MDNSW PhD Scholar, Sam Bryen, completes her thesis

I work at the Kids Neuroscience Centre, part of Kids Research at the Children’s Hospital at Westmead, in a team with many years of experience genetically diagnosing families with neuromuscular disorders. For the past 3 years MDNSW have supported me financially to complete my PhD degree, by providing me with the Sue Connor scholarship. I’m excited to announce that I have finally submitted my thesis last month!

Our team has a cohort of 227 families with neuromuscular disorders, which were referred to us from clinicians in Australia and New Zealand. The families that are referred to us typically have already undergone many genetic tests that haven’t revealed any answers. My PhD project focused on finding the genetic diagnosis for these undiagnosed families. Specifically, I studied genetic variants that disrupt the cellular process of pre-mRNA splicing, or “splicing variants” for short. Splicing variants are often missed by the standard genetic tests available for undiagnosed individuals with neuromuscular conditions. Therefore, by understanding how to better detect and interpret this type of genetic variant, we aimed to increase the diagnostic rates of neuromuscular disorders.

The work I did during my PhD helped to provide genetic answers for 51 affected individuals from 37 families, who presented with a range of neuromuscular conditions. To find a genetic diagnosis for these families, our team collaborated with the Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard in Boston. We sent DNA from our families to the Broad Institute, where they performed extensive genetic sequencing and provided us with large amounts of data to analysis. I spent many hours trawling through this data looking through the large numbers of genetic variants that each person has, searching for just the 1 or 2 variants that could be the cause of a neuromuscular condition. Once we found a plausible candidate we would then aim to provide functional evidence to show that this was (or was not) the cause of a neuromuscular condition. By performing experiments in our lab that look at DNA, RNA and/or protein extracted from blood, muscle, and/or skin fibroblasts, we were able to show how these genetic variants could lead to a muscle or nerve defect, enabling a diagnosis to be established for these 37 families.

A subset of these diagnoses led to the discovery of new or under recognised disease mechanisms associated with the splicing variants we identified. By publishing this data, we were able to share these discoveries with the scientific community. In total, my thesis contained six publications and two draft manuscripts describing the complex splicing variants and disease mechanisms we discovered. These studies and publications often involved the collective expertise of clinicians and scientist from all over the world. Whilst co-ordinating these large international projects was challenging; it was also rewarding to be able to contribute to diagnostic research overseas. The described molecular mechanisms and case reports within my thesis will continue to assist clinicians and variant curators globally to find a genetic diagnosis for families affected by genetic disorders.

The genetic diagnoses provided had far reaching benefits for affected individuals and their families, often ending long diagnostic odysseys of 10+ years. Clinical management for affected individuals were often guided by genetic findings. For example, two affected siblings with congenital myasthenic syndrome were prescribed salbutamol, a treatment known to be effective for the gene we identified as causal, which significantly improved their mobility and quality of life. Family planning options also became available for some families. I found it incredibly rewarding to be able to help these families find genetic answers.

To date, we have diagnosed 56% of families in our cohort and finding the genetic diagnosis for the remaining families continues to be a major focus of our research (where funding allows). In time, the diagnostic approaches we have taken will become increasingly accessible to affected individuals with suspected inherited neuromuscular diseases as the cost-effectiveness and clinical utility are realised. Already we are seeing increased availability of some of these sequencing technologies being used in standard diagnostic pipelines compared to when I first started my PhD. It is my hope that the work presented with my thesis will help pave the way for better detection and classification of splicing variants in the future. Accurately identifying and classifying splicing variants will take us one step closer to providing a genetic diagnosis for every family with a suspected genetic disorder.

I am incredibly grateful for all the financial support provided by MDNSW that enabled me to complete this body of work. I would also like to thank MDNSW for inviting me to the Neuromuscular Information and Research Days which enriched my understanding and appreciation of the challenges faced by those living with neuromuscular disorders. I am honoured to have been given the opportunity to help this inspirational community with my research. Thank you to the individuals and families in Australia and around the world who agreed to participate in this project.

  • Article written by Sam, Bryen, PhD Scholar