Spinal muscular atrophy (SMA) is a leading genetic cause of infant death, influenced by the copy number of two highly-homologous genes: SMN1 and SMN2. Although exome-seq is widely applied for genetic testing, SMA diagnosis and carrier screening have not been incorporated in routine exome-seq data analysis and lack of evaluation in clinical applications. We established a workflow for SMN gene copy number analysis based on unique-mapped reads on exon 7 of SMN genes and the control region. The workflow was retrospectively applied in the NICU cohort and validated with multiple ligation-dependent probe amplification. The predictions of our method are completely consistent with benchmark dataset (n=104). The retrospective analysis in the NICU cohort detected and confirmed eight SMN1 homozygous-deletions and 60 carriers (n=3,734). With multiple ligation-dependent probe amplification confirmation, the receiver operating characteristic curve analysis result showed the area under curve of 100% and 97.8%, respectively, in predicting SMN1 homozygous deletion and heterozygous deletion event, and 99.2% and 96.2%, respectively, in SMN2 deletion and duplication event. The results demonstrated favorable ability in both SMN1 and SMN2 copy number status prediction based on real clinical exome-seq data. This study provides a precise and portable workflow for both SMN1 and SMN2 copy number analysis based on exome-seq, assisting SMA diagnosing, carrier screening, and disease severity warning in clinical application.
Copyright © 2020. Published by Elsevier Inc.

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