Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection
| Autor: | Lauren Y. Cheng, David Zhang, Mitesh J. Borad, Lawrence N. Kwong, Ping Song, Phillip James, Sherry X. Chen, Daniel J. Turner, Deepak Thirunavukarasu |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Lung Neoplasms
QH301-705.5 Somatic cell Method Computational biology QH426-470 Biology Germline mutation Carcinoma Non-Small-Cell Lung Neoplasms Genetics False positive paradox Humans Digital polymerase chain reaction Biology (General) Melanoma Cancer Oncogene Myeloid leukemia High-Throughput Nucleotide Sequencing Variant allele Oncogenes Amplicon Human genetics Mutation detection Nanopore Sequencing Leukemia Myeloid Acute Mutation Non small cell Nanopore sequencing |
| Zdroj: | Genome Biology Genome Biology, Vol 22, Iss 1, Pp 1-17 (2021) |
| ISSN: | 1474-760X 1474-7596 |
| Popis: | Nanopore sequencing is more than 10-fold faster than sequencing-by-synthesis and provides reads that are roughly 100-fold longer. However, nanopore sequencing’s 7.5% intrinsic error rate renders it difficult to call somatic mutations with low variant allele frequencies (VAFs) without significant false positives. Here, we introduce the Oncogene Concatenated Enriched Amplicon Nanopore Sequencing (OCEANS) method, in which variants with low VAFs are selectively 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 constructed 4 distinct multi-gene OCEANS panels targeting recurrent mutations in acute myeloid leukemia, melanoma, non-small-cell lung cancer, and hepatocellular carcinoma. Comparison experiments against Illumina NGS showed 99.79% to 99.99% area under the receiver-operator curve for these panels on clinical FFPE tumor samples. Furthermore, we identified a significant number of mutations below the standard NGS limit of detection in clinical tissue samples using each OCEANS panel. Comparison against digital PCR on 10 of putative mutations at ≤1% VAF showed 9 concordant positive calls with VAFs between 0.02% and 0.66%. By overcoming the primary challenge of nanopore sequencing on detecting low VAF single nucleotide variant mutations, OCEANS is poised to enable same-day clinical sequencing panels. |
| Databáze: | OpenAIRE |
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