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, Cassandra Rastin, Laila Schenkel, Hanxin Lin, 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":null,"pages":null},"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, Cassandra Rastin, Laila Schenkel, Hanxin Lin, 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\":null,\"pages\":null},\"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}
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.
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.