Pulse-Field capillary electrophoresis of repeat-primed PCR amplicons for analysis of large repeats in Spinocerebellar Ataxia Type 10

Hashem, Vera I.; Tiwari, Anjana; Bewick, Brittani; Teive, Hélio Afonso Ghizoni; Moscovich, Mariana; Schuele, Birgitt; Bushara, Khalaf; Bower, Matt; Rasmussen, Astrid; Tsai, Yu Chih; Clark, Tyson A.; McFarland, Karen N.; Ashizawa, Tetsuo

doi:10.1371/journal.pone.0228789

Cited by 12 publications

(8 citation statements)

References 34 publications

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“…Intermediate-size alleles with reduced penetrance have also been reported [ 93 , 99 , 103 ]. Remarkably, in subjects with epileptic seizures, the repeat expansion is interrupted by inserted pentanucleotide motifs such as (ATTCC) n , (ATCCC) n , and (ATCCT) n that modify disease presentation [ 103 , 104 , 105 , 106 ]. Interestingly, the pathogenic repeat is in the poly-A tail of an Alu DNA element [ 107 ] similar to other pentanucleotide repeat mutations ( Figure 3 A).…”

Section: Pentanucleotide Repeats In Spinocerebellar Ataxiasmentioning

confidence: 99%

Molecular Mechanisms in Pentanucleotide Repeat Diseases

Loureiro

Castro

Figueiredo

et al. 2022

Cells

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The number of neurodegenerative diseases resulting from repeat expansion has increased extraordinarily in recent years. In several of these pathologies, the repeat can be transcribed in RNA from both DNA strands producing, at least, one toxic RNA repeat that causes neurodegeneration by a complex mechanism. Recently, seven diseases have been found caused by a novel intronic pentanucleotide repeat in distinct genes encoding proteins highly expressed in the cerebellum. These disorders are clinically heterogeneous being characterized by impaired motor function, resulting from ataxia or epilepsy. The role that apparently normal proteins from these mutant genes play in these pathologies is not known. However, recent advances in previously known spinocerebellar ataxias originated by abnormal non-coding pentanucleotide repeats point to a gain of a toxic function by the pathogenic repeat-containing RNA that abnormally forms nuclear foci with RNA-binding proteins. In cells, RNA foci have been shown to be formed by phase separation. Moreover, the field of repeat expansions has lately achieved an extraordinary progress with the discovery that RNA repeats, polyglutamine, and polyalanine proteins are crucial for the formation of nuclear membraneless organelles by phase separation, which is perturbed when they are expanded. This review will cover the amazing advances on repeat diseases.

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Section: Pentanucleotide Repeats In Spinocerebellar Ataxiasmentioning

confidence: 99%

Molecular Mechanisms in Pentanucleotide Repeat Diseases

Loureiro

Castro

Figueiredo

et al. 2022

Cells

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“…Both results suggest that the pure originally described ATTCT(n) expansion is not pathogenic, whereas repeat insertions or interruptions cause SCA10 symptoms. Only since it is possible to sequence through the entire repeat expansion from genomic DNA with long-read sequencing techniques is it possible to resolve the complete sequence of the ATXN10 repeat expansion fully, as it is not possible to decipher the sequence composition using Southern blot analysis, PCR electrophoresis or repeat-prime PCR 13 . Therefore, ATXN10 repeat expansions fall into a category of repeat expansions that only become clinically symptomatic when repeat interruptions are present.…”

Section: Reduced Disease Penetrance In Pure Attct Carriersmentioning

confidence: 99%

“…However, current clinical genetic diagnostics cannot determine the ATXN10 pentanucleotide repeat composition. More recent developments of repeat-prime PCR with the high-resolution pulse-field capillary electrophoresis analysis 13 and long-range sequencing 3 in the research setting allow for refinement of ATXN10 repeat composition.…”

Section: Introductionmentioning

confidence: 99%

ATTCT and ATTCC repeat expansions in the ATXN10 gene affect disease penetrance of spinocerebellar ataxia type 10

Torres

Zafar

Tsai

et al. 2022

Preprint

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Spinocerebellar ataxia type 10 (SCA10) is an autosomal-dominant disorder caused by an expanded pentanucleotide repeat in the ATXN10 gene. This repeat expansion, when fully penetrant, has a size of 850 to 4500 repeats. It has been shown that the repeat composition can be a modifier of disease, e.g., seizures.Here, we describe a Hispanic kindred in which we identified both pure (ATTCT)n expansions and mixed (ATTCT)n-(ATTCC)n in the same family. We used No-Amp targeted sequencing and optical genome mapping to decipher the composition of these repeat expansions. We found a considerable degree of mosaicism in the repeat expansion. This mosaicism was confirmed in skin fibroblasts from ATXN10 carriers with RNAScope in situ hybridization. All affected family members with the mixed ATXN10 repeat expansion showed typical clinical signs of spinocerebellar ataxia and epilepsy. In contrast, individuals with the pure ATXN10 expansion present with Parkinson’s disease or are unaffected even more than 20 years older than the average age at onset for SCA10.Our findings suggest that the pure (ATTCT)n expansion is non-pathogenic while repeat interruptions, e.g., (ATTCC)n, are necessary to cause SCA10. This mechanism has been recently described for several other repeat expansions, including SCA31 (BEAN1), SCA37 (DAB1), and three loci for benign adult familial myoclonic epilepsy BAFME (SAMD12, TNRC6A, RAPGEF2). Therefore, long-read sequencing and optical genome mapping of the entire genomic structure of repeat expansions is critical for clinical practice, and genetic counseling as variations in the repeat can affect disease penetrance, symptoms, and disease trajectory.

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“…In a study aimed at patients with SCA10, SMRT preferentially sequenced small repeat-sized alleles while failing to generate circular consensus sequences of expanded SCA10 repeats containing large (ATCCC) repeat interruptions. Researchers held that this was due to high GC content [ 128 ]. Hence, the constitution of repeats may influence the utility of SMRT.…”

Section: Single-molecule Real-time Sequencingmentioning

confidence: 99%

Next-Generation Sequencing Technologies and Neurogenetic Diseases

Sun

Shen

Fang

et al. 2021

Life

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Next-generation sequencing (NGS) technology has led to great advances in understanding the causes of Mendelian and complex neurological diseases. Owing to the complexity of genetic diseases, the genetic factors contributing to many rare and common neurological diseases remain poorly understood. Selecting the correct genetic test based on cost-effectiveness, coverage area, and sequencing range can improve diagnosis, treatments, and prevention. Whole-exome sequencing and whole-genome sequencing are suitable methods for finding new mutations, and gene panels are suitable for exploring the roles of specific genes in neurogenetic diseases. Here, we provide an overview of the classifications, applications, advantages, and limitations of NGS in research on neurological diseases. We further provide examples of NGS-based explorations and insights of the genetic causes of neurogenetic diseases, including Charcot–Marie–Tooth disease, spinocerebellar ataxias, epilepsy, and multiple sclerosis. In addition, we focus on issues related to NGS-based analyses, including interpretations of variants of uncertain significance, de novo mutations, congenital genetic diseases with complex phenotypes, and single-molecule real-time approaches.

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Pulse-Field capillary electrophoresis of repeat-primed PCR amplicons for analysis of large repeats in Spinocerebellar Ataxia Type 10

Cited by 12 publications

References 34 publications

Molecular Mechanisms in Pentanucleotide Repeat Diseases

Molecular Mechanisms in Pentanucleotide Repeat Diseases

ATTCT and ATTCC repeat expansions in the ATXN10 gene affect disease penetrance of spinocerebellar ataxia type 10

Next-Generation Sequencing Technologies and Neurogenetic Diseases

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