使用KAPA HyperChoice系统检测种系、体细胞和线粒体序列以及拷贝数变异的单个NGS靶向面板管道的临床验证。

IF 3.9 3区 医学 Q1 PATHOLOGY Expert Review of Molecular Diagnostics Pub Date : 2023-07-01 Epub Date: 2023-08-12 DOI:10.1080/14737159.2023.2245747
Jennifer Kerkhof, Cassandra Rastin, Laila Schenkel, Hanxin Lin, Bekim Sadikovic
{"title":"使用KAPA HyperChoice系统检测种系、体细胞和线粒体序列以及拷贝数变异的单个NGS靶向面板管道的临床验证。","authors":"Jennifer Kerkhof,&nbsp;Cassandra Rastin,&nbsp;Laila Schenkel,&nbsp;Hanxin Lin,&nbsp;Bekim Sadikovic","doi":"10.1080/14737159.2023.2245747","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Comprehensive molecular diagnostics are highly dependent on the technical performance of next-generation sequencing (NGS) pipelines, which are assessed by data quality, cost, turnaround time, and accuracy of detecting a range of sequence and copy number variants.</p><p><strong>Methods: </strong>A dataset of 285 clinically validated cases (205 retrospective and 80 prospective), carrying complex sequence and copy number variants and thousands of genetic polymorphisms underwent a clinical validation of the KAPA HyperChoice target enrichment system with parallel sample fidelity assessment across a number of NGS panels. The analysis included assessment of peripheral blood, urine, muscle and FFPE tissues.</p><p><strong>Results: </strong>High-quality and exceptionally uniform data with 100% coverage of all targeted panels were obtained, resulting in complete sensitivity and specificity for all variant types across nearly all panels and tissue types. Overall reduction in cost and turnaround times was obtained with the implementation of a parallel genotyping sample fidelity system.</p><p><strong>Conclusion: </strong>Results of the laboratory quality improvement study focused on a single NGS pipeline that includes both nuclear and mitochondrial genomes demonstrated utility in the clinical setting to assess a range of referral reasons, necessary due to the complex molecular etiology of human genetic disorders, while reducing costs and turnaround times.</p>","PeriodicalId":12113,"journal":{"name":"Expert Review of Molecular Diagnostics","volume":"23 9","pages":"827-841"},"PeriodicalIF":3.9000,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Clinical validation of a single NGS targeted panel pipeline using the KAPA HyperChoice system for detection of germline, somatic and mitochondrial sequence and copy number variants.\",\"authors\":\"Jennifer Kerkhof,&nbsp;Cassandra Rastin,&nbsp;Laila Schenkel,&nbsp;Hanxin Lin,&nbsp;Bekim Sadikovic\",\"doi\":\"10.1080/14737159.2023.2245747\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Comprehensive molecular diagnostics are highly dependent on the technical performance of next-generation sequencing (NGS) pipelines, which are assessed by data quality, cost, turnaround time, and accuracy of detecting a range of sequence and copy number variants.</p><p><strong>Methods: </strong>A dataset of 285 clinically validated cases (205 retrospective and 80 prospective), carrying complex sequence and copy number variants and thousands of genetic polymorphisms underwent a clinical validation of the KAPA HyperChoice target enrichment system with parallel sample fidelity assessment across a number of NGS panels. The analysis included assessment of peripheral blood, urine, muscle and FFPE tissues.</p><p><strong>Results: </strong>High-quality and exceptionally uniform data with 100% coverage of all targeted panels were obtained, resulting in complete sensitivity and specificity for all variant types across nearly all panels and tissue types. Overall reduction in cost and turnaround times was obtained with the implementation of a parallel genotyping sample fidelity system.</p><p><strong>Conclusion: </strong>Results of the laboratory quality improvement study focused on a single NGS pipeline that includes both nuclear and mitochondrial genomes demonstrated utility in the clinical setting to assess a range of referral reasons, necessary due to the complex molecular etiology of human genetic disorders, while reducing costs and turnaround times.</p>\",\"PeriodicalId\":12113,\"journal\":{\"name\":\"Expert Review of Molecular Diagnostics\",\"volume\":\"23 9\",\"pages\":\"827-841\"},\"PeriodicalIF\":3.9000,\"publicationDate\":\"2023-07-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Expert Review of Molecular Diagnostics\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1080/14737159.2023.2245747\",\"RegionNum\":3,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2023/8/12 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q1\",\"JCRName\":\"PATHOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Expert Review of Molecular Diagnostics","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1080/14737159.2023.2245747","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2023/8/12 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"PATHOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

背景:全面的分子诊断高度依赖于下一代测序(NGS)管道的技术性能,这是通过数据质量、成本、周转时间以及检测一系列序列和拷贝数变异的准确性来评估的。方法:对285例临床验证病例(205例回顾性病例和80例前瞻性病例)的数据集进行了KAPA HyperChoice靶点富集系统的临床验证,并对多个NGS面板进行了平行样本保真度评估。分析包括外周血、尿液、肌肉和FFPE组织的评估。结果:获得了100%覆盖所有靶向面板的高质量和异常均匀的数据,几乎所有面板和组织类型的所有变体类型都具有完全的敏感性和特异性。通过实施平行基因分型样本保真度系统,总体上降低了成本和周转时间。结论:实验室质量改进研究的结果集中在包括细胞核和线粒体基因组的单个NGS管道上,证明了在临床环境中评估一系列转诊原因的实用性,这是由于人类遗传疾病的复杂分子病因所必需的,同时降低了成本和周转时间。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Clinical validation of a single NGS targeted panel pipeline using the KAPA HyperChoice system for detection of germline, somatic and mitochondrial sequence and copy number variants.

Background: Comprehensive molecular diagnostics are highly dependent on the technical performance of next-generation sequencing (NGS) pipelines, which are assessed by data quality, cost, turnaround time, and accuracy of detecting a range of sequence and copy number variants.

Methods: A dataset of 285 clinically validated cases (205 retrospective and 80 prospective), carrying complex sequence and copy number variants and thousands of genetic polymorphisms underwent a clinical validation of the KAPA HyperChoice target enrichment system with parallel sample fidelity assessment across a number of NGS panels. The analysis included assessment of peripheral blood, urine, muscle and FFPE tissues.

Results: High-quality and exceptionally uniform data with 100% coverage of all targeted panels were obtained, resulting in complete sensitivity and specificity for all variant types across nearly all panels and tissue types. Overall reduction in cost and turnaround times was obtained with the implementation of a parallel genotyping sample fidelity system.

Conclusion: Results of the laboratory quality improvement study focused on a single NGS pipeline that includes both nuclear and mitochondrial genomes demonstrated utility in the clinical setting to assess a range of referral reasons, necessary due to the complex molecular etiology of human genetic disorders, while reducing costs and turnaround times.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
CiteScore
6.60
自引率
0.00%
发文量
71
审稿时长
1 months
期刊介绍: Expert Review of Molecular Diagnostics (ISSN 1473-7159) publishes expert reviews of the latest advancements in the field of molecular diagnostics including the detection and monitoring of the molecular causes of disease that are being translated into groundbreaking diagnostic and prognostic technologies to be used in the clinical diagnostic setting. Each issue of Expert Review of Molecular Diagnostics contains leading reviews on current and emerging topics relating to molecular diagnostics, subject to a rigorous peer review process; editorials discussing contentious issues in the field; diagnostic profiles featuring independent, expert evaluations of diagnostic tests; meeting reports of recent molecular diagnostics conferences and key paper evaluations featuring assessments of significant, recently published articles from specialists in molecular diagnostic therapy. Expert Review of Molecular Diagnostics provides the forum for reporting the critical advances being made in this ever-expanding field, as well as the major challenges ahead in their clinical implementation. The journal delivers this information in concise, at-a-glance article formats: invaluable to a time-constrained community.
期刊最新文献
Promising biomarkers of kawasaki disease: markers that aid in diagnosis. Strengths and limitations of molecular diagnostics for Pneumocystis jirovecii pneumonia. Genetic-based diagnostics of Parkinson's disease and other Parkinsonian syndromes. Biomarkers of treatment response in bladder cancer. Lipid-associated GWAS loci as important markers of the risk, severity, and clinical course of peripheral artery disease.
×
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
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 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 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1