Genome and <scp>RNA</scp> sequencing boost neuromuscular diagnoses to 62% from 34% with exome sequencing alone
Rhett G. Marchant, Samantha J. Bryen, Melanie Bahlo, Anita Cairns, Katherine R. Chao, Alastair Corbett, Mark R. Davis, Vijay Ganesh, Roula Ghaoui, Kristi Jones, Andrew J. Kornberg, Monkol Lek, Christina Liang, Daniel G. MacArthur, Emily C. Oates, Anne O’Donnell‐Luria, Gina O’Grady, Ikeoluwa Osei‐Owusu, Haloom Rafehi, Stephen Reddel, Richard Roxburgh, Monique M. Ryan, Sarah A. Sandaradura, Liam W. Scott, Elise Valkanas, Ben Weisburd, Helen Young, Frances J. Evesson, Leigh B. Waddell, Sandra T. Cooper
Abstract
OBJECTIVE: Most families with heritable neuromuscular disorders do not receive a molecular diagnosis. Here we evaluate diagnostic utility of exome, genome, RNA sequencing, and protein studies and provide evidence-based recommendations for their integration into practice. METHODS: In total, 247 families with suspected monogenic neuromuscular disorders who remained without a genetic diagnosis after standard diagnostic investigations underwent research-led massively parallel sequencing: neuromuscular disorder gene panel, exome, genome, and/or RNA sequencing to identify causal variants. Protein and RNA studies were also deployed when required. RESULTS: Integration of exome sequencing and auxiliary genome, RNA and/or protein studies identified causal or likely causal variants in 62% (152 out of 247) of families. Exome sequencing alone informed 55% (83 out of 152) of diagnoses, with remaining diagnoses (45%; 69 out of 152) requiring genome sequencing, RNA and/or protein studies to identify variants and/or support pathogenicity. Arrestingly, novel disease genes accounted for <4% (6 out of 152) of diagnoses while 36.2% of solved families (55 out of 152) harbored at least one splice-altering or structural variant in a known neuromuscular disorder gene. We posit that contemporary neuromuscular disorder gene-panel sequencing could likely provide 66% (100 out of 152) of our diagnoses today. INTERPRETATION: Our results emphasize thorough clinical phenotyping to enable deep scrutiny of all rare genetic variation in phenotypically consistent genes. Post-exome auxiliary investigations extended our diagnostic yield by 81% overall (34-62%). We present a diagnostic algorithm that details deployment of genomic and auxiliary investigations to obtain these diagnoses today most effectively. We hope this provides a practical guide for clinicians as they gain greater access to clinical genome and transcriptome sequencing.