Identification of Pathogenic Copy Number Variants in Mexican Patients With Inherited Retinal Dystrophies Applying an Exome Sequencing Data-Based Read-Depth Approach

Overview

Journal Mol Genet Genomic Med

Specialty Genetics

Date 2024 Oct 14

PMID 39400524

Authors

Gerardo E Fabian-Morales

Vianey Ordonez-Labastida

Froylan Garcia-Martinez

Luis Montes-Almanza

Juan C Zenteno

Affiliations

Soon will be listed here.

Abstract

Background: Retinal dystrophies (RDs) are the most common cause of inherited blindness worldwide and are caused by genetic defects in about 300 different genes. While targeted next-generation sequencing (NGS) has been demonstrated to be a reliable and efficient method to identify RD disease-causing variants, it doesn't routinely identify pathogenic structural variant as copy number variations (CNVs). Targeted NGS-based CNV detection has become a crucial step for RDs molecular diagnosis, particularly in cases without identified causative single nucleotide or Indels variants. Herein, we report the exome sequencing (ES) data-based read-depth bioinformatic analysis in a group of 30 unrelated Mexican RD patients with a negative or inconclusive genetic result after ES.

Methods: CNV detection was performed using ExomeDepth software, an R package designed to detect CNVs using exome data. Bioinformatic validation of identified CNVs was conducted through a commercially available CNV caller. All identified candidate pathogenic CNVs were orthogonally verified through quantitative PCR assays.

Results: Pathogenic or likely pathogenic CNVs were identified in 6 out of 30 cases (20%), and of them, a definitive molecular diagnosis was reached in 5 cases, for a final diagnostic rate of ~17%. CNV-carrying genes included CLN3 (2 cases), ABCA4 (novel deletion), EYS, and RPGRIP1.

Conclusions: Our results indicate that bioinformatic analysis of ES data is a reliable method for pathogenic CNV detection and that it should be incorporated in cases with a negative or inconclusive molecular result after ES.

References

Tian L, Chen C, Song Y, Zhang X, Xu K, Xie Y . Phenotype-Based Genetic Analysis Reveals Missing Heritability of ABCA4-Related Retinopathy: Deep Intronic Variants and Copy Number Variations. Invest Ophthalmol Vis Sci. 2022; 63(6):5. PMC: 9185996. DOI: 10.1167/iovs.63.6.5. View

Yang L, Fujinami K, Ueno S, Kuniyoshi K, Hayashi T, Kondo M . Genetic Spectrum of EYS-associated Retinal Disease in a Large Japanese Cohort: Identification of Disease-associated Variants with Relatively High Allele Frequency. Sci Rep. 2020; 10(1):5497. PMC: 7099090. DOI: 10.1038/s41598-020-62119-3. View

Van Schil K, Naessens S, Van de Sompele S, Carron M, Aslanidis A, Van Cauwenbergh C . Mapping the genomic landscape of inherited retinal disease genes prioritizes genes prone to coding and noncoding copy-number variations. Genet Med. 2017; 20(2):202-213. PMC: 5787040. DOI: 10.1038/gim.2017.97. View

Weisschuh N, Obermaier C, Battke F, Bernd A, Kuehlewein L, Nasser F . Genetic architecture of inherited retinal degeneration in Germany: A large cohort study from a single diagnostic center over a 9-year period. Hum Mutat. 2020; 41(9):1514-1527. DOI: 10.1002/humu.24064. View

Jarvela I, Mitchison H, Munroe P, ORawe A, Mole S, Syvanen A . Rapid diagnostic test for the major mutation underlying Batten disease. J Med Genet. 1996; 33(12):1041-2. PMC: 1050819. DOI: 10.1136/jmg.33.12.1041. View

Rosa J, Disner G, Pinto F, Lima C, Lopes-Ferreira M . Revisiting Retinal Degeneration Hallmarks: Insights from Molecular Markers and Therapy Perspectives. Int J Mol Sci. 2023; 24(17). PMC: 10488251. DOI: 10.3390/ijms241713079. View

Lee K, Garg S . Navigating the current landscape of clinical genetic testing for inherited retinal dystrophies. Genet Med. 2015; 17(4):245-52. DOI: 10.1038/gim.2015.15. View

Maggi J, Roberts L, Koller S, Rebello G, Berger W, Ramesar R . De Novo Assembly-Based Analysis of Exon ORF15 in an Indigenous African Cohort Overcomes Limitations of a Standard Next-Generation Sequencing (NGS) Data Analysis Pipeline. Genes (Basel). 2020; 11(7). PMC: 7396994. DOI: 10.3390/genes11070800. View

Wang F, Wang H, Tuan H, Nguyen D, Sun V, Keser V . Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. Hum Genet. 2013; 133(3):331-45. PMC: 3945441. DOI: 10.1007/s00439-013-1381-5. View

10.

de Ligt J, Boone P, Pfundt R, Vissers L, Richmond T, Geoghegan J . Detection of clinically relevant copy number variants with whole-exome sequencing. Hum Mutat. 2013; 34(10):1439-48. DOI: 10.1002/humu.22387. View

11.

Berger W, Kloeckener-Gruissem B, Neidhardt J . The molecular basis of human retinal and vitreoretinal diseases. Prog Retin Eye Res. 2010; 29(5):335-75. DOI: 10.1016/j.preteyeres.2010.03.004. View

12.

Hayman T, Millo T, Hendler K, Chowers I, Gross M, Banin E . Whole exome sequencing of 491 individuals with inherited retinal diseases reveals a large spectrum of variants and identification of novel candidate genes. J Med Genet. 2023; 61(3):224-231. DOI: 10.1136/jmg-2023-109482. View

13.

Bax N, Sangermano R, Roosing S, Thiadens A, Hoefsloot L, van den Born L . Heterozygous deep-intronic variants and deletions in ABCA4 in persons with retinal dystrophies and one exonic ABCA4 variant. Hum Mutat. 2014; 36(1):43-7. DOI: 10.1002/humu.22717. View

14.

Ku C, Hull S, Arno G, Vincent A, Carss K, Kayton R . Detailed Clinical Phenotype and Molecular Genetic Findings in CLN3-Associated Isolated Retinal Degeneration. JAMA Ophthalmol. 2017; 135(7):749-760. PMC: 5710208. DOI: 10.1001/jamaophthalmol.2017.1401. View

15.

Britten-Jones A, Gocuk S, Goh K, Huq A, Edwards T, Ayton L . The Diagnostic Yield of Next Generation Sequencing in Inherited Retinal Diseases: A Systematic Review and Meta-analysis. Am J Ophthalmol. 2023; 249:57-73. DOI: 10.1016/j.ajo.2022.12.027. View

16.

Plagnol V, Curtis J, Epstein M, Mok K, Stebbings E, Grigoriadou S . A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics. 2012; 28(21):2747-54. PMC: 3476336. DOI: 10.1093/bioinformatics/bts526. View

17.

Van Cauwenbergh C, Van Schil K, Cannoodt R, Bauwens M, Van Laethem T, De Jaegere S . arrEYE: a customized platform for high-resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs. Genet Med. 2016; 19(4):457-466. PMC: 5392597. DOI: 10.1038/gim.2016.119. View

18.

Conrad D, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y . Origins and functional impact of copy number variation in the human genome. Nature. 2009; 464(7289):704-12. PMC: 3330748. DOI: 10.1038/nature08516. View

19.

Ellingford J, Horn B, Campbell C, Arno G, Barton S, Tate C . Assessment of the incorporation of CNV surveillance into gene panel next-generation sequencing testing for inherited retinal diseases. J Med Genet. 2017; 55(2):114-121. PMC: 5800348. DOI: 10.1136/jmedgenet-2017-104791. View

20.

Khateb S, Hanany M, Khalaileh A, Beryozkin A, Meyer S, Abu-Diab A . Identification of genomic deletions causing inherited retinal degenerations by coverage analysis of whole exome sequencing data. J Med Genet. 2016; 53(9):600-7. DOI: 10.1136/jmedgenet-2016-103825. View