Whole genome analyses reveal no pathogenetic single nucleotide or structural differences between monozygotic twins discordant for amyotrophic lateral sclerosis

The contribution of genetic and environmental factors to the pathogenesis of sporadic amyotrophic lateral sclerosis (ALS) remains unclear. To investigate the genetic component of the disease, we performed whole genome sequencing on ALS discordant monozygotic twins. Illumina whole genome sequencing on white blood cell DNA of five ALS-discordant monozygotic twin pairs (10 samples in total) yielded ∼30x coverage per individual. All single nucleotide variants, indels, and structural variants (copy number variants, inversions and translocations) were called and evaluated for functional consequence, evolutionary conservation, population frequency and overlap with known ALS associated variants and genes. Results showed that no validated discordant coding or regulatory single nucleotide variants or indels were found, and nor were any genome-wide discordant structural variants detected. Concordant variants of particular interest were: 1) two rare, highly-conserved heterozygous non-synonymous variants in SYT9 and EWSR1, genes previously associated with ALS (out of 2044 rare heterozygous variants detected); 2) three rare homozygous missense variants; and 3) three novel copy number deletions that overlapped genes. In conclusion, no convincing coding or regulatory nucleotide or genome-wide structural differences were found between ALS discordant monozygotic twins. The results suggest that more work is needed to elucidate possible environmental, epigenetic, oligogenic and somatic genetic factors that could underlie susceptibility to sporadic ALS.

遗传与环境因素对散发性肌萎缩侧索硬化症（sporadic amyotrophic lateral sclerosis, ALS）发病机制的贡献迄今尚未阐明。为探究该病的遗传组分，我们对ALS表型不一致的同卵双胞胎开展了全基因组测序（whole genome sequencing）。针对5对ALS表型不一致的同卵双胞胎（共10份样本）的白细胞DNA进行Illumina全基因组测序，单样本测序覆盖度约为30倍。对所有单核苷酸变异（single nucleotide variants）、插入缺失（insertions and deletions, indels）以及结构变异（structural variants）进行了变异鉴定，并从功能影响、进化保守性、群体频率以及与已知ALS相关变异和基因的重叠性等维度开展评估。研究结果显示，未发现经过验证的表型不一致的编码区或调控区单核苷酸变异、插入缺失，也未检测到全基因组范围内表型不一致的结构变异。值得关注的一致性变异包括：1）在2044个检出的罕见杂合（heterozygous）变异中，2个分别位于SYT9与EWSR1基因的罕见且高度保守的杂合非同义变异（non-synonymous variants），此前这两个基因已被证实与ALS相关；2）3个罕见纯合（homozygous）错义变异（missense variants）；3）3个与基因区域重叠的新型拷贝数缺失变异（copy number deletions）。综上，在ALS表型不一致的同卵双胞胎之间，未发现具有说服力的编码区或调控区核苷酸差异，以及全基因组范围的结构差异。本研究结果提示，未来仍需开展更多研究，以阐明可能参与散发性ALS易感性的环境、表观遗传（epigenetic）、寡基因（oligogenic）及体细胞遗传（somatic genetic）等潜在因素。