Novel mutation identification and copy number variant detection via exome sequencing in congenital muscular dystrophy

• Published in: Molecular genetics & genomic medicine Vol. 8; no. 11; pp. e1387 - n/a
• Main Authors: Cauley, Edmund S., Pittman, Alan, Mummidivarpu, Swati, Karimiani, Ehsan G., Martinez, Samantha, Moroni, Isabella, Boostani, Reza, Podini, Daniele, Mora, Marina, Jamshidi, Yalda, Hoffman, Eric P., Manzini, M. Chiara
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.11.2020; John Wiley and Sons Inc; Wiley
• Subjects: Alleles; Biopsy; CNV analysis; Congenital diseases; congenital muscular dystrophy; Copy number; Data analysis; Deoxyribonucleic acid; DNA; Dystrophy; exome sequencing; Genomes; Genomics; Heterozygosity; LAMA2; Laminin; Magnetic resonance imaging; Medical imaging; Muscular dystrophy; Mutation; Neuroimaging; Nucleotides; Original; Patients; Proteins; Sequences; Splicing; congenital muscular dystrophy; exome sequencing; LAMA2; CNV analysis
• ISSN: 2324-9269; 2324-9269
• DOI: 10.1002/mgg3.1387

Background Congenital muscular dystrophy type 1A (MDC1A), also termed merosin‐deficient congenital muscular dystrophy (CMD), is a severe form of CMD caused by mutations in the laminin α2 gene (LAMA2). Of the more than 300 likely pathogenic variants found in the Leiden Open Variant Database, the majority are truncating mutations leading to complete LAMA2 loss of function, but multiple copy number variants (CNVs) have also been reported with variable frequency. Methods We collected a cohort of individuals diagnosed with likely MDC1A and sought to identify both single nucleotide variants and small and larger CNVs via exome sequencing by extending the analysis of sequencing data to detect splicing changes and CNVs. Results Standard exome analysis identified multiple novel LAMA2 variants in our cohort, but only four cases carried biallelic variants. Since likely truncating LAMA2 variants are often found in heterozygosity without a second allele, we performed additional splicing and CNV analysis on exome data and identified one splice change outside of the canonical sequences and three CNVs, in the remaining four cases. Conclusions Our findings support the expectation that a portion of MDC1A cases may be caused by at least one CNV allele and show how these changes can be effectively identified by additional analysis of existing exome data. Exome sequencing analysis can identify both novel single nucleotide variants (SNVs) and copy number variants (CNVs) in LAMA2 in congenital muscular dystrophy cases. When only one SNV allele is found, additional CNV analysis can provide a full genetic diagnosis.