Diagnostic Yield of NGS Tests for Hereditary Ataxia: a Systematic Review.

التفاصيل البيبلوغرافية
العنوان:	Diagnostic Yield of NGS Tests for Hereditary Ataxia: a Systematic Review.
المؤلفون:	Tenorio RB; Postgraduate Program in Internal Medicine, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil. genetica.curitiba@gmail.com., Camargo CHF; Postgraduate Program in Internal Medicine, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil.; Movement Disorders Sector, Neurology Service, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil., Donis KC; Medical Genetics Service, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil., Almeida CCB; Department of Nutrition, Federal University of Paraná, Curitiba, Paraná, Brazil., Teive HAG; Postgraduate Program in Internal Medicine, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil.; Movement Disorders Sector, Neurology Service, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil.
المصدر:	Cerebellum (London, England) [Cerebellum] 2024 Aug; Vol. 23 (4), pp. 1552-1565. Date of Electronic Publication: 2023 Nov 11.
نوع المنشور:	Systematic Review; Journal Article; Review
اللغة:	English
بيانات الدورية:	Publisher: Springer Country of Publication: United States NLM ID: 101089443 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1473-4230 (Electronic) Linking ISSN: 14734222 NLM ISO Abbreviation: Cerebellum Subsets: MEDLINE
أسماء مطبوعة:	Publication: <2006->: New York : Springer Original Publication: London : Martin Dunitz, c2002-
مواضيع طبية MeSH:	High-Throughput Nucleotide Sequencing*/methods, Humans ; Genetic Testing/methods ; Ataxia/genetics ; Ataxia/diagnosis
مستخلص:	Next-generation sequencing (NGS), comprising targeted panels (TP), exome sequencing (ES), and genome sequencing (GS) became robust clinical tools for diagnosing hereditary ataxia (HA). Determining their diagnostic yield (DY) is crucial for optimal clinical decision-making. We conducted a comprehensive systematic literature review on the DY of NGS tests for HA. We searched PubMed and Embase databases for relevant studies between 2016 and 2022 and manually examined reference lists of relevant reviews. Eligible studies described the DY of NGS tests in patients with ataxia as a significant feature. Data from 33 eligible studies showed a median DY of 43% (IQR = 9.5-100%). The median DY for TP and ES was 46% and 41.9%, respectively. Higher DY was associated with specific phenotype selection, such as episodic ataxia at 68.35% and early and late onset of ataxia at 46.4% and 54.4%. Parental consanguinity had a DY of 52.4% (p = 0.009), and the presumed autosomal recessive (AR) inheritance pattern showed 62.5%. There was a difference between the median DY of studies that performed targeted sequencing (tandem repeat expansion, TRE) screening and those that did not (p = 0.047). A weak inverse correlation was found between DY and the extent of previous genetic investigation (rho = - 0.323; p = 0.065). The most common genes were CACNA1A and SACS. DY was higher for presumed AR inheritance pattern, positive family history, and parental consanguinity. ES appears more advantageous due to the inclusion of rare genes that might be excluded in TP. (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
References:	Parodi L, Coarelli G, Stevanin G, Brice A, Durr A. Hereditary ataxias and paraparesias: clinical and genetic update. Curr Opin Neurol. 2018;31(4):462–71. https://doi.org/10.1097/WCO.0000000000000585 . (PMID: 10.1097/WCO.000000000000058529847346) Novis LE, Spitz M, Jardim M, Raskin S, Teive HAG. Evidence and practices of the use of next generation sequencing in patients with undiagnosed autosomal dominant cerebellar ataxias: a review. Arq Neuropsiquiatr. 2020;78(9):576–85. https://doi.org/10.1590/0004-282X20200017 . (PMID: 10.1590/0004-282X2020001732725052) Durr A. Autosomal dominant cerebellar ataxias: polyglutamine expansions and beyond. Lancet Neurol. 2010;9(9):885–94. https://doi.org/10.1016/S1474-4422(10)70183-6 . (PMID: 10.1016/S1474-4422(10)70183-620723845) Coarelli G, Wirth T, Tranchant C, Koenig M, Durr A, Anheim M. The inherited cerebellar ataxias: an update. J Neurol. 2023;270(1):208–22. https://doi.org/10.1007/s00415-022-11383-6 . (PMID: 10.1007/s00415-022-11383-636152050) Sawyer SL, Schwartzentruber J, Beaulieu CL, Dyment D, Smith A, Warman Chardon J, Yoon G, Rouleau GA, Suchowersky O, Siu V, Murphy L, Hegele RA, Marshall CR, FORGE Canada Consortium, Bulman DE, Majewski J, Tarnopolsky M, Boycott KM. Exome sequencing as a diagnostic tool for pediatric-onset ataxia. Hum Mutat. 2014;35(1):45–9. https://doi.org/10.1002/humu.22451 . (PMID: 10.1002/humu.2245124108619) Krygier M, Kwarciany M, Wasilewska K, Pienkowski VM, Krawczyńska N, Zielonka D, Kosińska J, Stawinski P, Rudzińska-Bar M, Boczarska-Jedynak M, Karaszewski B, Limon J, Sławek J, Płoski R, Rydzanicz M. A study in a Polish ataxia cohort indicates genetic heterogeneity and points to MTCL1 as a novel candidate gene. Clin Genet. 2019;95(3):415–9. https://doi.org/10.1111/cge.13489 . (PMID: 10.1111/cge.1348930548255) Weiss MM, Van der Zwaag B, Jongbloed JD, Vogel MJ, Brüggenwirth HT, Lekanne Deprez RH, Mook O, Ruivenkamp CA, van Slegtenhorst MA, van den Wijngaard A, Waisfisz Q, Nelen MR, van der Stoep N. Best practice guidelines for the use of next-generation sequencing applications in genome diagnostics: a national collaborative study of Dutch genome diagnostic laboratories. Hum Mutat. 2013;34(10):1313–21. https://doi.org/10.1002/humu.22368 . (PMID: 10.1002/humu.2236823776008) Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL. ACMG Laboratory Quality Assurance Committee. 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(5):405–24. https://doi.org/10.1038/gim.2015.30 . (PMID: 10.1038/gim.2015.30257418684544753) Kim M, Kim AR, Kim JS, et al. Clarification of undiagnosed ataxia using whole-exome sequencing with clinical implications. Parkinsonism Relat Disord. 2020;80:58–64. https://doi.org/10.1016/j.parkreldis.2020.08.040 . (PMID: 10.1016/j.parkreldis.2020.08.04032961395) Montaut S, Tranchant C, Drouot N, et al. Assessment of a targeted gene panel for identification of genes associated with movement disorders. JAMA Neurol. 2018;75(10):1234–45. https://doi.org/10.1001/jamaneurol.2018.1478 . (PMID: 10.1001/jamaneurol.2018.1478299130186233854) Galatolo D, Tessa A, Filla A, Santorelli FM. Clinical application of next generation sequencing in hereditary spinocerebellar ataxia: increasing the diagnostic yield and broadening the ataxia-spasticity spectrum. A retrospective analysis. Neurogenetics. 2018;19(1):1–8. https://doi.org/10.1007/s10048-017-0532-6 . (PMID: 10.1007/s10048-017-0532-629209898) Sterne JAC, Hernán MA, Reeves BC, Savović J, Berkman ND, Viswanathan M, et al. ROBINS-I: a tool for assessing risk of bias in non-randomized studies of interventions. BMJ. 2016;355:i4919. https://doi.org/10.1136/bmj.i4919 . (PMID: 10.1136/bmj.i4919277333545062054) Maksemous N, Roy B, Smith RA, Griffiths LR. Next-generation sequencing identifies novel CACNA1A gene mutations in episodic ataxia type 2. Mol Genet Genomic Med. 2016;4(2):211–22. https://doi.org/10.1002/mgg3.196 . (PMID: 10.1002/mgg3.196270665154799871) Maksemous N, Sutherland HG, Smith RA, Haupt LM, Griffiths LR. Comprehensive exonic sequencing of known ataxia genes in episodic ataxia. Biomedicines. 2020;8(5):134. https://doi.org/10.3390/biomedicines8050134 . (PMID: 10.3390/biomedicines8050134324662547277596) Coutelier M, Hammer MB, Stevanin G, Monin ML, Davoine CS, Mochel F, Labauge P, Ewenczyk C, Ding J, Gibbs JR, Hannequin D, Melki J, Toutain A, Laugel V, Forlani S, Charles P, Broussolle E, Thobois S, Afenjar A, et al. Spastic Paraplegia and Ataxia Network. Efficacy of exome-targeted capture sequencing to detect mutations in known cerebellar ataxia genes. JAMA Neurol. 2018;75(5):591–9. https://doi.org/10.1001/jamaneurol.2017.5121 . (PMID: 10.1001/jamaneurol.2017.5121294822235885259) Santos M, Damásio J, Carmona S, Neto JL, Dehghani N, Guedes LC, Barbot C, Barros J, Brás J, Sequeiros J, Guerreiro R. Molecular characterization of Portuguese patients with hereditary cerebellar ataxia. Cells. 2022;11(6):981. https://doi.org/10.3390/cells11060981 . (PMID: 10.3390/cells11060981353264328946949) Radziwonik W, Elert-Dobkowska E, Klimkowicz-Mrowiec A, Ziora-Jakutowicz K, Stepniak I, Zaremba J, Sulek A. Application of a custom NGS gene panel revealed a high diagnostic utility for molecular testing of hereditary ataxias. J Appl Genet. 2022;63(3):513–25. https://doi.org/10.1007/s13353-022-00701-3 . (PMID: 10.1007/s13353-022-00701-335588347) Németh AH, Kwasniewska AC, Lise S, Parolin Schnekenberg R, Becker EB, Bera KD, Shanks ME, Gregory L, Buck D, Zameel Cader M, Talbot K, de Silva R, Fletcher N, Hastings R, Jayawant S, Morrison PJ, Worth P, Taylor M, Tolmie J, et al. Next generation sequencing for molecular diagnosis of neurological disorders using ataxias as a model. Brain. 2013;136(Pt 10):3106–18. https://doi.org/10.1093/brain/awt236 . (PMID: 10.1093/brain/awt236240309523784284) Wan N, Chen Z, Wan L, Yuan H, Tang Z, Liu M, Peng Y, Peng L, Lei L, Xie Y, Deng Q, Wang S, Wang C, Peng H, Hou X, Shi Y, Long Z, Qiu R, Xia K, et al. Genetic etiology of a Chinese ataxia cohort: expanding the mutational spectrum of hereditary ataxias. Parkinsonism Relat Disord. 2021;89:120–7. https://doi.org/10.1016/j.parkreldis.2021.07.010 . (PMID: 10.1016/j.parkreldis.2021.07.01034284285) Hadjivassiliou M, Martindale J, Shanmugarajah P, et al. Causes of progressive cerebellar ataxia: prospective evaluation of 1500 patients. J Neurol Neurosurg Psychiatry. 2017;88:301–9. (PMID: 10.1136/jnnp-2016-31486327965395) Kang C, Liang C, Ahmad KE, et al. High degree of genetic heterogeneity for hereditary cerebellar ataxias in Australia. Cerebellum. 2019;18:137–46. https://doi.org/10.1007/s12311-018-0969-7 . (PMID: 10.1007/s12311-018-0969-730078120) da Graça FF, Peluzzo TM, Bonadia LC, Martinez ARM, Diniz de Lima F, Pedroso JL, Barsottini OGP, Gama MTD, Akçimen F, Dion PA, Rouleau GA, Marques W Jr, França MC Jr. Diagnostic yield of whole exome sequencing for adults with ataxia: a Brazilian perspective. Cerebellum. 2022;21(1):49–54. https://doi.org/10.1007/s12311-021-01268-1 . (PMID: 10.1007/s12311-021-01268-133956305) Cheng HL, Shao YR, Dong Y, Dong HL, Yang L, Ma Y, Shen Y, Wu ZY. Genetic spectrum and clinical features in a cohort of Chinese patients with autosomal recessive cerebellar ataxias. Transl Neurodegener. 2021;10(1):40. https://doi.org/10.1186/s40035-021-00264-z . (PMID: 10.1186/s40035-021-00264-z346634768522248) Sun M, Johnson AK, Nelakuditi V, Guidugli L, Fischer D, Arndt K, Ma L, Sandford E, Shakkottai V, Boycott K, Warman-Chardon J, Li Z, Del Gaudio D, Burmeister M, Gomez CM, Waggoner DJ, Das S. Targeted exome analysis identifies the genetic basis of disease in over 50% of patients with a wide range of ataxia-related phenotypes. Genet Med. 2019;21(1):195–206. https://doi.org/10.1038/s41436-018-0007-7 . (PMID: 10.1038/s41436-018-0007-729915382) Gauquelin L, Hartley T, Tarnopolsky M, Dyment DA, Brais B, Geraghty MT, Tétreault M, Ahmed S, Rojas S, Choquet K, Majewski J, Bernier F, Innes AM, Rouleau G, Suchowersky O, Boycott KM, Yoon G. Channelopathies are a frequent cause of genetic ataxias associated with cerebellar atrophy. Mov Disord Clin Pract. 2020;7(8):940–9. https://doi.org/10.1002/mdc3.13086 . (PMID: 10.1002/mdc3.13086331635657604675) Perez Maturo J, Zavala L, Vega P, González-Morón D, Medina N, Salinas V, Rosales J, Córdoba M, Arakaki T, Garretto N, Rodríguez-Quiroga S, Kauffman MA. Overwhelming genetic heterogeneity and exhausting molecular diagnostic process in chronic and progressive ataxias: facing it up with an algorithm, a gene, a panel at a time. J Hum Genet. 2020;65(10):895–902. https://doi.org/10.1038/s10038-020-0785-z . (PMID: 10.1038/s10038-020-0785-z32488064) Valence S, Cochet E, Rougeot C, Garel C, Chantot-Bastaraud S, Lainey E, Afenjar A, Barthez MA, Bednarek N, Doummar D, Faivre L, Goizet C, Haye D, Heron B, Kemlin I, Lacombe D, Milh M, Moutard ML, Riant F, et al. Exome sequencing in congenital ataxia identifies two new candidate genes and highlights a pathophysiological link between some congenital ataxias and early infantile epileptic encephalopathies. Genet Med. 2019;21(3):553–63. https://doi.org/10.1038/s41436-018-0089-2 . (PMID: 10.1038/s41436-018-0089-229997391) da Costa SCG, Rezende Filho FM, de Freitas JL, de Assis Pereira Matos PCA, Della-Ripa B, França MC Jr, Junior MW, Santos M, IVB C, Vale TC, Kok F, Alonso I, Pedroso JL, OGP B. Clinical and genetic characterization of Brazilian patients with ataxia and oculomotor apraxia. Mov Disord. 2022;37(6):1309–16. https://doi.org/10.1002/mds.29015 . (PMID: 10.1002/mds.2901535426160) Choi KD, Kim JS, Kim HJ, Jung I, Jeong SH, Lee SH, Kim DU, Kim SH, Choi SY, Shin JH, Kim DS, Park KP, Kim HS, Choi JH. Genetic variants associated with episodic ataxia in Korea. Sci Rep. 2017;7(1):13855. https://doi.org/10.1038/s41598-017-14254-7 . (PMID: 10.1038/s41598-017-14254-7290620945653837) Mutlu-Albayrak H, Kırat E, Gürbüz G. Childhood-onset autosomal recessive ataxias: a cross-sectional study from Turkey. Neurogenetics. 2020;21(1):59–66. https://doi.org/10.1007/s10048-019-00597-y . (PMID: 10.1007/s10048-019-00597-y31741144) Ignatius E, Isohanni P, Pohjanpelto M, Lahermo P, Ojanen S, Brilhante V, Palin E, Suomalainen A, Lönnqvist T, Carroll CJ. Genetic background of ataxia in children younger than 5 years in Finland. Neurol Genet. 2020;6(4):e444. https://doi.org/10.1212/NXG.0000000000000444 . (PMID: 10.1212/NXG.0000000000000444326376297323479) Shakya S, Kumari R, Suroliya V, Tyagi N, Joshi A, Garg A, Singh I, Kalikavil Puthanveedu D, Cherian A, Mukerji M, Srivastava AK, Faruq M. Whole exome and targeted gene sequencing to detect pathogenic recessive variants in early onset cerebellar ataxia. Clin Genet. 2019;96(6):566–74. https://doi.org/10.1111/cge.13625 . (PMID: 10.1111/cge.1362531429931) Arslan EA, Öncel İ, Ceylan AC, Topçu M, Topaloğlu H. Genetic and phenotypic features of patients with childhood ataxias diagnosed by next-generation sequencing gene panel. Brain Dev. 2020;42(1):6–18. https://doi.org/10.1016/j.braindev.2019.08.004 . (PMID: 10.1016/j.braindev.2019.08.00431493945) Ngo KJ, Rexach JE, Lee H, Petty LE, Perlman S, Valera JM, Deignan JL, Mao Y, Aker M, Posey JE, Jhangiani SN, Coban-Akdemir ZH, Boerwinkle E, Muzny D, Nelson AB, Hassin-Baer S, Poke G, Neas K, Geschwind MD, et al. A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders. Hum Mutat. 2020;41(2):487–501. https://doi.org/10.1002/humu.23946 . (PMID: 10.1002/humu.2394631692161) Bogdanova-Mihaylova P, Hebert J, Moran S, Murphy M, Ward D, Walsh RA, Murphy SM. Inherited cerebellar ataxias: 5-year experience of the Irish National Ataxia Clinic. Cerebellum. 2021;20(1):54–61. https://doi.org/10.1007/s12311-020-01180-0 . (PMID: 10.1007/s12311-020-01180-032816195) Fogel BL, Lee H, Deignan JL, Strom SP, Kantarci S, Wang X, Quintero-Rivera F, Vilain E, Grody WW, Perlman S, Geschwind DH, Nelson SF. Exome sequencing in the clinical diagnosis of sporadic or familial cerebellar ataxia. JAMA Neurol. 2014;71(10):1237–46. https://doi.org/10.1001/jamaneurol.2014.1944 . Erratum in: JAMA Neurol. 2015 Jan;72(1):128. (PMID: 10.1001/jamaneurol.2014.1944251339584324730) Pyle A, Smertenko T, Bargiela D, Griffin H, Duff J, Appleton M, Douroudis K, Pfeffer G, Santibanez-Koref M, Eglon G, Yu-Wai-Man P, Ramesh V, Horvath R, Chinnery PF. Exome sequencing in undiagnosed inherited and sporadic ataxias. Brain. 2015;138(Pt 2):276–83. https://doi.org/10.1093/brain/awu348 . (PMID: 10.1093/brain/awu34825497598) Vural A, Şimşir G, Tekgül Ş, Koçoğlu C, Akçimen F, Kartal E, Şen NE, Lahut S, Ömür Ö, Saner N, Gül T, Bayraktar E, Palvadeau R, Tunca C, Pirkevi Çetinkaya C, Gündoğdu Eken A, Şahbaz I, Kovancılar Koç M, Öztop Çakmak Ö, et al. The complex genetic landscape of hereditary ataxias in Turkey and implications in clinical practice. Mov Disord. 2021;36(7):1676–88. https://doi.org/10.1002/mds.28518 . (PMID: 10.1002/mds.2851833624863) Hamza W, Ali Pacha L, Hamadouche T, Muller J, Drouot N, Ferrat F, Makri S, Chaouch M, Tazir M, Koenig M, Benhassine T. Molecular and clinical study of a cohort of 110 Algerian patients with autosomal recessive ataxia. BMC Med Genet. 2015;16:36. https://doi.org/10.1186/s12881-015-0180-3 . (PMID: 10.1186/s12881-015-0180-3260682134630839) Balakrishnan S, Aggarwal S, Muthulakshmi M, Meena AK, Borgohain R, Mridula KR, Yareeda S, Ranganath P, Dalal A. Clinical and molecular spectrum of degenerative cerebellar ataxia: a single centre study. Neurol India. 2022;70(3):934–42. https://doi.org/10.4103/0028-3886.349660 . (PMID: 10.4103/0028-3886.34966035864621) Coutelier M, Coarelli G, Monin ML, Konop J, Davoine CS, Tesson C, Valter R, Anheim M, Behin A, Castelnovo G, Charles P, David A, Ewenczyk C, Fradin M, Goizet C, Hannequin D, Labauge P, Riant F, Sarda P, et al. A panel study on patients with dominant cerebellar ataxia highlights the frequency of channelopathies. Brain. 2017;140(6):1579–94. https://doi.org/10.1093/brain/awx081 . (PMID: 10.1093/brain/awx08128444220) Dong HL, Ma Y, Li QF, Du YC, Yang L, Chen S, Wu ZY. Genetic and clinical features of Chinese patients with mitochondrial ataxia identified by targeted next-generation sequencing. CNS Neurosci Ther. 2019;25(1):21–9. https://doi.org/10.1111/cns.12972 . (PMID: 10.1111/cns.1297229756269) Sanford Kobayashi E, et al. Approaches to long-read sequencing in a clinical setting to improve diagnostic rate. Scientific Reports. 2022;12(1):16945. https://doi.org/10.1038/s41598-022-20113-x .
فهرسة مساهمة:	Keywords: Cerebellar ataxia; Next-generation sequencing; Spinocerebellar ataxia; Targeted panels; Whole exome sequencing; Whole genome sequencing
تواريخ الأحداث:	Date Created: 20231110 Date Completed: 20240724 Latest Revision: 20240724
رمز التحديث:	20240726
DOI:	10.1007/s12311-023-01629-y
PMID:	37950147
قاعدة البيانات:	MEDLINE

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تدمد:	1473-4230
DOI:	10.1007/s12311-023-01629-y