16P Limitation of short-reads NGS sequencing on genomic DNA: interest of functional studies in the diagnosis of congenital Ullrich muscular dystrophy

• Published in: Neuromuscular disorders : NMD Vol. 43; p. 104441
• Main Authors: Metay, C., Ghanem, R., Toutain, A., Bloch, A., Blin, E., Jobic, V., Pham, T., Lejeune, E., Buratti, J., Keren, B., Ader, F., Richard, P.
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.10.2024
• ISSN: 0960-8966
• DOI: 10.1016/j.nmd.2024.07.223

COLVI related myopathies include phenotypes ranging from severe forms (Ullrich congenital muscular dystrophy) to more moderate forms (Bethlem myopathy). They result from abnormalities in the expression and/or secretion of collagen VI (COLVI), a component of the extracellular matrix which is formed by the assembly of 3 chains alpha 1, alpha 2 and alpha 3 each encoded by the COL6A1-A2-A3 genes. Their diagnosis is based on clinical criteria, muscle MRI and genetic analyses. We present the case of a patient with a typical COLVI related myopathy phenotype but for whom initial NGS panel analyzes were not conclusive. Complementary techniques of protein and transcriptional studies allowed confirming the diagnosis. Blood gDNA of the proband was sequenced on a NGS panel containing coding sequences of genes associated with retractile myopathies including COL6A1, COL6A2 and COL6A3. COLVI expression was carried out by immunostaining on fibroblasts obtained from a skin biopsy. A transcriptomic study by RNA-seq on mRNA from fibroblasts made it possible to analyze aberrant splicing of COL6A1-A2-A3. As no variant of interest was retained on the NGS panel, COLVI immunostaining on fibroblasts was carried out and showed an alteration of its secretion with absence of COLVI network. Subsequently, a transcriptomic approach by RNA-seq showed the skipping of exon 11 in the heterozygous state in COL6A1. Reanalysis of the NGS .bam files allowed characterizing the deletion consisting in a short CNV involving part of both exon 11 and intron 11 of COL6A1. Familial segregation could show this was a de novo event. Given the very evocative clinic and thanks to functional studies, we identified the causal genetic variant allowing us to confirm the diagnosis of Ullrich myopathy. This example illustrates the importance of clinician-biologist dialogue, the limits of analyzes on genomic DNA, and the complementarity of functional tests in order to reduce diagnostic wandering.