RT Journal
A1 Rafehi, Haloom
A1 Fearnley, Liam G.
A1 Read, Justin
A1 Snell, Penny
A1 Davies, Kayli C.
A1 Scott, Liam
A1 Gillies, Greta
A1 Thompson, Genevieve C.
A1 Field, Tess A.
A1 Eldo, Aleena
A1 Bodek, Simon
A1 Butler, Ernest
A1 Chen, Luke
A1 Drago, John
A1 Goel, Himanshu
A1 Hackett, Anna
A1 Halmagyi, G. Michael
A1 Hannaford, Andrew
A1 Kotschet, Katya
A1 Kumar, Kishore R.
A1 Kumble, Smitha
A1 Lee-Archer, Matthew
A1 Malhotra, Abhishek
A1 Paine, Mark
A1 Poon, Michael
A1 Pope, Kate
A1 Reardon, Katrina
A1 Ring, Steven
A1 Ronan, Anne
A1 Silsby, Matthew
A1 Smyth, Renee
A1 Stutterd, Chloe
A1 Wallis, Mathew
A1 Waterston, John
A1 Wellings, Thomas
A1 West, Kirsty
A1 Wools, Christine
A1 Wu, Kathy H.C.
A1 Szmulewicz, David J.
A1 Delatycki, Martin B.
A1 Bahlo, Melanie
A1 Lockhart, Paul J.
T1 A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia
JF Genome Research 
JO Genome Research 
YR 2025 
FD April 01 
VO 35 
IS 4 
SP 769 
OP 785 
DO 10.1101/gr.279634.124 
UL http://genome.cshlp.org/content/35/4/769.abstract 
AB 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.