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

IF 6.2 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Genome research Pub Date : 2025-02-27 DOI:10.1101/gr.279634.124

Haloom Rafehi, Liam G. Fearnley, Justin Read, Penny Snell, Kayli C. Davies, Liam Scott, Greta Gillies, Genevieve C. Thompson, Tess A. Field, Aleena Eldo, Simon Bodek, Ernest Butler, Luke Chen, John Drago, Himanshu Goel, Anna Hackett, G. Michael Halmagyi, Andrew Hannaford, Katya Kotschet, Kishore R. Kumar, Smitha Kumble, Matthew Lee-Archer, Abhishek Malhotra, Mark Paine, Michael Poon, Kate Pope, Katrina Reardon, Steven Ring, Anne Ronan, Matthew Silsby, Renee Smyth, Chloe Stutterd, Mathew Wallis, John Waterston, Thomas Wellings, Kirsty West, Christine Wools, Kathy H.C. Wu, David J. Szmulewicz, Martin B. Delatycki, Melanie Bahlo, Paul J. Lockhart

{"title":"A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia","authors":"Haloom Rafehi, Liam G. Fearnley, Justin Read, Penny Snell, Kayli C. Davies, Liam Scott, Greta Gillies, Genevieve C. Thompson, Tess A. Field, Aleena Eldo, Simon Bodek, Ernest Butler, Luke Chen, John Drago, Himanshu Goel, Anna Hackett, G. Michael Halmagyi, Andrew Hannaford, Katya Kotschet, Kishore R. Kumar, Smitha Kumble, Matthew Lee-Archer, Abhishek Malhotra, Mark Paine, Michael Poon, Kate Pope, Katrina Reardon, Steven Ring, Anne Ronan, Matthew Silsby, Renee Smyth, Chloe Stutterd, Mathew Wallis, John Waterston, Thomas Wellings, Kirsty West, Christine Wools, Kathy H.C. Wu, David J. Szmulewicz, Martin B. Delatycki, Melanie Bahlo, Paul J. Lockhart","doi":"10.1101/gr.279634.124","DOIUrl":null,"url":null,"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 (<em>n</em> = 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.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"55 4 1","pages":""},"PeriodicalIF":6.2000,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1101/gr.279634.124","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

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.

查看原文本刊更多论文

求助全文

约1分钟内获得全文求助全文

来源期刊

Genome research 生物-生化与分子生物学

CiteScore

12.40

自引率

1.40%

发文量

140

审稿时长

6 months

期刊介绍： Launched in 1995, Genome Research is an international, continuously published, peer-reviewed journal that focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine. Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. The journal also features exciting gene discoveries and reports of cutting-edge computational biology and high-throughput methodologies. New data in these areas are published as research papers, or methods and resource reports that provide novel information on technologies or tools that will be of interest to a broad readership. Complete data sets are presented electronically on the journal''s web site where appropriate. The journal also provides Reviews, Perspectives, and Insight/Outlook articles, which present commentary on the latest advances published both here and elsewhere, placing such progress in its broader biological context.