High Diagnostic Utility Incorporating a Targeted Neurodegeneration Gene Panel With MRI Brain Diagnostic Algorithms in Patients With Young-Onset Cognitive Impairment With Leukodystrophy

Using artificial intelligence and promoter-level transcriptome analysis to identify a biomarker as a possible prognostic predictor of cardiac complications in male patients with Fabry disease

Fabry disease is the most frequently occurring form of lysosomal disease in Japan, and is characterized by a wide variety of conditions. Primarily, the three major types of concerns associated with Fabry disease observed during adulthood that must be prevented are central nervous system, renal, and cardiac complications. Cardiac complications, such as cardiomyopathy, cardiac muscle fibrosis, and severe arrhythmia, are the most common mortality causes in patients with Fabry disease. To predict cardiac complications of Fabry disease, we extracted RNA from the venous blood of patients for cap analysis of gene expression (CAGE), performed likelihood ratio tests for each RNA expression dataset obtained from individuals with and without cardiac complications, and analyzed the correlation between cardiac functional factors observed using magnetic resonance imaging data extracted using artificial intelligence algorithms and RNA expression. Our findings showed that CHN1 expression was significantly higher in male Fabry disease patients with cardiac complications and that it could be associated with many cardiac functional factors. CHN1 encodes a GTPase-activating protein, chimerin 1, which is specific to the GTP-binding protein Rac (involved in oxidative stress generation and the promotion of myocardial fibrosis). Thus, CHN1 is a potential predictive biomarker of cardiac complications in Fabry disease; however, further studies are required to confirm this observation.

Spectrum of Leukodystrophy and Genetic Leukoencephalopathy in Indian Population Diagnosed by Clinical Exome Sequencing and Clinical Utility

Background and Objectives

Next-generation sequencing (NGS) has expedited the diagnostic process and unearthed many rare disorders in leukodystrophy (LD) and genetic leukoencephalopathy (gLE). Despite the progress in genomics, there is a paucity of data on the distribution of genetic white matter disorders (WMDs) and the diagnostic utility of NGS-based assays in a clinical setting. This study was initiated to explore the clinical, radiologic, and genetic spectrum of LD and gLE in the Indian population and also to estimate the diagnostic yield of clinical exome sequencing (CES).

Methods

This is a retrospective descriptive analysis of patients with a diagnosis of genetic WMDs from a single tertiary referral center who had CES performed as part of the diagnostic evaluation between January 2016 and December 2021. The demographic, clinical, radiologic, and genetic data were collected. The variants were classified using the American College of Medical Genetics and Genomics criteria. Pathogenic and likely pathogenic variants were included in the calculation of the diagnostic yield.

Results

In the study period, 138 patients were clinically diagnosed with either LD or gLE, of which 86 patients underwent CES. Pathogenic variants, likely pathogenic variants, and variants of uncertain significance with phenotype match were seen in 40 (41.8%), 13 (29.1%), and 15 (15.2%) patients, respectively. The mean age at onset in these 68 patients was 6.35 years (range 1 month-39 years), and 38 (55.9%) were male. LDs and gLE were diagnosed in 31 and 37 patients, respectively. 56 patients (71.8%) had autosomal recessive inheritance. The common clinical presentations were developmental delay (23.5%), psychomotor regression (20.6%), progressive myoclonic epilepsy syndrome (19.1%), and spastic ataxia (14.7%). Myelin disorders (48.5%) and leuko-axonopathies (41.2%) were the commonest type of disorders. The most frequently identified genes were ARSA, CLN5, ABCD1, CLN6, TPP1, HEXA, and L2HGDH. The diagnostic yield of the study was 61.6% (53/86), which increased to 79.1% when VUS with phenotype match were included.

Discussion

This study demonstrated a high diagnostic yield from proband-only CES in the evaluation of genetic WMDs and should be considered as a first-line investigation for genetic diagnosis.

Classification of Evidence

This study provides Class IV evidence that proband-only clinical exome sequencing is a useful "first-line investigation" for patients with genetic white matter disorders.

Modeling CSF-1 receptor deficiency diseases - how close are we?

The role of colony-stimulating factor-1 receptor (CSF-1R) in macrophage and organismal development has been extensively studied in mouse. Within the last decade, mutations in the CSF1R have been shown to cause rare diseases of both pediatric (Brain Abnormalities, Neurodegeneration, and Dysosteosclerosis, OMIM #618476) and adult (CSF1R-related leukoencephalopathy, OMIM #221820) onset. Here we review the genetics, penetrance, and histopathological features of these diseases and discuss to what extent the animal models of Csf1r deficiency currently available provide systems in which to study the underlying mechanisms involved.

Clinical and genetic spectrum of 104 Indian families with central nervous system white matter abnormalities

Genetic disorders with predominant central nervous system white matter abnormalities (CNS WMAs), also called leukodystrophies, are heterogeneous entities. We ascertained 117 individuals with CNS WMAs from 104 unrelated families. Targeted genetic testing was carried out in 16 families and 13 of them received a diagnosis. Chromosomal microarray (CMA) was performed for three families and one received a diagnosis. Mendeliome sequencing was used for testing 11 families and all received a diagnosis. Whole exome sequencing (WES) was performed in 80 families and was diagnostic in 52 (65%). Singleton WES was diagnostic for 50/75 (66.67%) families. Overall, genetic diagnoses were obtained in 77 families (74.03%). Twenty-two of 47 distinct disorders observed in this cohort have not been reported in Indian individuals previously. Notably, disorders of nuclear mitochondrial pathology were most frequent (9 disorders in 20 families). Thirty-seven of 75 (49.33%) disease-causing variants are novel. To sum up, the present cohort describes the phenotypic and genotypic spectrum of genetic disorders with CNS WMAs in our population. It demonstrates WES, especially singleton WES, as an efficient tool in the diagnosis of these heterogeneous entities. It also highlights possible founder events and recurrent disease-causing variants in our population and their implications on the testing strategy.