Nicola Whiffin^1
1University of Oxford 

Untranslated regions (UTRs) are the regions directly up- and down-stream of the protein-coding regions of a gene that are transcribed into RNA, but do not form part of the final protein sequence. They have very important roles in regulating RNA stability, RNA localisation, and the rate of protein translation. I will discuss a variety of approaches that we have used to identify UTR variants with a role in rare disease. I will also show tools that we have developed to aid in identification and annotation of these variants in clinical settings.

Retrotransposons, a type of mobile DNA that spread in the germline via a 'copy-and-paste' mechanism, occupy approximately half of the human genome. They are a major source of innovation in gene regulatory networks, as well as pathogenic mutations. The repetitive nature of retrotransposons has however left them understudied relative to their genomic footprint. My lab has pioneered the application of long-read 'omics approaches to study human retrotransposons. In this talk, I will give a general overview of how retrotransposons can contribute to disease and their potential use in diagnostics. I will then focus on our lung squamous cell carcinoma (LUSC) datasets, where are primarily composed of long-read Oxford Nanopore Technologies (ONT) methylome and Pacific Biosciences (PacBio) transcriptome sequencing. The results obtained from this cohort suggest retrotransposons can be used to discriminate tumour and non-tumour cells, and mined for potential immunotherapy targets.

David R. Thorburn^1,2,3
1Murdoch Children’s Research Institute, Melbourne, Australia

 ²University of Melbourne, Parkville, Australia 

³Victorian Clinical Genetics Services, Melbourne, Australia

In patients suspected of mitochondrial disease, a “genomics first” approach has largely replaced traditional enzyme and histochemical testing. Reported genomic diagnostic yields are typically 30-60% but depend on both the methods used and recruitment criteria. For example, our recent Australian Genomics Mito Flagship national study included 140 probands with pediatric- or adult-onset suspected mitochondrial disease . Initial sequencing used blood DNA. Proteomic or other follow-up analyses were performed when feasible. Overall diagnostic yield was 55%, but higher in paediatric-onset (71%) than adult-onset (31%) cases. 29% of diagnoses were in non-mito genes (mito mimics). These findings reflect the broad clinical features of mito that overlap hundreds of other conditions, along with ascertainment bias and loss of some mtDNA variants from blood in adults. 

MitoMDT is an MRFF-funded national study recruiting families with suspected mitochondrial disease to apply multi-Omic technologies seeking to improve overall diagnostic rates to over 70%. It combines researchers, clinicians and lab experts from around Australia with expertise in mitochondrial disease, genomics, transcriptomics, quantitative proteomics, metabolomics, computational biology and targeted functional testing. Initial results have provided evidence to upgrade VUS in multiple genes to Likely Pathogenic or Pathogenic as well as validating a novel disease gene.