinitis pigmentosa with erythrocytic microcytosis. Hum Mol Genet 2015; 25:44-56. [PMID: 26494905 DOI: 10.1093/hmg/ddv446] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/19/2015] [Indexed: 02/07/2023] Open
Abstract
Retinitis pigmentosa (RP) is a highly heterogeneous group of disorders characterized by degeneration of the retinal photoreceptor cells and progressive loss of vision. While hundreds of mutations in more than 100 genes have been reported to cause RP, discovering the causative mutations in many patients remains a significant challenge. Exome sequencing in an individual affected with non-syndromic RP revealed two plausibly disease-causing variants in TRNT1, a gene encoding a nucleotidyltransferase critical for tRNA processing. A total of 727 additional unrelated individuals with molecularly uncharacterized RP were completely screened for TRNT1 coding sequence variants, and a second family was identified with two members who exhibited a phenotype that was remarkably similar to the index patient. Inactivating mutations in TRNT1 have been previously shown to cause a severe congenital syndrome of sideroblastic anemia, B-cell immunodeficiency, recurrent fevers and developmental delay (SIFD). Complete blood counts of all three of our patients revealed red blood cell microcytosis and anisocytosis with only mild anemia. Characterization of TRNT1 in patient-derived cell lines revealed reduced but detectable TRNT1 protein, consistent with partial function. Suppression of trnt1 expression in zebrafish recapitulated several features of the human SIFD syndrome, including anemia and sensory organ defects. When levels of trnt1 were titrated, visual dysfunction was found in the absence of other phenotypes. The visual defects in the trnt1-knockdown zebrafish were ameliorated by the addition of exogenous human TRNT1 RNA. Our findings indicate that hypomorphic TRNT1 mutations can cause a recessive disease that is almost entirely limited to the retina.
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Affiliation(s)
- Adam P DeLuca
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - S Scott Whitmore
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | | | - Tasneem P Sharma
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | | | | | - Matthew C Weed
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Jill S Wiley
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Luke A Wiley
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Rebecca M Johnston
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Michael J Schnieders
- The Stephen A. Wynn Institute for Vision Research, Department of Biomedical Engineering, Department of Biochemistry, and
| | - Steven R Lentz
- Department of Internal Medicine; The University of Iowa, Iowa City, IA, USA
| | - Budd A Tucker
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Robert F Mullins
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Todd E Scheetz
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences, Department of Biomedical Engineering
| | - Edwin M Stone
- The Stephen A. Wynn Institute for Vision Research, Department of Ophthalmology and Visual Sciences
| | - Diane C Slusarski
- The Stephen A. Wynn Institute for Vision Research, Department of Biology,
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Identity-by-descent-guided mutation analysis and exome sequencing in consanguineous families reveals unusual clinical and molecular findings in retinal dystrophy. Genet Med 2014; 16:671-80. [PMID: 24625443 DOI: 10.1038/gim.2014.24] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/05/2014] [Indexed: 01/26/2023] Open
Abstract
PURPOSE Autosomal recessive retinal dystrophies are clinically and genetically heterogeneous, which hampers molecular diagnosis. We evaluated identity-by-descent-guided Sanger sequencing or whole-exome sequencing in 26 families with nonsyndromic (19) or syndromic (7) autosomal recessive retinal dystrophies to identify disease-causing mutations. METHODS Patients underwent genome-wide identity-by-descent mapping followed by Sanger sequencing (16) or whole-exome sequencing (10). Whole-exome sequencing data were filtered against identity-by-descent regions and known retinal dystrophy genes. The medical history was reviewed in mutation-positive families. RESULTS We identified mutations in 14 known retinal dystrophy genes in 20/26 (77%) families: ABCA4, CERKL, CLN3, CNNM4, C2orf71, IQCB1, LRAT, MERTK, NMNAT1, PCDH15, PDE6B, RDH12, RPGRIP1, and USH2A. Whole-exome sequencing in single individuals revealed mutations in either the largest or smaller identity-by-descent regions, and a compound heterozygous genotype in NMNAT1. Moreover, a novel deletion was found in PCDH15. In addition, we identified mutations in CLN3, CNNM4, and IQCB1 in patients initially diagnosed with nonsyndromic retinal dystrophies. CONCLUSION Our study emphasized that identity-by-descent-guided mutation analysis and/or whole-exome sequencing are powerful tools for the molecular diagnosis of retinal dystrophy. Our approach uncovered unusual molecular findings and unmasked syndromic retinal dystrophies, guiding future medical management. Finally, elucidating ABCA4, LRAT, and MERTK mutations offers potential gene-specific therapeutic perspectives.
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