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Raggio V, Dell'Oca N, Simoes C, Tapié A, Medici C, Costa G, Rodriguez S, Greif G, Garrone E, Rovella ML, Gonzalez V, Halty M, González G, Shin JY, Shin SY, Kim C, Seo JS, Graña M, Naya H, Spangenberg L. Whole genome sequencing reveals a frameshift mutation and a large deletion in YY1AP1 in a girl with a panvascular artery disease. Hum Genomics 2021; 15:28. [PMID: 33971976 PMCID: PMC8108437 DOI: 10.1186/s40246-021-00328-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/26/2021] [Indexed: 11/10/2022] Open
Abstract
Background Rare diseases are pathologies that affect less than 1 in 2000 people. They are difficult to diagnose due to their low frequency and their often highly heterogeneous symptoms. Rare diseases have in general a high impact on the quality of life and life expectancy of patients, which are in general children or young people. The advent of high-throughput sequencing techniques has improved diagnosis in several different areas, from pediatrics, achieving a diagnostic rate of 41% with whole genome sequencing (WGS) and 36% with whole exome sequencing, to neurology, achieving a diagnostic rate between 47 and 48.5% with WGS. This evidence has encouraged our group to pursue a molecular diagnosis using WGS for this and several other patients with rare diseases. Results We used whole genome sequencing to achieve a molecular diagnosis of a 7-year-old girl with a severe panvascular artery disease that remained for several years undiagnosed. We found a frameshift variant in one copy and a large deletion involving two exons in the other copy of a gene called YY1AP1. This gene is related to Grange syndrome, a recessive rare disease, whose symptoms include stenosis or occlusion of multiple arteries, congenital heart defects, brachydactyly, syndactyly, bone fragility, and learning disabilities. Bioinformatic analyses propose these mutations as the most likely cause of the disease, according to its frequency, in silico predictors, conservation analyses, and effect on the protein product. Additionally, we confirmed one mutation in each parent, supporting a compound heterozygous status in the child. Conclusions In general, we think that this finding can contribute to the use of whole genome sequencing as a diagnosis tool of rare diseases, and in particular, it can enhance the set of known mutations associated with different diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-021-00328-1.
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Affiliation(s)
- Víctor Raggio
- Departamento de Genética, Facultad de Medicina, Universidad de la República, General Flores 2125, 11800, Montevideo, Uruguay
| | - Nicolas Dell'Oca
- Departamento de Genética, Facultad de Medicina, Universidad de la República, General Flores 2125, 11800, Montevideo, Uruguay
| | - Camila Simoes
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Alejandra Tapié
- Departamento de Genética, Facultad de Medicina, Universidad de la República, General Flores 2125, 11800, Montevideo, Uruguay
| | - Conrado Medici
- Cátedra de Neuropediatría, Centro Hospitalario Pereira Rossell, Facultad de Medicina, Universidad de la República, General Flores, 2125, Montevideo, Uruguay
| | - Gonzalo Costa
- Cátedra de Neuropediatría, Centro Hospitalario Pereira Rossell, Facultad de Medicina, Universidad de la República, General Flores, 2125, Montevideo, Uruguay
| | - Soledad Rodriguez
- Departamento de Genética, Facultad de Medicina, Universidad de la República, General Flores 2125, 11800, Montevideo, Uruguay
| | - Gonzalo Greif
- Molecular Biology Unit, Institut Pasteur de Montevideo, Mataojo, 2020, Montevideo, Uruguay
| | - Estefania Garrone
- Departamento de Pediatría, Centro Hospitalario Pereira Rossell, Facultad de Medicina, Universidad de la República, General Flores 2125, 11800, Montevideo, Uruguay
| | - María Laura Rovella
- Departamento de Pediatría, Centro Hospitalario Pereira Rossell, Facultad de Medicina, Universidad de la República, General Flores 2125, 11800, Montevideo, Uruguay
| | - Virgina Gonzalez
- Departamento de Pediatría, Centro Hospitalario Pereira Rossell, Facultad de Medicina, Universidad de la República, General Flores 2125, 11800, Montevideo, Uruguay
| | - Margarita Halty
- Departamento de Pediatría, Nefrología pediátrica, Centro Hospitalario Pereira Rossell, Facultad de Medicina, Universidad de la República, General Flores 2125, 11800, Montevideo, Uruguay
| | - Gabriel González
- Cátedra de Neuropediatría, Centro Hospitalario Pereira Rossell, Facultad de Medicina, Universidad de la República, General Flores, 2125, Montevideo, Uruguay
| | - Jong-Yeon Shin
- Precision Medicine Institute, Macrogen Inc., Seoul, 08511, South Korea
| | - Sang-Yoon Shin
- Precision Medicine Institute, Macrogen Inc., Seoul, 08511, South Korea
| | - Changhoon Kim
- Bioinformatics Institute, Macrogen Inc., Seoul, 08511, South Korea
| | - Jeong-Sun Seo
- Precision Medicine Institute, Macrogen Inc., Seoul, 08511, South Korea.,Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Martin Graña
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Hugo Naya
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay.,Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Av Gral Eugenio Garzón 780, 12900, Montevideo, Uruguay
| | - Lucia Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay. .,Department of Informatics and Computer Science, Universidad Católica del Uruguay, 8 de Octubre 2738, 11600, Montevideo, Uruguay.
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Alves A, Alonso R, Cuevas A, Margarida AM, Pereira C A, Jannes E C, J. Krieger E, Arroyo R, Schreier L, Corral P, Bañares G V, Araujo M, Asenjo S, Stoll M, Dell'Oca N, Reyes X, Ressia A, Campo R, Merchan A, Magaña-Torres Teresa M, Vasques-Cardenas N A, Mata P, Santos R, Bourbon M. Molecular Aspects Of Homozygous Familial Hypercholesterolemia In Ibero-American Countries. Atherosclerosis 2019. [DOI: 10.1016/j.atherosclerosis.2019.06.654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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