TY - JOUR
T1 - SMRT sequencing of long tandem nucleotide repeats in SCA10 reveals unique insight of repeat expansion structure
AU - McFarl, Karen N.
AU - Liu, Jilin
AU - Landrian, Ivette
AU - Godiska, Ronald
AU - Shanker, Savita
AU - Yu, Fahong
AU - Farmerie, William G.
AU - Ashizawa, Tetsuo
N1 - Funding Information:
This work was supported by NIH grants (NS083564 and NS041547) and a University of Florida Opportunity Grant to TA.
Publisher Copyright:
© 2015 McFarland et al.
PY - 2015/8/21
Y1 - 2015/8/21
N2 - 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.
AB - 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.
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U2 - 10.1371/journal.pone.0135906
DO - 10.1371/journal.pone.0135906
M3 - Article
C2 - 26295943
AN - SCOPUS:84942930007
SN - 1932-6203
VL - 10
JO - PLoS ONE
JF - PLoS ONE
IS - 8
M1 - e0135906
ER -