[P3-123] Enhanced Detection of CNVs in LAMA2 using NGS/CGH Microarrays and Breakpoints Study
Autosomal recessive laminin-2 deficient congenital muscular dystrophy (CMD) is caused by mutations in the LAMA2 gene. Approximately 20% of the mutations associated with laminin-2 deficient CMD are gross deletions or duplications, that is, copy number variation (CNV). In previous study, we diagnosed 82 cases from 69 families with laminin-2 deficient muscular dystrophy genetically. Among them, there were 27 cases from 25 families have deletions of one or more exons using current multiplex ligation-dependent probe amplification (MLPA) method. However, MLPA has limits of resolution and cannot identify precise breakpoints of LAMA2 CNVs. Here, we developed a whole genome sequencing of LAMA2 using NGS and a high-density oligonucleotide-based comparative genomic hybridization (CGH) microarray targeting LAMA2 gene. We have found three Chinese CMD patients carrying exon 4 deletion in previous study. In this study, we identified another four MLPA-negative patients carrying exon 4 deletion using CGH. Totally, there are 27 cases (from 82 cases) have CNVs, the allele frequency which carry CNVs is 18.3%. We performed further study to identify the breakpoints. In addition, a specific polymerase chain reaction assay was used to confirm the identical deletion of 5823 bp involving LAMA2 exon 4 in all seven patients and their carrier parents. Our observations suggest that this deletion could be derived from a founder in the Chinese population. A 5-bp microhomology was shown at the deletion junctions, suggesting that the CNV mutational mechanism is of microhomology-mediated break-induced replication.