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. 2021 May;42(5):626-638.
doi: 10.1002/humu.24191. Epub 2021 Mar 19.

A single NGS-based assay covering the entire genomic sequence of the DMD gene facilitates diagnostic and newborn screening confirmatory testing

Babi R R Nallamilli  1 , Alka Chaubey  1 , C A Valencia  1 , Leah Stansberry  1 , Andrea M Behlmann  1 , Zeqiang Ma  1 , Abhinav Mathur  1 , Suresh Shenoy  1 , Vidya Ganapathy  2 , Lakshmanan Jagannathan  1 , Vinish Ramachander  1 , Alessandra Ferlini  3 , Lora Bean  1 , Madhuri Hegde  1
Affiliations

A single NGS-based assay covering the entire genomic sequence of the DMD gene facilitates diagnostic and newborn screening confirmatory testing

Babi R R Nallamilli et al. Hum Mutat. 2021 May.

Abstract

Molecular diagnosis for Duchenne and Becker muscular dystrophies (DMD/BMD) involves a two-tiered approach for detection of deletions/duplications using MLPA or array CGH, followed by sequencing of coding and flanking intronic regions to detect sequence variants, which is time-consuming and expensive. We have developed a comprehensive next-generation sequencing (NGS)-based single-step assay to sequence the entire 2.2 Mb of the DMD gene to detect all copy number and sequence variants in both index males and carrier females. Assay validation was 100% concordant with other methodologies. A total of 772 samples have been tested, of which 62% (N = 480) were index cases with a clinical suspicion of DMD. Carrier testing females account for 38% (N = 292). Molecular diagnosis was confirmed in 86% (N = 413) of the index cases. Intragenic deletions and duplications (single-exon or multi-exon) were detected in 60% (N = 247) and 14% (N = 58) of the index cases, respectively. Full-sequence analysis of the entire gene allows for detection of deep intronic pathogenic variants and accurate breakpoint detection of CNVs involving similar exons, which could have an impact on the outcome of clinical trials. This comprehensive assay is highly sensitive for diagnostic testing for DMD and is also suitable for confirmatory testing for newborn screening for DMD.

Keywords: DMD; Duchenne muscular dystrophy; molecular diagnosis; newborn screening; next-generation sequencing.

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