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Álvarez-Cuesta JA, Mora-Batista C, Reyes-Carreto R, Carrillo-Rodes FJ, Fitz SJT, González-Zaldivar Y, Vargas-De-León C. On the Cut-Off Value of the Anteroposterior Diameter of the Midbrain Atrophy in Spinocerebellar Ataxia Type 2 Patients. Brain Sci 2024; 14:53. [PMID: 38248268 PMCID: PMC10813098 DOI: 10.3390/brainsci14010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
(1) Background: Spinocerebellar ataxias (SCA) is a term that refers to a group of hereditary ataxias, which are neurological diseases characterized by degeneration of the cells that constitute the cerebellum. Studies suggest that magnetic resonance imaging (MRI) supports diagnoses of ataxias, and linear measurements of the aneteroposterior diameter of the midbrain (ADM) have been investigated using MRI. These measurements correspond to studies in spinocerebellar ataxia type 2 (SCA2) patients and in healthy subjects. Our goal was to obtain the cut-off value for ADM atrophy in SCA2 patients. (2) Methods: This study evaluated 99 participants (66 SCA2 patients and 33 healthy controls). The sample was divided into estimations (80%) and validation (20%) samples. Using the estimation sample, we fitted a logistic model using the ADM and obtained the cut-off value through the inverse of regression. (3) Results: The optimal cut-off value of ADM was found to be 18.21 mm. The area under the curve (AUC) of the atrophy risk score was 0.957 (95% CI: 0.895-0.991). Using this cut-off on the validation sample, we found a sensitivity of 100.00% (95% CI: 76.84%-100.00%) and a specificity of 85.71% (95% CI: 42.13%-99.64%). (4) Conclusions: We obtained a cut-off value that has an excellent discriminatory capacity to identify SCA2 patients.
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Affiliation(s)
- José Alberto Álvarez-Cuesta
- Centro de Investigación y Rehabilitación de las Ataxias Hereditarias, VPWP+RM5, Holguín 80100, Cuba; (J.A.Á.-C.); (F.J.C.-R.); (Y.G.-Z.)
| | - Camilo Mora-Batista
- Facultad de Matemáticas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39087, Mexico;
| | - Ramón Reyes-Carreto
- Facultad de Matemáticas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39087, Mexico;
| | - Frank Jesus Carrillo-Rodes
- Centro de Investigación y Rehabilitación de las Ataxias Hereditarias, VPWP+RM5, Holguín 80100, Cuba; (J.A.Á.-C.); (F.J.C.-R.); (Y.G.-Z.)
| | | | - Yanetza González-Zaldivar
- Centro de Investigación y Rehabilitación de las Ataxias Hereditarias, VPWP+RM5, Holguín 80100, Cuba; (J.A.Á.-C.); (F.J.C.-R.); (Y.G.-Z.)
| | - Cruz Vargas-De-León
- División de Investigación, Hospital Juárez de México, Ciudad de México 07760, Mexico
- Laboratorio de Modelación Bioestadística para la Salud, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
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Chiara M, Zambelli F, Picardi E, Horner DS, Pesole G. Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data. Brief Bioinform 2019; 21:1971-1986. [DOI: 10.1093/bib/bbz099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/22/2019] [Accepted: 07/09/2019] [Indexed: 01/19/2023] Open
Abstract
Abstract
A number of studies have reported the successful application of single-molecule sequencing technologies to the determination of the size and sequence of pathological expanded microsatellite repeats over the last 5 years. However, different custom bioinformatics pipelines were employed in each study, preventing meaningful comparisons and somewhat limiting the reproducibility of the results. In this review, we provide a brief summary of state-of-the-art methods for the characterization of expanded repeats alleles, along with a detailed comparison of bioinformatics tools for the determination of repeat length and sequence, using both real and simulated data. Our reanalysis of publicly available human genome sequencing data suggests a modest, but statistically significant, increase of the error rate of single-molecule sequencing technologies at genomic regions containing short tandem repeats. However, we observe that all the methods herein tested, irrespective of the strategy used for the analysis of the data (either based on the alignment or assembly of the reads), show high levels of sensitivity in both the detection of expanded tandem repeats and the estimation of the expansion size, suggesting that approaches based on single-molecule sequencing technologies are highly effective for the detection and quantification of tandem repeat expansions and contractions.
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Affiliation(s)
- Matteo Chiara
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
| | - Federico Zambelli
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70126 Bari, Italy
| | - David S Horner
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70126 Bari, Italy
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