A comprehensive WGS-based pipeline for the identification of new candidate genes in inherited retinal dystrophies
Open accessAbstract
To enhance the use of Whole Genome Sequencing (WGS) in clinical practice, it is still necessary to standardize data analysis pipelines. Herein, we aimed to define a WGS-based algorithm for the accurate interpretation of variants in inherited retinal dystrophies (IRD). This study comprised 429 phenotyped individuals divided into three cohorts. A comparison of 14 pathogenicity predictors, and the re-definition of its cutoffs, were performed using panel-sequencing curated data from 209 genetically diagnosed individuals with IRD (training cohort). The optimal tool combinations, previously validated in 50 additional IRD individuals, were also tested in patients with hereditary cancer (n = 109), and with neurological diseases (n = 47) to evaluate the translational value of this approach (validation cohort). Then, our workflow was applied for the WGS-data analysis of 14 individuals from genetically undiagnosed IRD families (discovery cohort). The statistical analysis showed that the optimal filtering combination included CADDv1.6, MAPP, Grantham, and SIFT tools. Our pipeline allowed the identification of one homozygous variant in the candidate gene CFAP20 (c.337 C > T; p.Arg113Trp), a conserved ciliary gene, which was abundantly expressed in human retina and was located in the photoreceptors layer. Although further studies are needed, we propose CFAP20 as a candidate gene for autosomal recessive retinitis pigmentosa. Moreover, we offer a translational strategy for accurate WGS-data prioritization, which is essential for the advancement of personalized medicine.
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González-del Pozo et al. identified CFAP20 as a putative cause of autosomal recessive RP from a cohort of 14 whole genome sequences from genetically undiagnosed IRD patients.
“González-del Pozo et al.72 identified CFAP20 as a putative cause of autosomal recessive RP from a cohort of 14 whole genome sequences from genetically undiagnosed IRD patients”
From The inner junction protein CFAP20 functions in motile and non-motile cilia and is critical for vision (2022) · cites this paper as [72]
The Introduction and Discussion identify CFAP20 as a candidate cause of autosomal recessive retinitis pigmentosa, and the Methods (Subjects and previous NGS studies; page unavailable) confirm that all 14 discovery-cohort individuals underwent WGS. But only nine were affected; the other five were unaffected family members, so the claim inaccurately describes all 14 sequences as coming from genetically undiagnosed IRD patients. (LLM, conf=0.87)
Experimental — accuracy not yet measuredOne individual with homozygous p.(Arg113Trp) CFAP20 variants segregated with disease.
“this study identified one individual with homozygous p.(Arg113Trp) CFAP20 variants that segregated with disease.”
From The inner junction protein CFAP20 functions in motile and non-motile cilia and is critical for vision (2022) · cites this paper as [72]
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Pozo, M. G., Martín-Sánchez, M., Bravo‐Gil, N., Méndez‐Vidal, C., Chimenea, Á., Rodríguez-de-la-Rúa-Franch, E., Borrego, S., & Antiñolo, G. (2018) · Scientific Reports · doi:10.1038/s41598-018-31511-5 · Cited by 26 · see citing works
Self-citationOn the Wrong Track: Alterations of Ciliary Transport in Inherited Retinal Dystrophies
Sánchez-Bellver, L., Toulis, V., & Marfany, G. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.623734 · Cited by 25 · see citing works
Effective variant filtering and expected candidate variant yield in studies of rare human diseasePreprint
Pedersen, B. S., Brown, J. M., Dashnow, H., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.13.249532 · Cited by 21 · see citing works
Méndez‐Vidal, C., Pozo, M. G., Vela‐Boza, A., et al. (2013) · PubMed · Cited by 20 · see citing works
Self-citationMoye, A. R., Singh, R. K., Kimler, V. A., Dilan, T. L., Munezero, D., Saravanan, T., Goldberg, A. F. X., & Ramamurthy, V. (2018) · Molecular Biology of the Cell · doi:10.1091/mbc.e18-01-0040 · Cited by 20 · see citing works
A founder Alu insertion in RP1 gene in Japanese patients with retinitis pigmentosa
Nishiguchi, K. M., Fujita, K., Ikeda, Y., et al. (2020) · Japanese Journal of Ophthalmology · doi:10.1007/s10384-020-00732-5 · Cited by 18 · see citing works
Optimizing Genetic Diagnosis of Neurodevelopmental Disorders in the Clinical Setting
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Toulis, V., Cortés‐González, V., de Castro‐Miró, M., Sallum, J. M. F., Mora, J. C., Villanueva‐Mendoza, C., Ciccioli, M., Gonzàlez‐Duarte, R., Valero, R., & Marfany, G. (2020) · Genes · doi:10.3390/genes11040378 · Cited by 14 · see citing works
Confirming TBC1D32 ‐related ciliopathy in humans
Alsahan, N., & Alkuraya, F. S. (2020) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.61717 · Cited by 13 · see citing works
Improve your Galaxy text life: The Query Tabular Tool
Johnson, J. E., Kumar, P., Easterly, C., et al. (2019) · F1000Research · doi:10.12688/f1000research.16450.2 · Cited by 9 · see citing works
Martín-Sánchez, M., Bravo‐Gil, N., Pozo, M. G., Méndez‐Vidal, C., Fernández-Suárez, E., Rodríguez-de-la-Rúa-Franch, E., Borrego, S., & Antiñolo, G. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21249355 · Cited by 9 · see citing works
Self-citationImprove your Galaxy text life: The Query Tabular Tool
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Braddock, S. R., Lipinski, R. J., & Carey, J. C. (2020) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.61514 · Cited by 5 · see citing works
RPGeNet v2.0: expanding the universe of retinal disease gene interactions network
Arenas-Galnares, R., Castillo-Lara, S., Toulis, V., et al. (2019) · Database · doi:10.1093/database/baz120 · Cited by 3 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Chrystal, P. W., Lambacher, N. J., Doucette, L. P., Bellingham, J., Schiff, E. R., Noel, N. C. L., Li, C., Tsiropoulou, S., Casey, G. A., Zhai, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33820-w · Cited by 31 · see citing works
“While our study was in revision, Gonzálezdel Pozo et al.(72) identified CFAP20 as a putative cause of autosomal recessive RP from a cohort of 14 whole genome sequences from genetically undiagnosed IRD patients; this study identified one individual with homozygous p.”
Result
- Authors
- González-del Pozo, M., Fernández-Suárez, E., Bravo-Gil, N., Méndez-Vidal, C., Martín-Sánchez, M., Rodríguez-de la Rúa, E., Ramos-Jiménez, M., Morillo-Sánchez, M. J., Borrego, S., & Antiñolo, G.
- Affiliations
- Consejo Superior de Investigaciones Científicas (ES)
- Hospital Universitario Virgen Macarena (ES)
- Centre for Biomedical Network Research on Rare Diseases (ES)
- Corresponding author
- Borrego, Salud
- Antiñolo, Guillermo
- ORCID
- Venue
- npj Genomic Medicine
- Published
- 2022-03-04
- Volume
- 7
- Issue
- 1
- Pages
- 17-17
- ISSN
- 2056-7944 (ISSN-L)
- PMC
- PMC8897414
- OpenAlex
- W4214907201
- Cited by
- 21
- References
- 97
- Citations by year
- 2026: 3 · 2025: 8 · 2024: 4 · 2023: 4 · 2022: 2
- FWCI
- 2.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- npj Genomic Medicine (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RISalud Institutional Health Repository of Andalucía (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- idUS (Universidad de Sevilla) (submittedVersion, cc-by-nc-nd)
- Funders
- European Commission
- Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (RH-0118-2020, CTS-1664)
- Ministerio de Economía y Competitividad (FI19/00091, PI18-00612, 00612)
- Instituto de Salud Carlos III (PI21/00244, FI19/00091, PI18/00612)
- European Regional Development Fund
- European Social Fund
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Retinal Development and Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and Kidney Cyst Diseases
- Keywords
- inherited retinal disease, variant pathogenicity prediction, variant filtering, CADD, MAPP, SIFT, autosomal recessive retinitis pigmentosa, candidate gene identification, ciliary genes, photoreceptors, hereditary cancer, neurological disorders
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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