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Journal of Translational Medicine
Published in: Journal of Translational Medicine 1/2020

01-12-2020 | Pigmentary Retinopathy | Research

Unmasking Retinitis Pigmentosa complex cases by a whole genome sequencing algorithm based on open-access tools: hidden recessive inheritance and potential oligogenic variants

Authors: María González-del Pozo, Elena Fernández-Suárez, Marta Martín-Sánchez, Nereida Bravo-Gil, Cristina Méndez-Vidal, Enrique Rodríguez-de la Rúa, Salud Borrego, Guillermo Antiñolo

Published in: Journal of Translational Medicine | Issue 1/2020

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Abstract

Background

Retinitis Pigmentosa (RP) is a clinically and genetically heterogeneous disorder that results in inherited blindness. Despite the large number of genes identified, only ~ 60% of cases receive a genetic diagnosis using targeted-sequencing. The aim of this study was to design a whole genome sequencing (WGS) based approach to increase the diagnostic yield of complex Retinitis Pigmentosa cases.

Methods

WGS was conducted in three family members, belonging to one large apparent autosomal dominant RP family that remained unsolved by previous studies, using Illumina TruSeq library preparation kit and Illumina HiSeq X platform. Variant annotation, filtering and prioritization were performed using a number of open-access tools and public databases. Sanger sequencing of candidate variants was conducted in the extended family members.

Results

We have developed and optimized an algorithm, based on the combination of different open-access tools, for variant prioritization of WGS data which allowed us to reduce significantly the number of likely causative variants pending to be manually assessed and segregated. Following this algorithm, four heterozygous variants in one autosomal recessive gene (USH2A) were identified, segregating in pairs in the affected members. Additionally, two pathogenic alleles in ADGRV1 and PDZD7 could be contributing to the phenotype in one patient.

Conclusions

The optimization of a diagnostic algorithm for WGS data analysis, accompanied by a hypothesis-free approach, have allowed us to unmask the genetic cause of the disease in one large RP family, as well as to reassign its inheritance pattern which implies differences in the clinical management of these cases. These results contribute to increasing the number of cases with apparently dominant inheritance that carry causal mutations in recessive genes, as well as the possible involvement of various genes in the pathogenesis of RP in one patient. Moreover, our WGS-analysis approach, based on open-access tools, can easily be implemented by other researchers and clinicians to improve the diagnostic yield of additional patients with inherited retinal dystrophies.
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Literature
1.
Verbakel SK, van Huet RAC, Boon CJF, den Hollander AI, Collin RWJ, Klaver CCW, Hoyng CB, Roepman R, Klevering BJ. Non-syndromic retinitis pigmentosa. Prog Retin Eye Res. 2018;66:157–86.PubMedCrossRef
2.
3.
Yuan Z, Li B, Xu M, Chang EY, Li H, Yang L, Wu S, Soens ZT, Li Y, Wong LC, et al. The phenotypic variability of HK1-associated retinal dystrophy. Sci Rep. 2017;7:017–07629.CrossRef
4.
Hull S, Arno G, Plagnol V, Chamney S, Russell-Eggitt I, Thompson D, Ramsden SC, Black GC, Robson A, Holder GE, et al. The phenotypic variability of retinal dystrophies associated with mutations in CRX, with report of a novel macular dystrophy phenotype. Invest Ophthalmol Vis Sci. 2014;55:6934–44.PubMedCrossRef
5.
6.
Martin-Merida I, Avila-Fernandez A, Del Pozo-Valero M, Blanco-Kelly F, Zurita O, Perez-Carro R, Aguilera-Garcia D, Riveiro-Alvarez R, Arteche A, Trujillo-Tiebas MJ, et al. Genomic landscape of sporadic Retinitis Pigmentosa: findings from 877 Spanish Cases. Ophthalmology. 2019;126:1181–8.PubMedCrossRef
7.
Bravo-Gil N, Gonzalez-Del Pozo M, Martin-Sanchez M, Mendez-Vidal C, la Rodriguez-de la Rua E, Borrego S, Antinolo G. Unravelling the genetic basis of simplex Retinitis Pigmentosa cases. Sci Rep. 2017;7:41937.PubMedPubMedCentralCrossRef
8.
Birtel J, Gliem M, Mangold E, Muller PL, Holz FG, Neuhaus C, Lenzner S, Zahnleiter D, Betz C, Eisenberger T, et al. Next-generation sequencing identifies unexpected genotype-phenotype correlations in patients with retinitis pigmentosa. PLoS ONE. 2018;13:e0207958.PubMedPubMedCentralCrossRef
9.
Churchill JD, Bowne SJ, Sullivan LS, Lewis RA, Wheaton DK, Birch DG, Branham KE, Heckenlively JR, Daiger SP. Mutations in the X-linked retinitis pigmentosa genes RPGR and RP2 found in 8.5% of families with a provisional diagnosis of autosomal dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2013;54:1411–6.PubMedPubMedCentralCrossRef
10.
Jones KD, Wheaton DK, Bowne SJ, Sullivan LS, Birch DG, Chen R, Daiger SP. Next-generation sequencing to solve complex inherited retinal dystrophy: a case series of multiple genes contributing to disease in extended families. Mol Vis. 2017;23:470–81.PubMedPubMedCentral
11.
Chen X, Sheng X, Liu Y, Li Z, Sun X, Jiang C, Qi R, Yuan S, Wang X, Zhou G, et al. Distinct mutations with different inheritance mode caused similar retinal dystrophies in one family: a demonstration of the importance of genetic annotations in complicated pedigrees. J Transl Med. 2018;16:018–1522.CrossRef
12.
Mendez-Vidal C, Bravo-Gil N, Gonzalez-Del Pozo M, Vela-Boza A, Dopazo J, Borrego S, Antinolo G. Novel RP1 mutations and a recurrent BBS1 variant explain the co-existence of two distinct retinal phenotypes in the same pedigree. BMC Genet. 2014;15:143.PubMedPubMedCentralCrossRef
13.
Duncan JL, Pierce EA, Laster AM, Daiger SP, Birch DG, Ash JD, Iannaccone A, Flannery JG, Sahel JA, Zack DJ, Zarbin MA. Inherited retinal degenerations: current landscape and knowledge gaps. Transl Vis Sci Technol. 2018;7:6.PubMedPubMedCentralCrossRef
14.
Nanda A, McClements ME, Clouston P, Shanks ME, MacLaren RE. The location of Exon 4 mutations in RP1 raises challenges for genetic counseling and gene therapy. Am J Ophthalmol. 2019;202:23–9.PubMedCrossRef
15.
Dias MF, Joo K, Kemp JA, Fialho SL, da Silva Cunha A Jr., Woo SJ, Kwon YJ. Molecular genetics and emerging therapies for retinitis pigmentosa: basic research and clinical perspectives. Prog Retin Eye Res. 2018;63:107–31.PubMedCrossRef
16.
Bravo-Gil N, Mendez-Vidal C, Romero-Perez L, Gonzalez-del Pozo M, Rodriguez-de la Rua E, Dopazo J, Borrego S, Antinolo G. Improving the management of inherited retinal dystrophies by targeted sequencing of a population-specific gene panel. Sci Rep. 2016;6:1–10.CrossRef
17.
Wang X, Wang H, Sun V, Tuan HF, Keser V, Wang K, Ren H, Lopez I, Zaneveld JE, Siddiqui S, et al. Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing. J Med Genet. 2013;50:674–88.PubMedCrossRef
18.
Shanks ME, Downes SM, Copley RR, Lise S, Broxholme J, Hudspith KA, Kwasniewska A, Davies WI, Hankins MW, Packham ER, et al. Next-generation sequencing (NGS) as a diagnostic tool for retinal degeneration reveals a much higher detection rate in early-onset disease. Eur J Hum Genet. 2013;21:274–80.PubMedCrossRef
19.
Consugar MB, Navarro-Gomez D, Place EM, Bujakowska KM, Sousa ME, Fonseca-Kelly ZD, Taub DG, Janessian M, Wang DY, Au ED, et al. Panel-based genetic diagnostic testing for inherited eye diseases is highly accurate and reproducible, and more sensitive for variant detection, than exome sequencing. Genet Med. 2015;17:253–61.PubMedCrossRef
20.
Farrar GJ, Carrigan M, Dockery A, Millington-Ward S, Palfi A, Chadderton N, Humphries M, Kiang AS, Kenna PF, Humphries P. Toward an elucidation of the molecular genetics of inherited retinal degenerations. Hum Mol Genet. 2017;26:R2–11.PubMedPubMedCentralCrossRef
21.
Carss KJ, Arno G, Erwood M, Stephens J, Sanchis-Juan A, Hull S, Megy K, Grozeva D, Dewhurst E, Malka S, et al. Comprehensive rare variant analysis via whole-genome sequencing to determine the molecular pathology of inherited retinal disease. Am J Hum Genet. 2017;100:75–90.CrossRefPubMed
22.
Zeitz C, Michiels C, Neuille M, Friedburg C, Condroyer C, Boyard F, Antonio A, Bouzidi N, Milicevic D, Veaux R, et al. Where are the missing gene defects in inherited retinal disorders? Intronic and synonymous variants contribute at least to 4% of CACNA1F-mediated inherited retinal disorders. Hum Mutat. 2019;40:765–87.CrossRefPubMed
23.
24.
Ellingford JM, Barton S, Bhaskar S, Williams SG, Sergouniotis PI, O’Sullivan J, Lamb JA, Perveen R, Hall G, Newman WG, et al. Whole genome sequencing increases molecular diagnostic yield compared with current diagnostic testing for inherited retinal disease. Ophthalmology. 2016;123:1143–50.PubMedCrossRef
25.
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:2009–10.
26.
27.
28.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303.PubMedPubMedCentralCrossRef
29.
30.
Zhu M, Need AC, Han Y, Ge D, Maia JM, Zhu Q, Heinzen EL, Cirulli ET, Pelak K, He M, et al. Using ERDS to infer copy-number variants in high-coverage genomes. Am J Hum Genet. 2012;91:408–21.PubMedPubMedCentralCrossRef
31.
Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004;32:D493–6.PubMedPubMedCentralCrossRef
32.
MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW. The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 2014;42:29.CrossRef
33.
Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP. DECIPHER: database of chromosomal imbalance and phenotype in humans using ensembl resources. Am J Hum Genet. 2009;84:524–33.PubMedPubMedCentralCrossRef
34.
Kotlar AV, Trevino CE, Zwick ME, Cutler DJ, Wingo TS. Bystro: rapid online variant annotation and natural-language filtering at whole-genome scale. Genome Biol. 2018;19:018–1387.CrossRef
35.
Desmet FO, Hamroun D, Lalande M, Collod-Beroud G, Claustres M, Beroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 2009;37:1.CrossRef
36.
Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol. 2004;11:377–94.PubMedCrossRef
37.
Reese MG, Eeckman FH, Kulp D, Haussler D. Improved splice site detection in Genie. J Comput Biol. 1997;4:311–23.PubMedCrossRef
38.
Liquori A, Vache C, Baux D, Blanchet C, Hamel C, Malcolm S, Koenig M, Claustres M, Roux AF. Whole USH2A gene sequencing identifies several new deep intronic mutations. Hum Mutat. 2016;37:184–93.PubMedCrossRef
39.
Sim NL, Kumar P, Hu J, Henikoff S, Schneider G, Ng PC. SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res. 2012;40:11.CrossRef
40.
41.
42.
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405–24.PubMedPubMedCentralCrossRef
43.
Wildeman M, van Ophuizen E, den Dunnen JT, Taschner PE. Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Hum Mutat. 2008;29:6–13.PubMedCrossRef
44.
Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019;47:D886–94.PubMedCrossRef
45.
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15:1034–50.PubMedPubMedCentralCrossRef
46.
47.
Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47:D607–13.CrossRefPubMed
48.
Gullapalli RR, Desai KV, Santana-Santos L, Kant JA, Becich MJ. Next generation sequencing in clinical medicine: challenges and lessons for pathology and biomedical informatics. J Pathol Inform. 2012;3:2153–3539.
49.
Schwarze K, Buchanan J, Taylor JC, Wordsworth S. Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature. Genet Med. 2018;20:1122–30.PubMedCrossRef
50.
McGee TL, Seyedahmadi BJ, Sweeney MO, Dryja TP, Berson EL. Novel mutations in the long isoform of the USH2A gene in patients with Usher syndrome type II or non-syndromic retinitis pigmentosa. J Med Genet. 2010;47:499–506.PubMedCrossRef
51.
Baux D, Blanchet C, Hamel C, Meunier I, Larrieu L, Faugere V, Vache C, Castorina P, Puech B, Bonneau D, et al. Enrichment of LOVD-USHbases with 152 USH2A genotypes defines an extensive mutational spectrum and highlights missense hotspots. Hum Mutat. 2014;35:1179–86.PubMedCrossRef
52.
Aller E, Najera C, Millan JM, Oltra JS, Perez-Garrigues H, Vilela C, Navea A, Beneyto M. Genetic analysis of 2299delG and C759F mutations (USH2A) in patients with visual and/or auditory impairments. Eur J Hum Genet. 2004;12:407–10.PubMedCrossRef
53.
Lenassi E, Vincent A, Li Z, Saihan Z, Coffey AJ, Steele-Stallard HB, Moore AT, Steel KP, Luxon LM, Heon E, et al. A detailed clinical and molecular survey of subjects with nonsyndromic USH2A retinopathy reveals an allelic hierarchy of disease-causing variants. Eur J Hum Genet. 2015;23:1318–27.PubMedPubMedCentralCrossRef
54.
Gonzalez-Del Pozo M, Martin-Sanchez M, Bravo-Gil N, Mendez-Vidal C, Chimenea A, Rodriguez-de la Rua E, Borrego S, Antinolo G. Searching the second hit in patients with inherited retinal dystrophies and monoallelic variants in ABCA4, USH2A and CEP290 by whole-gene targeted sequencing. Sci Rep. 2018;8:018–31511.CrossRef
55.
Ebermann I, Phillips JB, Liebau MC, Koenekoop RK, Schermer B, Lopez I, Schafer E, Roux AF, Dafinger C, Bernd A, et al. PDZD7 is a modifier of retinal disease and a contributor to digenic Usher syndrome. J Clin Invest. 2010;120:1812–23.PubMedPubMedCentralCrossRef
56.
Aparisi MJ, Aller E, Fuster-Garcia C, Garcia-Garcia G, Rodrigo R, Vazquez-Manrique RP, Blanco-Kelly F, Ayuso C, Roux AF, Jaijo T, Millan JM. Targeted next generation sequencing for molecular diagnosis of Usher syndrome. Orphanet J Rare Dis. 2014;9:014–0168.CrossRef
57.
Gifford CA, Ranade SS, Samarakoon R, Salunga HT, de Soysa TY, Huang Y, Zhou P, Elfenbein A, Wyman SK, Bui YK, et al. Oligogenic inheritance of a human heart disease involving a genetic modifier. Science. 2019;364:865–70.PubMedPubMedCentralCrossRef
58.
Zaghloul NA, Liu Y, Gerdes JM, Gascue C, Oh EC, Leitch CC, Bromberg Y, Binkley J, Leibel RL, Sidow A, et al. Functional analyses of variants reveal a significant role for dominant negative and common alleles in oligogenic Bardet-Biedl syndrome. Proc Natl Acad Sci U S A. 2010;107:10602–7.PubMedPubMedCentralCrossRef
59.
Daiger SP, Bowne SJ, Sullivan LS. Genes and mutations causing autosomal dominant Retinitis Pigmentosa. Cold Spring Harb Perspect Med. 2014;5:a017129.PubMedCrossRef
60.
Rose AM, Bhattacharya SS. Variant haploinsufficiency and phenotypic non-penetrance in PRPF31-associated retinitis pigmentosa. Clin Genet. 2016;90:118–26.CrossRefPubMed
61.
DuPont M, Jones EM, Xu M, Chen R. Investigating the disease association of USH2A p.C759F variant by leveraging large retinitis pigmentosa cohort data. Ophthalmic Genet. 2018;39:291–2.CrossRefPubMed
62.
Gonzalez-Del Pozo M, Bravo-Gil N, Mendez-Vidal C, Montero-de-Espinosa I, Millan JM, Dopazo J, Borrego S, Antinolo G. Re-evaluation casts doubt on the pathogenicity of homozygous USH2A p.C759F. Am J Med Genet A. 2015;167:1597–600.CrossRef
63.
Estrada-Cuzcano A, Koenekoop RK, Senechal A, De Baere EB, de Ravel T, Banfi S, Kohl S, Ayuso C, Sharon D, Hoyng CB, et al. BBS1 mutations in a wide spectrum of phenotypes ranging from nonsyndromic retinitis pigmentosa to Bardet–Biedl syndrome. Arch Ophthalmol. 2012;130:1425–32.CrossRefPubMed
64.
Webb TR, Parfitt DA, Gardner JC, Martinez A, Bevilacqua D, Davidson AE, Zito I, Thiselton DL, Ressa JH, Apergi M, et al. Deep intronic mutation in OFD1, identified by targeted genomic next-generation sequencing, causes a severe form of X-linked retinitis pigmentosa (RP23). Hum Mol Genet. 2012;21:3647–54.PubMedPubMedCentralCrossRef
65.
Zheng SL, Zhang HL, Lin ZL, Kang QY. Whole-exome sequencing identifies USH2A mutations in a pseudo-dominant Usher syndrome family. Int J Mol Med. 2015;36:1035–41.PubMedPubMedCentralCrossRef
Metadata
Title
Unmasking Retinitis Pigmentosa complex cases by a whole genome sequencing algorithm based on open-access tools: hidden recessive inheritance and potential oligogenic variants
Authors
María González-del Pozo
Elena Fernández-Suárez
Marta Martín-Sánchez
Nereida Bravo-Gil
Cristina Méndez-Vidal
Enrique Rodríguez-de la Rúa
Salud Borrego
Guillermo Antiñolo
Publication date
01-12-2020
Publisher
BioMed Central
Published in
Journal of Translational Medicine / Issue 1/2020
Electronic ISSN: 1479-5876
DOI
https://doi.org/10.1186/s12967-020-02258-3

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