SMRT Sequencing of Long Tandem Nucleotide Repeats in SCA10 Reveals Unique Insight of Repeat Expansion Structure.
SMRT Sequencing of Long Tandem Nucleotide Repeats in SCA10 Reveals Unique Insight of Repeat Expansion Structure.
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DOI：
10.1371/journal.pone.0135906
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Ashizawa T
中科院分区：
文献类型：
--
作者：
McFarland KN;Liu J;Landrian I;Godiska R;Shanker S;Yu F;Farmerie WG;Ashizawa T
一个大的，非编码ATTCT重复扩增导致神经退行性疾病，脊髓小脑共济失调10型（SCA10）。在SCA10患者的一个子集中，中断基序存在于扩展的5'端，并且与癫痫发作强烈相关。因此，中断基序是癫痫表型的预测因子，并被假设为SCA10中的表型修饰因子。然而，SCA10扩增的确切内部序列结构仍然是未知的，这是由于目前的技术限制，用于跨串联核苷酸重复的长延伸段进行测序。我们使用第三代测序技术，单分子真实的时间（SMRT）测序，获得全长连续扩增序列，长度从2.5到4.4 kb，从三个SCA10患者具有不同的临床表现。我们获得了跨越整个扩展长度的序列，并确定了SCA10扩展中已知和新中断基序的结构。扩展SCA10等位基因的确切中断模式将使我们能够进一步研究这些中断序列对导致SCA10癫痫表型的致病性修饰的潜在贡献。我们的研究结果还表明，SMRT测序是有用的破译长串联重复构成的“差距”在人类基因组序列。
A large, non-coding ATTCT repeat expansion causes the neurodegenerative disorder, spinocerebellar ataxia type 10 (SCA10). In a subset of SCA10 patients, interruption motifs are present at the 5’ end of the expansion and strongly correlate with epileptic seizures. Thus, interruption motifs are a predictor of the epileptic phenotype and are hypothesized to act as a phenotypic modifier in SCA10. Yet, the exact internal sequence structure of SCA10 expansions remains unknown due to limitations in current technologies for sequencing across long extended tracts of tandem nucleotide repeats. We used the third generation sequencing technology, Single Molecule Real Time (SMRT) sequencing, to obtain full-length contiguous expansion sequences, ranging from 2.5 to 4.4 kb in length, from three SCA10 patients with different clinical presentations. We obtained sequence spanning the entire length of the expansion and identified the structure of known and novel interruption motifs within the SCA10 expansion. The exact interruption patterns in expanded SCA10 alleles will allow us to further investigate the potential contributions of these interrupting sequences to the pathogenic modification leading to the epilepsy phenotype in SCA10. Our results also demonstrate that SMRT sequencing is useful for deciphering long tandem repeats that pose as “gaps” in the human genome sequence.