A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia

Rafehi, H; Fearnley, LG; Read, J; Snell, P; Davies, KC; Scott, L; Gillies, G; Thompson, GC; Field, TA; Eldo, A; Bodek, S; Butler, E; Chen, L; DRAGO, J; Goel, H; Hackett, A; Halmagyi, GM; Hannaford, A; Kotschet, K; Kumar, KR; Kumble, S; Lee-Archer, M; Malhotra, A; PAINE, M; Poon, M; Pope, K; Reardon, K; Ring, S; Ronan, A; Silsby, M; Smyth, R; Stutterd, C; Wallis, M; Waterston, J; Wellings, T; West, K; Wools, C; Wu, KHC; Szmulewicz, DJ; Delatycki, MB; Bahlo, M; Lockhart, PJ

Author(s): Rafehi, H; Fearnley, LG; Read, J; Snell, P; Davies, KC; Scott, L; Gillies, G; Thompson, GC; Field, TA; Eldo, A; Bodek, S; Butler, E; Chen, L; DRAGO, J; Goel, H; Hackett, A; Halmagyi, GM; Hannaford, A; Kotschet, K; Kumar, KR; Kumble, S; Lee-Archer, M; Malhotra, A; PAINE, M; Poon, M; Pope, K; Reardon, K; Ring, S; Ronan, A; Silsby, M; Smyth, R; Stutterd, C; Wallis, M; Waterston, J; Wellings, T; West, K; Wools, C; Wu, KHC; Szmulewicz, DJ; Delatycki, MB; Bahlo, M; Lockhart, PJ;
Details: Publication Year 2025-04-14,Volume 35,Issue #4,Page 769-785
Journal Title: Genome Reearch
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.
Publisher: CSH Press
Keywords: Humans; Male; Female; *Cerebellar Ataxia/genetics/diagnosis; Middle Aged; Adult; Prospective Studies; *High-Throughput Nucleotide Sequencing/methods; DNA Repeat Expansion; *Genetic Testing/methods; Sequence Analysis, DNA/methods; Aged; Whole Genome Sequencing/methods; Adolescent; Genome, Human
Research Division(s): Genetics and Gene Regulation
PubMed ID: 40015980
Publisher's Version: https://doi.org/10.1101/gr.279634.124
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2025-05-05 08:40:26

Last Modified: 2025-05-05 08:40:35