SMRT sequencing of long tandem nucleotide repeats in SCA10 reveals unique insight of repeat expansion structure

Karen N. McFarl, Jilin Liu, Ivette Landrian, Ronald Godiska, Savita Shanker, Fahong Yu, William G. Farmerie, Tetsuo Ashizawa

Research output: Contribution to journalArticle

25 Scopus citations

Abstract

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 fulllength 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.

Original languageEnglish (US)
Article numbere0135906
JournalPLoS ONE
Volume10
Issue number8
DOIs
StatePublished - Aug 21 2015

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Fingerprint Dive into the research topics of 'SMRT sequencing of long tandem nucleotide repeats in SCA10 reveals unique insight of repeat expansion structure'. Together they form a unique fingerprint.

Cite this