{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T04:19:07Z","timestamp":1784693947516,"version":"3.55.0"},"reference-count":33,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T00:00:00Z","timestamp":1766707200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan","award":["BR24992933"],"award-info":[{"award-number":["BR24992933"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background: Duchenne muscular dystrophy (DMD) results from pathogenic variants in the DMD gene, one of the most significant and most mutation-prone genes in the human genome. Although global mutation registries are well developed, genetic data from Central Asian populations remain extremely limited, leaving essential gaps in regional epidemiology and in the understanding of genotype\u2013phenotype patterns. Methods: We conducted a retrospective analysis of patients with genetically confirmed dystrophinopathy in Kazakhstan. Variants were identified using multiplex ligation-dependent probe amplification (MLPA) for exon-level copy number alterations and next-generation sequencing (NGS) with Sanger confirmation for sequence-level changes. All variants were classified under ACMG guidelines. Statistical modelling incorporated mutation-class grouping, exon-hotspot mapping, reading-frame status, CPK stratification, chi-squared association testing, Spearman correlations, Kaplan\u2013Meier ambulation survival curves, and multivariable logistic and Cox regression. Results: multi-exon deletions were the predominant mutation class, with a marked concentration within the canonical hotspot spanning exons 44\u201355. Recurrent deletions affecting exons 46\u201350 and 45\u201350 appeared in several unrelated patients. NGS confirmed severe protein-truncating variants, including p. Lys1049* and p. Ser861Ilefs*7. Phenotypic severity followed a consistent hierarchy: hotspot-associated deletions and early truncating variants showed the earliest loss of ambulation, whereas splice-site variants and duplications demonstrated the mildest courses. CPK levels correlated with the extent of genomic involvement, though extreme elevations did not consistently predict early functional decline. Regression models identified hotspot localization and out-of-frame effect as independent predictors of ambulation loss. Conclusions: This study provides the first statistically modelled characterisation of DMD gene mutations in Kazakhstan. While the mutational landscape largely mirrors global patterns, notable variability in clinical severity suggests the presence of population-specific modifiers. Integrating comprehensive molecular diagnostics with statistical-genetics approaches enhances prognostic accuracy and supports the development of mutation-targeted therapeutic strategies in Central Asia.<\/jats:p>","DOI":"10.3390\/genes17010020","type":"journal-article","created":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T00:50:42Z","timestamp":1766969442000},"page":"20","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Statistical Genetics of DMD Gene Mutations in a Kazakhstan Cohort: MLPA\/NGS Variant Validation and Genotype\u2013Phenotype Modelling"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0186-978X","authenticated-orcid":false,"given":"Aizhan","family":"Moldakaryzova","sequence":"first","affiliation":[{"name":"Department of Molecular Biology and Medical Genetics, Asfendiyarov Kazakh National Medical University, Zheltoksan 37A Street, Almaty 050012, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dias","family":"Dautov","sequence":"additional","affiliation":[{"name":"Centre for Orphan Diseases with Neurological Manifestations in Children at the Republican Children\u2019s Clinical Hospital \u201cAksai\u201d of KazNMU Named After S.D. Asfendiyarov, Tautagan 2a, Almaty 050000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7770-8427","authenticated-orcid":false,"given":"Saken","family":"Khaidarov","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Medical Genetics, Asfendiyarov Kazakh National Medical University, Zheltoksan 37A Street, Almaty 050012, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1420-7486","authenticated-orcid":false,"given":"Saniya","family":"Ossikbayeva","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetic Research Center JS, Kazakh Institute of Oncology and Radiology, Almaty 050022, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0969-5983","authenticated-orcid":false,"given":"Dilyara","family":"Kaidarova","sequence":"additional","affiliation":[{"name":"First Vice-Rector, Asfendiyarov Kazakh National Medical University, Tole-Bi Street 94, Almaty 050012, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/0092-8674(87)90504-6","article-title":"Complete cloning of the Duchenne muscular dystrophy (DMD) cDNA and preliminary genomic organization of the DMD gene","volume":"50","author":"Koenig","year":"1987","journal-title":"Cell"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1016\/0092-8674(87)90579-4","article-title":"Dystrophin: The protein product of the Duchenne muscular dystrophy locus","volume":"51","author":"Hoffman","year":"1987","journal-title":"Cell"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1136\/jmedgenet-2015-103387","article-title":"The importance of genetic diagnosis for Duchenne muscular dystrophy","volume":"53","author":"Ginjaar","year":"2016","journal-title":"J. Med. Genet."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1016\/S0140-6736(02)07815-7","article-title":"The muscular dystrophies","volume":"359","author":"Emery","year":"2002","journal-title":"Lancet"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1002\/humu.22758","article-title":"The TREAT-NMD DMD Global Database: Analysis of more than 7,000 Duchenne muscular dystrophy mutations","volume":"36","author":"Bladen","year":"2015","journal-title":"Hum. Mutat."},{"key":"ref_6","first-page":"665","article-title":"Mutation spectrum of the dystrophin gene in Japanese patients with Duchenne\/Becker muscular dystrophy","volume":"127","author":"Takeshima","year":"2010","journal-title":"Hum. Genet."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/0888-7543(88)90113-9","article-title":"An explanation for the phenotypic differences between patients bearing partial deletions of the DMD locus","volume":"2","author":"Monaco","year":"1988","journal-title":"Genomics"},{"key":"ref_8","first-page":"181","article-title":"Phenotype variability in dystrophinopathies: Exceptions to the reading-frame rule","volume":"54","author":"Zimowski","year":"2020","journal-title":"Neurol. Neurochir. Pol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1016\/j.ncl.2014.05.002","article-title":"Duchenne and Becker muscular dystrophies","volume":"32","author":"Flanigan","year":"2014","journal-title":"Neurol. Clin."},{"key":"ref_10","first-page":"711","article-title":"The \u201creading-frame rule\u201d in Duchenne muscular dystrophy: Still valid?","volume":"28","author":"Bello","year":"2018","journal-title":"Neuromuscul. Disord."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1002\/humu.20367","article-title":"Duplications in the DMD gene","volume":"27","author":"White","year":"2006","journal-title":"Hum. Mutat."},{"key":"ref_12","unstructured":"Ankala, A., Kohn, J.N., and Hegde, S. (2015). Dystrophinopathies: Clinical and genetic testing strategies. Neurol. Genet., 1."},{"key":"ref_13","first-page":"6220","article-title":"Exon skipping applications in Duchenne muscular dystrophy","volume":"21","author":"Lim","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"ref_14","first-page":"541","article-title":"Development of exon skipping therapies for Duchenne muscular dystrophy: A critical review","volume":"16","author":"Straub","year":"2017","journal-title":"Lancet Neurol."},{"key":"ref_15","first-page":"451","article-title":"Assessment of the safety and efficacy of ataluren for nonsense mutation DMD","volume":"381","author":"Mendell","year":"2013","journal-title":"Lancet"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/S1474-4422(09)70271-6","article-title":"Diagnosis and management of Duchenne muscular dystrophy, part 1","volume":"9","author":"Bushby","year":"2010","journal-title":"Lancet Neurol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e57","DOI":"10.1093\/nar\/gnf056","article-title":"MLPA: A novel multiplex PCR method for detection of deletions\/duplications","volume":"30","author":"Schouten","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/gim.2015.30","article-title":"Standards and guidelines for the interpretation of sequence variants (ACMG-AMP)","volume":"17","author":"Richards","year":"2015","journal-title":"Genet. Med."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1038\/nrg1916","article-title":"A tutorial on statistical genetics","volume":"7","author":"Balding","year":"2006","journal-title":"Nat. Rev. Genet."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1946","DOI":"10.1002\/sim.6082","article-title":"Multiple testing and survival analysis","volume":"33","author":"Goeman","year":"2014","journal-title":"Stat. Med."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Khaidarov, S., Hejran, A.B., Moldakaryzova, A., Izmailova, S., Nurgaliyeva, B., Beisenova, A., Mustafaeva, A., Nurzhanova, K., Belova, Y., and Satbayeva, E. (2025). An Anti-HIV Drug Is Highly Effective Against SARS-CoV-2 In Vitro and Has Potential Benefit for Long COVID Treatment. Viruses, 17.","DOI":"10.3390\/v17091170"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"306","DOI":"10.5535\/arm.2017.41.2.306","article-title":"Correlation of Serum Creatine Kinase Level With Pulmonary Function in Duchenne Muscular Dystrophy","volume":"41","author":"Kim","year":"2017","journal-title":"Ann. Rehabil. Med."},{"key":"ref_23","first-page":"35","article-title":"Changes of serum creatine kinase levels in children with Duchenne muscular dystrophy","volume":"10","author":"Sun","year":"2008","journal-title":"Zhongguo Dang Dai Er Ke Za Zhi"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/0022-510X(91)90068-I","article-title":"Serum creatine-kinase (CK) and pyruvate-kinase (PK) activities in Duchenne (DMD) as compared with Becker (BMD) muscular dystrophy","volume":"102","author":"Zatz","year":"1991","journal-title":"J. Neurol. Sci."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1002\/ana.23819","article-title":"LTBP4 genotype predicts age of ambulatory loss in Duchenne muscular dystrophy","volume":"73","author":"Flanigan","year":"2013","journal-title":"Ann. Neurol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1212\/WNL.0b013e318207afeb","article-title":"SPP1 genotype is a determinant of disease severity in Duchenne muscular dystrophy","volume":"76","author":"Pegoraro","year":"2011","journal-title":"Neurology"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Kosac, A., Pesovic, J., Radenkovic, L., Brkusanin, M., Radovanovic, N., Djurisic, M., Radivojevic, D., Mladenovic, J., Ostojic, S., and Kovacevic, G. (2022). LTBP4, SPP1, and CD40 Variants: Genetic Modifiers of Duchenne Muscular Dystrophy Analyzed in Serbian Patients. Genes, 13.","DOI":"10.3390\/genes13081385"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1016\/j.ajhg.2016.08.023","article-title":"Association Study of Exon Variants in the NF-\u03baB and TGF\u03b2 Pathways Identifies CD40 as a Modifier of Duchenne Muscular Dystrophy","volume":"99","author":"Bello","year":"2016","journal-title":"Am. J. Hum. Genet."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"14143","DOI":"10.1038\/ncomms14143","article-title":"Evidence for ACTN3 as a genetic modifier of Duchenne muscular dystrophy","volume":"8","author":"Hogarth","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"e2406","DOI":"10.1212\/WNL.0000000000201163","article-title":"Evaluating Genetic Modifiers of Duchenne Muscular Dystrophy Disease Progression Using Modeling and MRI","volume":"99","author":"Barnard","year":"2022","journal-title":"Neurology"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1136\/thorax-2023-220811","article-title":"Development of respiratory care guidelines for Duchenne muscular dystrophy","volume":"79","author":"Childs","year":"2024","journal-title":"Thorax"},{"key":"ref_32","first-page":"3801","article-title":"Cardiovascular Disease in Duchenne Muscular Dystrophy","volume":"11","author":"Schultz","year":"2022","journal-title":"J. Clin. Med."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Sales, T.L.S., Pereira, D.N., Gomes, V.M.R., de Aguiar, G.G., and Marcolino, M.S. (2025). Efficacy of tenofovir on clinical outcomes of COVID-19: A review of clinical trials. BMC Infect. Dis., 25.","DOI":"10.1186\/s12879-025-11359-7"}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/1\/20\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T01:03:13Z","timestamp":1766970193000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/1\/20"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,26]]},"references-count":33,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1]]}},"alternative-id":["genes17010020"],"URL":"https:\/\/doi.org\/10.3390\/genes17010020","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,26]]}}}