基于串联增强扩增子的纳孔测序实现快速、准确且经济实惠的体细胞突变检测
Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection.
机构信息
NuProbe USA Inc, Houston, TX, USA.
Department of Bioengineering, Rice University, Houston, TX, USA.
出版信息
Genome Biol. 2021 Sep 6;22(1):227. doi: 10.1186/s13059-021-02449-1.
Abstract
We develop the Oncogene Concatenated Enriched Amplicon Nanopore Sequencing (OCEANS) method, in which variants with low variant allele frequency (VAFs) are amplified and subsequently concatenated for Nanopore Sequencing. OCEANS allows accurate detection of somatic mutations with VAF limits of detection between 0.05 and 1%. We construct 4 distinct multi-gene OCEANS panels targeting recurrent mutations in acute myeloid leukemia, melanoma, non-small- cell lung cancer, and hepatocellular carcinoma and validate them on clinical samples. By demonstrating detection of low VAF single nucleotide variant mutations using Nanopore Sequencing, OCEANS is poised to enable same-day clinical sequencing panels.
摘要
我们开发了 Oncogene Concatenated Enriched Amplicon Nanopore Sequencing（OCEANS）方法，该方法对低变异等位基因频率（VAF）的变体进行扩增，然后连接起来进行 Nanopore 测序。OCEANS 允许对 VAF 检测限在 0.05%至 1%之间的体细胞突变进行准确检测。我们构建了 4 个不同的针对急性髓系白血病、黑色素瘤、非小细胞肺癌和肝细胞癌中常见突变的多基因 OCEANS 检测 panel，并在临床样本上对其进行了验证。通过证明使用 Nanopore Sequencing 检测低 VAF 的单核苷酸变异突变，OCEANS 有望实现当天的临床测序 panel。
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本文引用的文献
1
Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing.
Nat Biomed Eng. 2021 Jul;5(7):690-701. doi: 10.1038/s41551-021-00713-0. Epub 2021 May 3.
2
Nanopore sequencing and its application to the study of microbial communities.
Comput Struct Biotechnol J. 2021 Mar 7;19:1497-1511. doi: 10.1016/j.csbj.2021.02.020. eCollection 2021.
3
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing.
Nat Methods. 2021 Feb;18(2):165-169. doi: 10.1038/s41592-020-01041-y. Epub 2021 Jan 11.
4
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Nat Biotechnol. 2020 Sep;38(9):1044-1053. doi: 10.1038/s41587-020-0503-6. Epub 2020 May 4.
5
Integrating genomic features for non-invasive early lung cancer detection.
Nature. 2020 Apr;580(7802):245-251. doi: 10.1038/s41586-020-2140-0. Epub 2020 Mar 25.
6
The repertoire of mutational signatures in human cancer.
Nature. 2020 Feb;578(7793):94-101. doi: 10.1038/s41586-020-1943-3. Epub 2020 Feb 5.
7
High-Fidelity Nanopore Sequencing of Ultra-Short DNA Targets.
Anal Chem. 2019 May 21;91(10):6783-6789. doi: 10.1021/acs.analchem.9b00856. Epub 2019 May 10.
8
Considerations and quality controls when analyzing cell-free tumor DNA.
Biomol Detect Quantif. 2019 Feb 13;17:100078. doi: 10.1016/j.bdq.2018.12.003. eCollection 2019 Mar.
9
A multi-task convolutional deep neural network for variant calling in single molecule sequencing.
Nat Commun. 2019 Mar 1;10(1):998. doi: 10.1038/s41467-019-09025-z.
10
A universal SNP and small-indel variant caller using deep neural networks.
Nat Biotechnol. 2018 Nov;36(10):983-987. doi: 10.1038/nbt.4235. Epub 2018 Sep 24.
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