Benchmarking nanopore sequencing and rapid genomics feasibility: validation at a quaternary hospital in New Zealand.

IF 4.7 2区医学 Q1 GENETICS & HEREDITY

NPJ Genomic Medicine Pub Date : 2024-11-08 DOI:10.1038/s41525-024-00445-5

Denis M Nyaga, Peter Tsai, Clare Gebbie, Hui Hui Phua, Patrick Yap, Polona Le Quesne Stabej, Sophie Farrow, Jing Rong, Gergely Toldi, Eric Thorstensen, Zornitza Stark, Sebastian Lunke, Kimberley Gamet, Jodi Van Dyk, Mark Greenslade, Justin M O'Sullivan

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引用次数: 0

Abstract

Approximately 200 critically ill infants and children in New Zealand are in high-dependency care, many suspected of having genetic conditions, requiring scalable genomic testing. We adopted an acute care genomics protocol from an accredited laboratory and established a clinical pipeline using Oxford Nanopore Technologies PromethION 2 solo system and Fabric GEM™ software. Benchmarking of the pipeline was performed using Global Alliance for Genomics and Health benchmarking tools and Genome in a Bottle samples (HG002-HG007). Evaluation of single nucleotide variants resulted in a precision and recall of 0.997 and 0.992, respectively. Small indel identification approached a precision of 0.922 and recall of 0.838. Large genomic variations from Coriell Copy Number Variation Reference Panel 1 were reliably detected with ~2 M long reads. Finally, we present results obtained from fourteen trio samples, ten of which were processed in parallel with a clinically accredited short-read rapid genomic testing pipeline (Newborn Genomics Programme; NCT06081075; 2023-10-12).

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纳米孔测序和快速基因组学可行性基准：新西兰一家四级医院的验证。

新西兰约有 200 名重症婴幼儿需要高度依赖护理，其中许多人被怀疑患有遗传疾病，需要进行可扩展的基因组测试。我们采用了一家认证实验室的急症护理基因组学方案，并使用牛津纳米孔技术公司的 PromethION 2 solo 系统和 Fabric GEM™ 软件建立了临床流水线。使用全球基因组学与健康联盟（Global Alliance for Genomics and Health）的基准工具和瓶中基因组样本（HG002-HG007）对管道进行了基准测试。单核苷酸变异评估的精确度和召回率分别为 0.997 和 0.992。小片段识别的精确度为 0.922，召回率为 0.838。用 ~2 M 长读数可以可靠地检测到来自 Coriell Copy Number Variation Reference Panel 1 的大基因组变异。最后，我们介绍了 14 个三组样本的结果，其中 10 个样本是与临床认可的短读数快速基因组检测管道（新生儿基因组计划；NCT06081075；2023-10-12）同时处理的。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

NPJ Genomic Medicine Biochemistry, Genetics and Molecular Biology-Molecular Biology

CiteScore

9.40

自引率

1.90%

发文量

审稿时长

17 weeks

期刊介绍： npj Genomic Medicine is an international, peer-reviewed journal dedicated to publishing the most important scientific advances in all aspects of genomics and its application in the practice of medicine. The journal defines genomic medicine as "diagnosis, prognosis, prevention and/or treatment of disease and disorders of the mind and body, using approaches informed or enabled by knowledge of the genome and the molecules it encodes." Relevant and high-impact papers that encompass studies of individuals, families, or populations are considered for publication. An emphasis will include coupling detailed phenotype and genome sequencing information, both enabled by new technologies and informatics, to delineate the underlying aetiology of disease. Clinical recommendations and/or guidelines of how that data should be used in the clinical management of those patients in the study, and others, are also encouraged.