Poster Presentation 41st Lorne Genome Conference 2020

Advances in repeat expansion disorders: New tools for faster diagnosis and novel gene discovery (#204)

Melanie Bahlo 1 , Haloom Rafehi 1 , David J Szmulewicz 2 , Rick M Tankard 3 , Egor Dolzhenko 4 , Michael A Eberle 4 , Mark F Bennett 1 , Martin B Delatycki 5 , Paul J Lockhart 6
  1. Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
  2. Cerebellar Ataxia Clinic, Neuroscience Department, Alfred Health, Melbourne, VIC, Australia
  3. Mathematics and Statistics, Murdoch University, Perth, WA, Australia
  4. Illumina, San Diego, California, USA
  5. Victorian Clinical Genetics Service, Murdoch Childrens Research Institute, Melbourne, VIC, Australia
  6. Bruce Lefroy Centre, Murdoch Childrens Research Institute, Parkville, VIC, Australia

NGS technologies are revolutionizing diagnostics and clinical medicine. However, these approaches have previously proven inefficient at identifying pathogenic repeat expansions (RE), which underlie at least 30 inherited human conditions such as ataxia, Fragile X and Friedreich ataxia. These disorders occur when a short tandem repeat (STR) is expanded beyond a locus-specific threshold. RE disorders display a broad onset age and can present with overlapping phenotypes, making clinical and molecular diagnoses challenging. Traditionally, molecular testing for RE has utilised single-gene PCR-based methods, however these can be slow and costly and often yield no result. We recently developed exSTRa (expanded short tandem repeat algorithm, [1]), which interrogates NGS data to identify RE. We demonstrated the tool could identify 11 of 12 common RE with high specificity and sensitivity, suggesting considerable clinical utility in comparison to current molecular testing methods.

One limitation of exSTRa and similar RE detection algorithms is the need to provide the genomic co-ordinates of STRs to be interrogated [2], precluding genome-wide discovery of novel RE. Here we applied a pipeline of bioinformatics tools, testing for both novel and known RE, to a cohort of 22 families with a clinical diagnosis of cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS). Genome-wide analysis identified a novel recessively inherited intronic RE [(AAGGG)exp] in the gene encoding Replication Factor C1 (RFC1). Genetic analyses confirmed the pathogenic RE in 18 CANVAS families, demonstrating it is the predominant cause of this disorder [3].

In conclusion, these studies have demonstrated that improved bioinformatics tools increase the diagnostic utility of NGS to determine the genetic basis of a heterogeneous group of clinically overlapping neurogenetic disorders. They provide a powerful new approach for the identification of novel RE and add to the evidence base for implementation of WGS as cost effective single test for molecular diagnostics.

  1. Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data. Tankard RM, Bennett MF, Degorski P, Delatycki MB, Lockhart PJ, Bahlo M. Am J Hum Genet. 2018;103(6):858-873.
  2. Recent advances in the detection of repeat expansions with short-read next-generation sequencing. Bahlo M, Bennett MF, Degorski P, Tankard RM, Delatycki MB, Lockhart PJ. F1000Res. 2018;7. pii: F1000 Faculty Rev-736.
  3. Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS. Rafehi H, Szmulewicz DJ, Bennett MF, Sobreira NLM, Pope K, Smith KR, Gillies G, Diakumis P, Dolzhenko E, Eberle MA, Barcina MG, Breen DP, Chancellor AM, Cremer PD, Delatycki MB, Fogel BL, Hackett A, Halmagyi GM, Kapetanovic S, Lang A, Mossman S, Mu W, Patrikios P, Perlman SL, Rosemergy I, Storey E, Watson SRD, Wilson MA, Zee DS, Valle D, Amor DJ, Bahlo M, Lockhart PJ. Am J Hum Genet. 2019;105(1):151-165.