RNA Sequencing for Solid Tumor Fusion Gene Detection: Proficiency Testing Practice and Performance Comparison.

IF 3.7 3区 医学 Q2 MEDICAL LABORATORY TECHNOLOGY
Julia A Bridge, Kevin C Halling, Joel T Moncur, Rhona J Souers, Meera R Hameed, Helen Fernandes, Angshumoy Roy, Lea Surrey, Laura J Tafe, Patricia Vasalos, Dolores H Lopez-Terrada
{"title":"RNA Sequencing for Solid Tumor Fusion Gene Detection: Proficiency Testing Practice and Performance Comparison.","authors":"Julia A Bridge, Kevin C Halling, Joel T Moncur, Rhona J Souers, Meera R Hameed, Helen Fernandes, Angshumoy Roy, Lea Surrey, Laura J Tafe, Patricia Vasalos, Dolores H Lopez-Terrada","doi":"10.5858/arpa.2023-0047-CP","DOIUrl":null,"url":null,"abstract":"<p><strong>Context: </strong>Next-generation sequencing-based approaches using RNA have increasingly been used by clinical laboratories for the detection of fusion genes, intragenic rearrangements, and exon-skipping events. Correspondingly, the College of American Pathologists (CAP) has advanced RNA sequencing proficiency testing (PT) to ensure optimal performance of these assays.</p><p><strong>Objective: </strong>To report on laboratory performance and practices of RNA sequencing for the detection of fusion genes, intragenic rearrangements, and exon-skipping events using CAP PT data from 8 mailings (2018-A through 2021-B).</p><p><strong>Design: </strong>CAP PT RNA sequencing program results from 153 laboratories across 24 proficiency test specimens, interrogating 22 distinct engineered fusion transcripts, were analyzed for correct identification of the fusion event, associated performance variables, and laboratory practices.</p><p><strong>Results: </strong>Overall, the 4-year program detection rate (sensitivity) was 95.5% (1486 of 1556 results). False-negative rates were 3.6% (53 of 1463) and 18.3% (17 of 93) for fusion gene and intragenic rearrangement/exon-skipping events, respectively. Only 19 false-positive results were reported among the 8 PT mailings, and most were likely the result of preanalytical or postanalytical errors. There were no practice characteristics (eg, instrumentation, sequencing method) significantly associated with the fusion detection results.</p><p><strong>Conclusions: </strong>These data reveal a high overall sensitivity and specificity for fusion gene detection by participating laboratories using clinical RNA sequencing. Performance was comparable across all laboratories, regardless of methodology. The fraction of false-negative results for intragenic rearrangement/exon-skipping events was greater than that for the chimeric fusion genes. False-negative results could not be attributed to any specific practice characteristics.</p>","PeriodicalId":8305,"journal":{"name":"Archives of pathology & laboratory medicine","volume":null,"pages":null},"PeriodicalIF":3.7000,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Archives of pathology & laboratory medicine","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.5858/arpa.2023-0047-CP","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"MEDICAL LABORATORY TECHNOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Context: Next-generation sequencing-based approaches using RNA have increasingly been used by clinical laboratories for the detection of fusion genes, intragenic rearrangements, and exon-skipping events. Correspondingly, the College of American Pathologists (CAP) has advanced RNA sequencing proficiency testing (PT) to ensure optimal performance of these assays.

Objective: To report on laboratory performance and practices of RNA sequencing for the detection of fusion genes, intragenic rearrangements, and exon-skipping events using CAP PT data from 8 mailings (2018-A through 2021-B).

Design: CAP PT RNA sequencing program results from 153 laboratories across 24 proficiency test specimens, interrogating 22 distinct engineered fusion transcripts, were analyzed for correct identification of the fusion event, associated performance variables, and laboratory practices.

Results: Overall, the 4-year program detection rate (sensitivity) was 95.5% (1486 of 1556 results). False-negative rates were 3.6% (53 of 1463) and 18.3% (17 of 93) for fusion gene and intragenic rearrangement/exon-skipping events, respectively. Only 19 false-positive results were reported among the 8 PT mailings, and most were likely the result of preanalytical or postanalytical errors. There were no practice characteristics (eg, instrumentation, sequencing method) significantly associated with the fusion detection results.

Conclusions: These data reveal a high overall sensitivity and specificity for fusion gene detection by participating laboratories using clinical RNA sequencing. Performance was comparable across all laboratories, regardless of methodology. The fraction of false-negative results for intragenic rearrangement/exon-skipping events was greater than that for the chimeric fusion genes. False-negative results could not be attributed to any specific practice characteristics.

用于实体瘤融合基因检测的 RNA 测序:能力验证实践与性能比较。
背景:临床实验室越来越多地使用基于下一代RNA测序的方法来检测融合基因、基因内重排和外显子缺失事件。相应地,美国病理学家学会(CAP)推进了 RNA 测序能力验证(PT),以确保这些检测方法的最佳性能:利用 8 次邮件(2018-A 至 2021-B)中的 CAP PT 数据,报告用于检测融合基因、基因内重排和外显子跳断事件的 RNA 测序的实验室性能和实践:对来自 153 个实验室的 24 份能力验证样本的 CAP PT RNA 测序项目结果进行了分析,其中涉及 22 个不同的工程融合转录本,分析了融合事件的正确识别、相关性能变量和实验室实践:总体而言,4 年计划的检测率(灵敏度)为 95.5%(1556 项结果中的 1486 项)。融合基因和基因内重排/外显子缺失事件的假阴性率分别为 3.6%(1463 项中的 53 项)和 18.3%(93 项中的 17 项)。在 8 份 PT 邮件中,仅报告了 19 个假阳性结果,其中大部分可能是分析前或分析后出错所致。没有任何实践特征(如仪器、测序方法)与融合检测结果显著相关:这些数据显示,参与研究的实验室使用临床RNA测序法检测融合基因的总体灵敏度和特异性都很高。无论采用哪种方法,所有实验室的检测结果都具有可比性。基因内重排/外显子缺失事件的假阴性结果比例高于嵌合型融合基因。假阴性结果不能归因于任何特定的实践特点。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
CiteScore
9.20
自引率
2.20%
发文量
369
审稿时长
3-8 weeks
期刊介绍: Welcome to the website of the Archives of Pathology & Laboratory Medicine (APLM). This monthly, peer-reviewed journal of the College of American Pathologists offers global reach and highest measured readership among pathology journals. Published since 1926, ARCHIVES was voted in 2009 the only pathology journal among the top 100 most influential journals of the past 100 years by the BioMedical and Life Sciences Division of the Special Libraries Association. Online access to the full-text and PDF files of APLM articles is free.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信