MLPA identification of dystrophin mutations and in silico evaluation of the predicted protein in dystrophinopathy cases from India

BMC Medical Genetics

Research Article

Seena Vengalil¹  Atchayaram Nalini¹  Kiran Polavarapu¹  Veeramani Preethish-Kumar¹  Narayanappa Gayathri²  Sekar Deepha²  Meera Purushottam³ 

[1] Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India;Department of Neuropathology, Neuromuscular Laboratory, Bengaluru, Karnataka, India;Molecular Genetics Laboratory, Neurobiology Research Centre, Department of Psychiatry, National Institute of Mental Health and Neurosciences, Hosur Road, 560029, Bangalore, Karnataka, India;

关键词: DMD;    MLPA;    PROVEAN;    Hydrophobicity profile;    eDystrophin;   

DOI  :  10.1186/s12881-017-0431-6

 received in 2016-04-11, accepted in 2017-05-31,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundDuchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive disorders caused by mutations in the DMD gene. The aim of this study was to predict the effect of gene mutations on the dystrophin protein and study its impact on clinical phenotype.MethodsIn this study, 415 clinically diagnosed patients were tested for mutations by Multiplex ligation dependent probe amplification (MLPA). Muscle biopsy was performed in 34 patients with negative MLPA. Phenotype-genotype correlation was done using PROVEAN, hydrophobicity and eDystrophin analysis. We have utilized bioinformatics tools in order to evaluate the observed mutations both at the level of primary as well as secondary structure.ResultsMutations were identified in 75.42% cases, of which there were deletions in 91.6% and duplications in 8.30%. As per the reading frame rule, 84.6% out-of frame and 15.3% in-frame mutations were noted. Exon 50 was the most frequently deleted exon and the exon 45–52 region was the hot-spot for deletions in this cohort. There was no correlation noted between age of onset or creatine kinase (CK) values with extent of gene mutation. The PROVEAN analysis showed a deleterious effect in 94.5% cases and a neutral effect in 5.09% cases. Mutations in exon 45–54 (out of frame) and exon 46–54 (in-frame) regions in the central rod domain of dystrophin showed more negative scores compared to other domains in the present study. Hydrophobicity profile analysis showed that the hydrophobic regions I & III were equally affected. Analysis of deletions in hinge III hydrophobic region by the eDystrophin programme also predicted a hybrid repeat seen to be associated with a BMD like disease progression, thus making the hinge III region relatively tolerant to mutations.ConclusionsWe found that, while the predictions made by the software utilized might have overall significance, the results were not convincing on a case by case basis. This reflects the inadequacy of the currently available tools and also underlines the possible inadequacy of MLPA to detect other minor mutations that might enhance or suppress the effect of the primary mutation in this large gene. Next Generation Sequencing or targeted Sanger sequencing on a case by case basis might improve phenotype- genotype correlation.

【 授权许可】

CC BY   
© The Author(s). 2017