Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases

Mizuguchi, Takeshi; Toyota, Tomoko; Adachi, Hiroaki; Miyake, Noriko; Matsumoto, Naomichi; Miyatake, Satoko

doi:10.1038/s10038-018-0551-7

Cited by 35 publications

(32 citation statements)

References 33 publications

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“…SCA8 can harbor Interruptions within the CTG�CAG expansion by one or more CCG�CGG, CTA�TAG, CTC�GAG, CCA�TGG, or CTT�AAG trinucleotides which can duplicate when transmitted from one generation to the next [23]. BAFME is caused by a large (TTTCA) repeat insertion adjacent to the (TAAAA) n repeat in the intronic SAMD12, TNRC6A and RAPGEF2 [24]. AR-CANVAS is caused by biallelic pentanucleotide repeat expansion where the normal (AAAAG) n intronic repeat in the gene encoding Replication Factor C1 (RFC1) is replaced by a large (AAGGG) n expansion [17].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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Large expansions of microsatellite DNA cause several neurological diseases. In Spinocerebellar ataxia type 10 (SCA10), the repeat interruptions change disease phenotype; an (ATTCC) n or a (ATCCT) n /(ATCCC) n interruption within the (ATTCT) n repeat is associated with the robust phenotype of ataxia and epilepsy while mostly pure (ATTCT) n may have reduced penetrance. Large repeat expansions of SCA10, and many other microsatellite expansions, can exceed 10,000 base pairs (bp) in size. Conventional next generation sequencing (NGS) technologies are ineffective in determining internal sequence contents or size of these expanded repeats. Using repeat primed PCR (RP-PCR) in conjunction with a high-sensitivity pulsed-field capillary electrophoresis fragment analyzer (FEMTO-Pulse, Agilent, Santa Clara, CA) (RP-FEMTO hereafter), we successfully determined sequence content of large expansion repeats in genomic DNA of SCA10 patients and transformed yeast artificial chromosomes containing SCA10 repeats. This RP-FEMTO is a simple and economical methodology which could complement emerging NGS for very long sequence reads such as Single Molecule, Real-Time (SMRT) and nanopore sequencing technologies.

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Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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“…Of these, the repeat expansion in intron four of SAMD12 was the most frequent and was observed in 48 out of 51 FCMTE families 9 . These findings were subsequently validated in additional Japanese and Chinese families with FCMTE 10–13 . Here, we present a large multigenerational Chinese family with more than twenty individuals with FCMTE symptoms from five generations that we have been studying for 23 years.…”

Section: Introductionmentioning

confidence: 71%

Clinical and genomic analysis of a large Chinese family with familial cortical myoclonic tremor with epilepsy and SAMD12 intronic repeat expansion

et al. 2021

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Objective Our goal was to perform detailed clinical and genomic analysis of a large multigenerational Chinese family with 21 individuals showing symptoms of Familial Cortical Myoclonic Tremor with Epilepsy (FCMTE) that we have followed for over 20 years. Methods Patients were subjected to clinical evaluation, routine EEG, and structural magnetic resonance imaging. Whole exome sequencing, repeat‐primed PCR, long‐range PCR, and PacBio sequencing were performed to characterize the disease‐causing mutation in this family. Results All evaluated patients manifested adult‐onset seizures and presented with progressive myoclonic postural tremors starting after the third or fourth decade of life. Seizures typically diminished markedly in frequency with implementation of antiseizure medications but did not completely cease. The electroencephalogram of affected individuals showed generalized or multifocal spikes and slow wave complexes. An expansion of TTTTA motifs with addition of TTTCA motifs in intron 4 of SAMD12 was identified to segregate with the disease phenotype in this family. Furthermore, we found that the mutant allele is unstable and can undergo both contraction and expansion by changes in the number of repeat motifs each time it is passed to the next generation. The size of mutant allele varied from 5 to 5.5 kb with 549‐603 copies of TTTTA and 287‐343 copies of TTTCA repeat motifs in this family. Significance Our study provides a detailed description of clinical progression of FCMTE symptoms and its management with antiseizure medications. Our method of repeat analysis by PacBio sequencing of long‐range PCR products does not require high‐quality DNA and hence can be easily applied to other families to elucidate any correlation between the repeat size and phenotypic variables, such as, age of onset, and severity of symptoms.

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“…Whole‐genome long‐read sequencing has been utilized to investigate the structure of the (TTTCA) n insertion and the accompanying (TTTTA) n expansion in SAMD12 . However, the accurate structure has not been able to be identified because of the very common insertion and deletion (indel) errors in long‐read sequencing, and the very limited reads (only two to four) spanning the repeat expansion region .…”

Section: Discussionmentioning

confidence: 99%

“…14,16,17 However, the accurate structure has not been able to be identified because of the very common insertion and deletion (indel) errors in long-read sequencing, and the very limited reads (only two to four) spanning the repeat expansion region. 14,16,17 To tackle this issue, we performed targeted long-read sequencing using LR-PCR products from 2 patients and 1 asymptomatic carrier in this study. This targeted long-read sequencing approach enabled us to reveal the accurate structures of the expanded repeats and gain a better understanding of the repeat expansions in FCMTE1.…”

Section: Discussionmentioning

confidence: 99%

Intronic (TTTGA)_n insertion in SAMD12 also causes familial cortical myoclonic tremor with epilepsy

et al. 2019

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Background Intronic (TTTCA)n insertions in the SAMD12, TNRC6A, and RAPGEF2 genes have been identified as causes of familial cortical myoclonic tremor with epilepsy. Objective To identify the cause of familial cortical myoclonic tremor with epilepsy pedigrees without (TTTCA)n insertions in SAMD12, TNRC6A, and RAPGEF2. Methods Repeat‐primed polymerase chain reaction, long‐range polymerase chain reaction, and Sanger sequencing were performed to identify the existence of a novel (TTTGA)n insertion. Targeted long‐read sequencing was performed to confirm the accurate structure of the (TTTGA)n insertion. Results We identified a novel expanded intronic (TTTGA)n insertion at the same site as the previously reported (TTTCA)n insertion in SAMD12. This insertion cosegregated with familial cortical myoclonic tremor with epilepsy in 1 Chinese pedigree with no (TTTCA)n insertion. In the targeted long‐read sequencing of 2 patients and 1 asymptomatic carrier in this pedigree, with 1 previously reported (TTTCA)n‐insertion–carrying patient as a positive control, a respective total of 302, 159, 207, and 50 on‐target subreads (predicated accuracy: ≥90%) spanning the target repeat expansion region were generated. These sequencing data revealed the accurate repeat expansion structures as (TTTTA)114‐123(TTTGA)108‐116 in the pedigree and (TTTTA)38(TTTCA)479 in (TTTCA)n‐insertion–carrying patient. Conclusion The targeted long‐read sequencing helped us to elucidate the accurate structures of the (TTTGA)n and (TTTCA)n insertions. Our finding offers a novel possible cause for familial cortical myoclonic tremor with epilepsy and might shed light on the identification of genetic causes of this disease in pedigrees with no detected (TTTCA)n insertion in the reported causative genes. © 2019 International Parkinson and Movement Disorder Society

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Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases

Cited by 35 publications

References 33 publications

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

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

Clinical and genomic analysis of a large Chinese family with familial cortical myoclonic tremor with epilepsy and SAMD12 intronic repeat expansion

Intronic (TTTGA)_n insertion in SAMD12 also causes familial cortical myoclonic tremor with epilepsy

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Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases

Cited by 35 publications

References 33 publications

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

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

Clinical and genomic analysis of a large Chinese family with familial cortical myoclonic tremor with epilepsy and SAMD12 intronic repeat expansion

Intronic (TTTGA)n insertion in SAMD12 also causes familial cortical myoclonic tremor with epilepsy

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Intronic (TTTGA)_n insertion in SAMD12 also causes familial cortical myoclonic tremor with epilepsy