Complete sequencing of expanded SAMD12 repeats by long-read sequencing and Cas9-mediated enrichment.

A pentanucleotide TTTCA repeat insertion into a polymorphic TTTTA repeat element in SAMD12 causes benign adult familial myoclonic epilepsy. Although the precise determination of the entire SAMD12 repeat sequence is important for molecular diagnosis and research, obtaining this sequence remains challenging when using conventional genomic/genetic methods, and even short-read and long-read next-generation sequencing technologies have been insufficient. Incomplete information regarding expanded repeat sequences may hamper our understanding of the pathogenic roles played by varying numbers of repeat units, genotype-phenotype correlations, and mutational mechanisms. Here, we report a new approach for the precise determination of the entire expanded repeat sequence and present a workflow designed to improve the diagnostic rates in various repeat expansion diseases. We examined 34 clinically diagnosed benign adult familial myoclonic epilepsy patients, from 29 families using repeat-primed PCR, Southern blot, and long-read sequencing with Cas9-mediated enrichment. Two cases with questionable results from repeat-primed PCR and/or Southern blot were confirmed as pathogenic using long-read sequencing with Cas9-mediated enrichment, resulting in the identification of pathogenic SAMD12 repeat expansions in 76% of examined families (22/29). Importantly, long-read sequencing with Cas9-mediated enrichment was able to provide detailed information regarding the sizes, configurations, and compositions of the expanded repeats. The inserted TTTCA repeat size and the proportion of TTTCA sequences among the overall repeat sequences were highly variable, and a novel repeat configuration was identified. A genotype-phenotype correlation study suggested that the insertion of even short (TTTCA)14 repeats contributed to the development of benign adult familial myoclonic epilepsy. However, the sizes of the overall TTTTA and TTTCA repeat units are also likely to be involved in the pathology of benign adult familial myoclonic epilepsy. Seven unsolved SAMD12-negative cases were investigated using whole-genome long-read sequencing, and infrequent, disease-associated, repeat expansions were identified in two cases. The strategic workflow resolved two questionable SAMD12-positive cases and two previously SAMD12-negative cases, increasing the diagnostic yield from 69% (20/29 families) to 83% (24/29 families). This study indicates the significant utility of long-read sequencing technologies to explore the pathogenic contributions made by various repeat units in complex repeat expansions and to improve the overall diagnostic rate.

Long-read whole-genome sequencing identified a partial MBD5 deletion in an exome-negative patient with neurodevelopmental disorder.

Whole-exome sequencing (WES) can detect not only single-nucleotide variants in causal genes, but also pathogenic copy-number variations using several methods. However, there may be overlooked pathogenic variations in the out of target genome regions of WES analysis (e.g., promoters), leaving many patients undiagnosed. Whole-genome sequencing (WGS) can potentially analyze such regions. We applied long-read nanopore WGS and our recently developed analysis pipeline "dnarrange" to a patient who was undiagnosed by trio-based WES analysis, and identified a heterozygous 97-kb deletion partially involving 5'-untranslated exons of MBD5, which was outside the WES target regions. The phenotype of the patient, a 32-year-old male, was consistent with haploinsufficiency of MBD5. The transcript level of MBD5 in the patient's lymphoblastoid cells was reduced. We therefore concluded that the partial MBD5 deletion is the culprit for this patient. Furthermore, we found other rare structural variations (SVs) in this patient, i.e., a large inversion and a retrotransposon insertion, which were not seen in 33 controls. Although we considered that they are benign SVs, this finding suggests that our pipeline using long-read WGS is useful for investigating various types of potentially pathogenic SVs. In conclusion, we identified a 97-kb deletion, which causes haploinsufficiency of MBD5 in a patient with neurodevelopmental disorder, demonstrating that long-read WGS is a powerful technique to discover pathogenic SVs.

Sarcoplasmic MxA expression: A valuable marker of dermatomyositis.

OBJECTIVE: To evaluate the diagnostic value of myxovirus resistance A (MxA) expression in the cytoplasm of myofibers in the diagnosis of dermatomyositis (DM). METHODS: We assessed the sensitivity and specificity of the sarcoplasmic expression of MxA in muscles with DM by immunohistochemistry in consecutive cases of DM (n = 34) and other idiopathic inflammatory myopathies (n = 120: 8 with polymyositis, 16 with anti-tRNA-synthetase antibody-associated myositis, 46 with immune-mediated necrotizing myopathy, and 50 with inclusion body myositis) and compared them with conventional pathologic hallmarks of DM, including perifascicular atrophy (PFA) and membrane attack complex (MAC) deposition on endomysial capillaries. RESULTS: The sensitivity and specificity of sarcoplasmic MxA expression were 71% and 98%, respectively. While the specificity was almost comparable to that of PFA and capillary MAC deposition, the sensitivity was higher, with PFA showing 47% sensitivity and 98% specificity and capillary MAC deposition showing 35% sensitivity and 93% specificity. Of note, in patients with DM with typical skin rash but no PFA, 44% of the samples showed sarcoplasmic MxA expression, which was higher than the 17% sensitivity of capillary MAC deposition in the population. CONCLUSIONS: Sarcoplasmic MxA expression detected by immunohistochemistry is a more sensitive marker of DM than the conventional hallmarks, indicating its practical utility in the diagnosis of DM. It may well be included in the routine immunohistochemistry panel for myositis. CLASSIFICATION OF EVIDENCE: This study provides Class II evidence that immunohistochemistry-detected sarcoplasmic MxA expression accurately identifies patients with dermatomyositis.

Hepatitis C virus infection in inclusion body myositis: A case-control study.

OBJECTIVE: To clarify whether there is any association between inclusion body myositis (IBM) and hepatitis C virus (HCV) infection. METHODS: We assessed the prevalence of HCV infection in 114 patients with IBM whose muscle biopsies were analyzed pathologically for diagnostic purpose from 2002 to 2012 and in 44 age-matched patients with polymyositis diagnosed in the same period as a control by administering a questionnaire survey to the physicians in charge. We also compared clinicopathologic features including the duration from onset to development of representative symptoms of IBM and the extent of representative pathologic changes between patients with IBM with and without HCV infection. RESULTS: A significantly higher number of patients with IBM (28%) had anti-HCV antibodies as compared with patients with polymyositis (4.5%; odds ratio 8.2, 95% confidence interval 1.9-36) and the general Japanese population in their 60s (3.4%). Furthermore, between patients with IBM with and without HCV infection, we did not find any significant difference in the clinicopathologic features, indicating that the 2 groups have essentially the same disease regardless of HCV infection. CONCLUSION: Our results provide the statistical evidence for an association between IBM and HCV infection, suggesting a possible pathomechanistic link between the 2 conditions.

Anti-myelin oligodendrocyte glycoprotein (MOG) antibodies in a Japanese boy with recurrent optic neuritis.

BACKGROUND: Myelin oligodendrocyte glycoprotein (MOG) localizes on the outermost surface of the myelin sheath and oligodendrocytes in the central nervous system (CNS). Autoantibodies against MOG are reportedly found in patients with spectrum of inflammatory demyelinating diseases of the CNS, including acute disseminated encephalomyelitis, multiple sclerosis, and neuromyelitis optica. In addition, recent studies have emphasized an association between anti-MOG antibodies and optic neuritis. PATIENT: We present the first case report of a 7-year-old Japanese boy who was positive for anti-MOG antibodies. He experienced four episodes of unilateral optic neuritis and one seizure event. Magnetic resonance imaging revealed T2-hyperintense lesions in the subcortical white matter and midbrain. Although he fulfilled the diagnostic criteria for multiple sclerosis, recombinant interferon beta did not prevent recurrence. Established cell-based immunoassays revealed that he was positive for anti-MOG antibodies and negative for anti-aquaporin 4 antibodies. CONCLUSIONS: Our case report supports the relationship between anti-MOG antibodies and recurrent optic neuritis. Additional studies are needed to establish the clinical significance of anti-MOG antibodies for diagnosis, treatment, and prognosis.

Utility of real-time three-dimensional echocardiography for Duchenne muscular dystrophy with echocardiographic limitations.

Duchenne muscular dystrophy (DMD) is strongly associated with a unique form of dilated cardiomyopathy. Cardiac complications are the leading cause of death in DMD; thus, longitudinal assessments and early intervention for cardiac dysfunction are necessary to improve prognosis. Two-dimensional echocardiography, which is routinely used for cardiac assessment, has some limitations for quantitative analyses in DMD patients with thoracic deformities and regional wall motion abnormalities in the left ventricle. Recently, real-time three-dimensional echocardiography has emerged as a feasible tool for cardiac assessment in various cardiac diseases. The aim of this study was to examine the utility of this technology in DMD. We evaluated left ventricular ejection fraction (LVEF), a major parameter of left ventricular function, in 17 male DMD patients. LVEF values measured by real-time three-dimensional echocardiography were compared with those determined by two established nuclear cardiology methods: "the first-pass method of radionuclide angiocardiography" and "quantitative electrocardiogram-gated single-photon emission computed tomography". A good correlation was observed for LVEF values, particularly between real-time three-dimensional echocardiography and "the first-pass method of radionuclide angiocardiography" (r=0.90, p<0.05). Thus, real-time three-dimensional echocardiography can provide an accurate measurement of LVEF in DMD patients with echocardiographic limitations.

Acid phosphatase-positive globular inclusions is a good diagnostic marker for two patients with adult-onset Pompe disease lacking disease specific pathology.

Diagnosis of adult-onset Pompe disease is sometimes challenging because of its clinical similarities to muscular dystrophy and the paucity of disease-specific vacuolated fibers in the skeletal muscle pathology. We describe two patients with adult-onset Pompe disease whose muscle pathology showed no typical vacuolated fibers but did show unique globular inclusions with acid phosphatase activity. The acid phosphatase-positive globular inclusions may be a useful diagnostic marker for adult-onset Pompe disease even when typical vacuolated fibers are absent.