Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection
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 o...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2021-09-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-021-02449-1 |
| _version_ | 1819023616932577280 |
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| author | Deepak Thirunavukarasu Lauren Y. Cheng Ping Song Sherry X. Chen Mitesh J. Borad Lawrence Kwong Phillip James Daniel J. Turner David Yu Zhang |
| author_facet | Deepak Thirunavukarasu Lauren Y. Cheng Ping Song Sherry X. Chen Mitesh J. Borad Lawrence Kwong Phillip James Daniel J. Turner David Yu Zhang |
| author_sort | Deepak Thirunavukarasu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T04:41:44Z |
| format | Article |
| id | doaj.art-4bf551b9432b4350a7d2d7853a93be54 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-21T04:41:44Z |
| publishDate | 2021-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-4bf551b9432b4350a7d2d7853a93be542022-12-21T19:15:41ZengBMCGenome Biology1474-760X2021-09-0122111710.1186/s13059-021-02449-1Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detectionDeepak Thirunavukarasu0Lauren Y. Cheng1Ping Song2Sherry X. Chen3Mitesh J. Borad4Lawrence Kwong5Phillip James6Daniel J. Turner7David Yu Zhang8NuProbe USA IncDepartment of Bioengineering, Rice UniversityDepartment of Bioengineering, Rice UniversityNuProbe USA IncDepartment of Oncology, Mayo ClinicDepartment of Translational Molecular Pathology, The University of Texas MD Anderson Cancer CenterOxford Nanopore TechnologiesOxford Nanopore TechnologiesNuProbe USA IncAbstract 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.https://doi.org/10.1186/s13059-021-02449-1Nanopore SequencingCancerMutation detection |
| spellingShingle | Deepak Thirunavukarasu Lauren Y. Cheng Ping Song Sherry X. Chen Mitesh J. Borad Lawrence Kwong Phillip James Daniel J. Turner David Yu Zhang Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection Genome Biology Nanopore Sequencing Cancer Mutation detection |
| title | Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection |
| title_full | Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection |
| title_fullStr | Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection |
| title_full_unstemmed | Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection |
| title_short | Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection |
| title_sort | oncogene concatenated enriched amplicon nanopore sequencing for rapid accurate and affordable somatic mutation detection |
| topic | Nanopore Sequencing Cancer Mutation detection |
| url | https://doi.org/10.1186/s13059-021-02449-1 |
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