@article{Rafehi01042025,
author = {Rafehi, Haloom and Fearnley, Liam G. and Read, Justin and Snell, Penny and Davies, Kayli C. and Scott, Liam and Gillies, Greta and Thompson, Genevieve C. and Field, Tess A. and Eldo, Aleena and Bodek, Simon and Butler, Ernest and Chen, Luke and Drago, John and Goel, Himanshu and Hackett, Anna and Halmagyi, G. Michael and Hannaford, Andrew and Kotschet, Katya and Kumar, Kishore R. and Kumble, Smitha and Lee-Archer, Matthew and Malhotra, Abhishek and Paine, Mark and Poon, Michael and Pope, Kate and Reardon, Katrina and Ring, Steven and Ronan, Anne and Silsby, Matthew and Smyth, Renee and Stutterd, Chloe and Wallis, Mathew and Waterston, John and Wellings, Thomas and West, Kirsty and Wools, Christine and Wu, Kathy H.C. and Szmulewicz, David J. and Delatycki, Martin B. and Bahlo, Melanie and Lockhart, Paul J.}, 
title = {A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia},
volume = {35}, 
number = {4}, 
pages = {769-785}, 
year = {2025}, 
doi = {10.1101/gr.279634.124}, 
abstract ={The cerebellar ataxias (CAs) are a heterogeneous group of disorders characterized by progressive incoordination. Seventeen repeat expansion (RE) loci have been identified as the primary genetic cause and account for >80% of genetic diagnoses. Despite this, diagnostic testing is limited and inefficient, often utilizing single gene assays. This study evaluates the effectiveness of long- and short-read sequencing as diagnostic tools for CA. We recruited 110 individuals (48 females, 62 males) with a clinical diagnosis of CA. Short-read genome sequencing (SR-GS) was performed to identify pathogenic RE and also non-RE variants in 356 genes associated with CA. Independently, long-read sequencing with adaptive sampling (LR-AS) was performed to identify pathogenic RE. SR-GS provided a genetic diagnosis for 38% of the cohort (40/110) including seven non-RE pathogenic variants. RE causes disease in 33 individuals, with the most common condition being SCA27B (n = 24). In comparison, LR-AS identified pathogenic RE in 29 individuals. RE identification for the two methods was concordant apart from four SCA27B cases not detected by LR-AS due to low read depth. For both technologies manual review of the RE alignment enhances diagnostic outcomes. Orthogonal testing for SCA27B revealed a 15% and 0% false positive rate for SR-GS and LR-AS, respectively. In conclusion, both technologies are powerful screening tools for CA. SR-GS is a mature technology currently used by diagnostic providers, requiring only minor changes in bioinformatic workflows to enable CA diagnostics. LR-AS offers considerable advantages in the context of RE detection and characterization but requires optimization before clinical implementation.}, 
URL = {http://genome.cshlp.org/content/35/4/769.abstract}, 
eprint = {http://genome.cshlp.org/content/35/4/769.full.pdf+html}, 
journal = {Genome Research} 
}