Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection

Genome Biology

Ping Song¹  Lauren Y. Cheng¹  Mitesh J. Borad²  Lawrence Kwong³  Sherry X. Chen⁴  Deepak Thirunavukarasu⁴  David Yu Zhang⁵  Daniel J. Turner⁶  Phillip James⁶ 

[1] Department of Bioengineering, Rice University, Houston, TX, USA;Department of Oncology, Mayo Clinic, Phoenix, AZ, USA;Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;NuProbe USA Inc, Houston, TX, USA;NuProbe USA Inc, Houston, TX, USA;Department of Bioengineering, Rice University, Houston, TX, USA;Oxford Nanopore Technologies, Oxford, UK;

关键词: Nanopore Sequencing;    Cancer;    Mutation detection;   

DOI  :  10.1186/s13059-021-02449-1

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY