We developed a diagnostic method for repeat expansion diseases using a long-read sequencer to improve currently available, low throughput diagnostic methods. We employed the real-time target enrichment system of the nanopore GridION sequencer using the adaptive sampling option, in which software-based target assignment is available without prior sample enrichment, and built an analysis pipeline that prioritized the disease-causing loci. Twenty-two patients with various neurological and neuromuscular diseases, including 12 with genetically diagnosed repeat expansion diseases and 10 manifesting cerebellar ataxia, but without genetic diagnosis, were analyzed. We first sequenced the 12 molecularly diagnosed patients and accurately confirmed expanded repeats in all with uniform depth of coverage across the loci. Next, we applied our method and a conventional method to 10 molecularly undiagnosed patients. Our method corrected inaccurate diagnoses of two patients by the conventional method. Our method is superior to conventional diagnostic methods in terms of speed, accuracy, and comprehensiveness.

Amyotrophic lateral sclerosis (ALS) is a devastating progressive motor neuron disease that affects people of all ethnicities. Approximately 90% of ALS cases are sporadic and thought to have multifactorial pathogenesis. To understand the genetics of sporadic ALS, we conducted a genome-wide association study using 1,173 sporadic ALS cases and 8,925 controls in a Japanese population. A combined meta-analysis of our Japanese cohort with individuals of European ancestry revealed a significant association at the ACSL5 locus (top SNP p = 2.97 × 10⁻⁸). We validated the association with ACSL5 in a replication study with a Chinese population and an independent Japanese population (1941 ALS cases, 3821 controls; top SNP p = 1.82 × 10⁻⁴). In the combined meta-analysis, the intronic ACSL5 SNP rs3736947 showed the strongest association (p = 7.81 × 10⁻¹¹). Using a gene-based analysis of the full multi-ethnic dataset, we uncovered additional genes significantly associated with ALS: ERGIC1, RAPGEF5, FNBP1, and ATXN3. These results advance our understanding of the genetic basis of sporadic ALS.

The biodiversity of photosynthetic eukaryotes, traditionally recognized as nine algal divisions or phyla, is attributed to two kinds of endosymbiotic events involving plastids: primary endosymbiosis and secondary endosymbiosis. Therefore, the phylogenetic positions of primary photosynthetic eukaryotes are fundamental for understanding the evolution of eukaryotic cells and establishing higher taxonomic concepts of eukaryotes. Recently, Rodríguez-Ezpeleta et al. (2005) demonstrated the strong monophyly of the three groups of primary photosynthetic eukaryotes (green plants, glaucophytes, and red algae) based on 143 nuclear genes. However, they analyzed only two divisions of the secondary phototrophs belonging to the Stramenopiles–Alveolata (SA) lineage, and their 143 genes included rapidly evolving genes. Here, we reexamine the phylogeny of the primary phototrophs based on slowly evolving nuclear genes selected mainly from the data matrix of Rodríguez-Ezpeleta et al. (2005), using additional operational taxonomic units (OTUs) of a free-living, secondary phototrophic group (Haptophyta) and of Excavata (Heterolobosea and Reclinomonas) that do not belong to the SA lineage. Our phylogenetic results demonstrate the robust non-monophyly of the primary phototrophs and the basal position of red algae within the bikonts, suggesting the loss of plastids in certain eukaryotic lineages under the assumption of the single plastid primary endosymbiosis.