Poster Presentation 44th Lorne Genome Conference 2023

Genetic and transcriptomic sequencing analysis unveil the molecular genetics of neuromuscular disorders: a selection of case studies (#239)

Chiara Folland 1 , Mridul Johari 1 , Vijay S Ganesh 2 3 4 , Ben Weisburd 2 , Jevin Parmar 1 , Catriona McLean 5 6 , Paul Kennedy 5 6 , Andrew Kornberg 7 8 , Anne O'Donnell-Luria 2 4 9 , Heidi L Rehm 2 9 , Anita Cairns 10 , Phillipa J Lamont 11 , Igor Stevanovski 12 13 , Sanjog Chintalaphani 12 13 14 , Ira Deveson 12 13 14 , Gina Ravenscroft 1 15
  1. Centre for Medical Research, Harry Perkins Institute of Medical Research, Perth, WA, Australia
  2. Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
  3. Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
  4. Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
  5. Department of Anatomical Pathology, Alfred Health, Melbourne, Victoria, Australia
  6. Department of Medicine, Central Clinical School, Monash University, Melbourne, Victoria, Australia
  7. Murdoch Children's Research Institute, Melbourne, Victoria, Australia
  8. Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia
  9. Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
  10. Department of Neurosciences, Queensland Children's Hospital, Brisbane, QLD, Australia
  11. Neurogenetic Unit, Royal Perth Hospital, Perth, WA, Australia
  12. Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia
  13. Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, NSW, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
  14. School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
  15. School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia

Neuromuscular disorders (NMDs) are caused by genetic defects affecting the motoneurons, peripheral nerves, neuromuscular junctions, or skeletal muscle. Progress in the genetic diagnosis of NMD patients has been greatly accelerated since the implementation of high throughput sequencing technologies. However, approximately 50% of patients with NMDs do not have a molecular diagnosis following diagnostic gene panel or exome sequencing. Here we investigated the underlying molecular genetics of NMD patients for whom conventional diagnostic testing failed to yield a genetic diagnosis. Our approach leveraged a combination of short-read genome sequencing (GS), muscle transcriptome sequencing, and targeted programmable long-read sequencing. Where applicable, informatic tools including seqr, Expansion Hunter, Expansion Hunter De Novo, STRipy, OUTRIDER and FRASER were used to explore the breadth of genetic and transcriptomic variation, including short tandem repeat expansions, aberrant gene expression, and aberrant splicing events. We exemplify the utility of these approaches to achieve a genetic diagnosis through case studies. Transcriptome-guided GS analysis resolved a complex DMD inversion and a DIP2B ‘CGG’ expansion in a Duchenne muscular dystrophy patient with autism spectrum disorder. Long-read sequencing was used to validate and genotype these genetic findings. Using short- and long-read sequencing we identified a NOP56 hexanucleotide repeat expansion and clarified the repeat size in a spinocerebellar ataxia family. In a third example, using GS and seqr we identified a homozygous frameshift variant in the C-terminal region of JPH1 (NM_020647.4: c.1738del, p.(Leu580Trpfs*16) in a congenital myopathy patient. Previously, a heterozygous missense variant in JPH1 was implicated as a possible genetic modifier of GDAP1-associated Charcot-Marie-Tooth. Here, OUTRIDER identified significantly reduced expression of the JPH1 transcript in patient muscle transcriptome data. Investigations are ongoing to understand how loss-of-function JPH1 variants may result in a myopathy. Together, these case studies highlight the importance of leveraging multiple sequencing technologies to uncover the hidden heritability of NMD patients.