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通过多重 CRISPR-Cas9 富集和长读长纳米孔测序检测伙伴独立融合基因。

Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing.

机构信息

Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands.

Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan, Amsterdam, Netherlands.

出版信息

Nat Commun. 2020 Jun 5;11(1):2861. doi: 10.1038/s41467-020-16641-7.

DOI:10.1038/s41467-020-16641-7
PMID:32504042
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7275081/
Abstract

Fusion genes are hallmarks of various cancer types and important determinants for diagnosis, prognosis and treatment. Fusion gene partner choice and breakpoint-position promiscuity restricts diagnostic detection, even for known and recurrent configurations. Here, we develop FUDGE (FUsion Detection from Gene Enrichment) to accurately and impartially identify fusions. FUDGE couples target-selected and strand-specific CRISPR-Cas9 activity for fusion gene driver enrichment - without prior knowledge of fusion partner or breakpoint-location - to long read nanopore sequencing with the bioinformatics pipeline NanoFG. FUDGE has flexible target-loci choices and enables multiplexed enrichment for simultaneous analysis of several genes in multiple samples in one sequencing run. We observe on-average 665 fold breakpoint-site enrichment and identify nucleotide resolution fusion breakpoints within 2 days. The assay identifies cancer cell line and tumor sample fusions irrespective of partner gene or breakpoint-position. FUDGE is a rapid and versatile fusion detection assay for diagnostic pan-cancer fusion detection.

摘要

融合基因是各种癌症类型的标志，也是诊断、预后和治疗的重要决定因素。融合基因伙伴的选择和断点位置的混杂限制了诊断检测，即使是对于已知和反复出现的结构。在这里，我们开发了 FUDGE（融合从基因富集检测）来准确和公正地识别融合。FUDGE 将靶向选择和链特异性 CRISPR-Cas9 活性与长读长纳米孔测序相结合，具有生物信息学管道 NanoFG-无需事先了解融合伙伴或断点位置-用于融合基因驱动子富集。FUDGE 具有灵活的靶标选择，可以在一次测序运行中同时对多个样本中的多个基因进行多路复用富集。我们观察到平均 665 倍的断点位置富集，并在 2 天内确定核苷酸分辨率的融合断点。该检测方法可以识别癌症细胞系和肿瘤样本融合，而与伙伴基因或断点位置无关。FUDGE 是一种快速而通用的融合检测方法，用于诊断性泛癌融合检测。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c615/7275081/5e2f22c75a15/41467_2020_16641_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c615/7275081/7a8d757cfe9e/41467_2020_16641_Fig1_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c615/7275081/6844d6612423/41467_2020_16641_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c615/7275081/9cfcfb2ae02d/41467_2020_16641_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c615/7275081/5e2f22c75a15/41467_2020_16641_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c615/7275081/7a8d757cfe9e/41467_2020_16641_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c615/7275081/9a1ebf959e8a/41467_2020_16641_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c615/7275081/65aaff90ecf9/41467_2020_16641_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c615/7275081/c85f1705f144/41467_2020_16641_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c615/7275081/6844d6612423/41467_2020_16641_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c615/7275081/9cfcfb2ae02d/41467_2020_16641_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c615/7275081/5e2f22c75a15/41467_2020_16641_Fig7_HTML.jpg

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