Journal Article

Long-read sequencing identified intronic repeat expansions in SAMD12 from Chinese pedigrees affected with familial cortical myoclonic tremor with epilepsy

Zeng, Sheng, Hu, Zheng-mao, Zhang, Mei-yun, Wang, Xue-jing, Fang, Li, Li, Jin-chen, Li, Nan, Jiang, Hong, Wang, Jun-ling, Hao, Jun-wei, Liao, Wei-ping, Teng, Jun-fang, Tang, Bei-sha, Yin, Xiao-meng, Liu, Qian, Yang, Qi, Shi, Fu-dong, Xia, Kun, Ding, Xue-bing, Wang, Kai, Liu, Jing-yu, Liang, Fan

2019

Overview

The locus for familial cortical myoclonic tremor with epilepsy (FCMTE) has long been mapped to 8q24 in linkage studies, but the causative mutations remain unclear. Recently, expansions of intronic TTTCA and TTTTA repeat motifs within were found to be involved in the pathogenesis of FCMTE in Japanese pedigrees. We aim to identify the causative mutations of FCMTE in Chinese pedigrees. We performed genetic linkage analysis by microsatellite markers in a five-generation Chinese pedigree with 55 members. We also used array-comparative genomic hybridisation (CGH) and next-generation sequencing (NGS) technologies (whole-exome sequencing, capture region deep sequencing and whole-genome sequencing) to identify the causative mutations in the disease locus. Recently, we used low-coverage (~10×) long-read genome sequencing (LRS) on the PacBio Sequel and Oxford Nanopore platforms to identify the causative mutations, and used repeat-primed PCR for validation of the repeat expansions. Linkage analysis mapped the disease locus to 8q23.3-24.23. Array-CGH and NGS failed to identify causative mutations in this locus. LRS identified the intronic TTTCA and TTTTA repeat expansions in as the causative mutations, thus corroborating the recently published results in Japanese pedigrees. We identified the pentanucleotide repeat expansion in as the causative mutation in Chinese FCMTE pedigrees. Our study also suggested that LRS is an effective tool for molecular diagnosis of genetic disorders, especially for neurological diseases that cannot be positively diagnosed by conventional clinical microarray and NGS technologies.

• Publisher: BMJ Publishing Group LTD
• Subject: Adult / Chromosome 8 / Chromosomes / Comparative Genomic Hybridization / Cortex / Epilepsies, Myoclonic - diagnosis / Epilepsies, Myoclonic - genetics / Epilepsy / Family medical history / Female / Genes / Genetic analysis / Genetic Association Studies - methods / Genetic disorders / Genetic markers / Genomes / Humans / Hybridization / Introns / Linkage analysis / Male / Microsatellites / Mutation / Nerve Tissue Proteins - genetics / Neurological diseases / Next-generation sequencing / Pathogenesis / Pedigree / Phenotype / Sequence Analysis, DNA / Tandem Repeat Sequences / Tremor / Whole Exome Sequencing / Whole Genome Sequencing