Browsing by Author "Scott, Hamish S. (7402297583)"

Purpose: We set out to develop a publicly available tool that could accurately diagnose spinal muscular atrophy (SMA) in exome, genome, or panel sequencing data sets aligned to a GRCh37, GRCh38, or T2T reference genome. Methods: The SMA Finder algorithm detects the most common genetic causes of SMA by evaluating reads that overlap the c.840 position of the SMN1 and SMN2 paralogs. It uses these reads to determine whether an individual most likely has 0 functional copies of SMN1. Results: We developed SMA Finder and evaluated it on 16,626 exomes and 3911 genomes from the Broad Institute Center for Mendelian Genomics, 1157 exomes and 8762 panel samples from Tartu University Hospital, and 198,868 exomes and 198,868 genomes from the UK Biobank. SMA Finder's false-positive rate was below 1 in 200,000 samples, its positive predictive value was greater than 96%, and its true-positive rate was 29 out of 29. Most of these SMA diagnoses had initially been clinically misdiagnosed as limb-girdle muscular dystrophy. Conclusion: Our extensive evaluation of SMA Finder on exome, genome, and panel sequencing samples found it to have nearly 100% accuracy and demonstrated its ability to reduce diagnostic delays, particularly in individuals with milder subtypes of SMA. Given this accuracy, the common misdiagnoses identified here, the widespread availability of clinical confirmatory testing for SMA, and the existence of treatment options, we propose that it is time to add SMN1 to the American College of Medical Genetics list of genes with reportable secondary findings after genome and exome sequencing. © 2024 American College of Medical Genetics and Genomics

The significance of the autoimmune regulator (Aire) transcription regulator in establishing central tolerance has recently been elucidated in great detail. Still, the role of Aire in medullary thymic epithelial cell (mTEC) physiology is not fully understood. To shed more light on this issue, we studied the ultrastructure of mTECs in Aire-deficient thymus. We show that all types of mTECs show ultrastructural signs of activation and increased intracellular traffic, which suggests that in the absence of Aire their physiology is impaired. Type 6 'large' mTECs are fully developed in Aire-deficient mice and more frequent than in the normal thymus. The frequency of type 5 'undifferentiated' mTECs is also increased. Collectively, our results suggest that the role of Aire in the physiology of mTECs could be more profound and not restricted only to the presentation of self-tissue-restricted antigens and/or apoptosis of end-stage fully mature cell types. © 2010 Australasian Society for Immunology Inc. All rights reserved.

The significance of the autoimmune regulator (Aire) transcription regulator in establishing central tolerance has recently been elucidated in great detail. Still, the role of Aire in medullary thymic epithelial cell (mTEC) physiology is not fully understood. To shed more light on this issue, we studied the ultrastructure of mTECs in Aire-deficient thymus. We show that all types of mTECs show ultrastructural signs of activation and increased intracellular traffic, which suggests that in the absence of Aire their physiology is impaired. Type 6 'large' mTECs are fully developed in Aire-deficient mice and more frequent than in the normal thymus. The frequency of type 5 'undifferentiated' mTECs is also increased. Collectively, our results suggest that the role of Aire in the physiology of mTECs could be more profound and not restricted only to the presentation of self-tissue-restricted antigens and/or apoptosis of end-stage fully mature cell types. © 2010 Australasian Society for Immunology Inc. All rights reserved.