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...
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Autor*in:	Deepak Thirunavukarasu [verfasserIn] Lauren Y. Cheng [verfasserIn] Ping Song [verfasserIn] Sherry X. Chen [verfasserIn] Mitesh J. Borad [verfasserIn] Lawrence Kwong [verfasserIn] Phillip James [verfasserIn] Daniel J. Turner [verfasserIn] David Yu Zhang [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	Nanopore Sequencing Cancer Mutation detection

Übergeordnetes Werk:	In: Genome Biology - BMC, 2014, 22(2021), 1, Seite 17
Übergeordnetes Werk:	volume:22 ; year:2021 ; number:1 ; pages:17

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/s13059-021-02449-1

Katalog-ID:	DOAJ07684224X

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allfields	10.1186/s13059-021-02449-1 doi (DE-627)DOAJ07684224X (DE-599)DOAJ4bf551b9432b4350a7d2d7853a93be54 DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Deepak Thirunavukarasu verfasserin aut Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Nanopore Sequencing Cancer Mutation detection Biology (General) Genetics Lauren Y. Cheng verfasserin aut Ping Song verfasserin aut Sherry X. Chen verfasserin aut Mitesh J. Borad verfasserin aut Lawrence Kwong verfasserin aut Phillip James verfasserin aut Daniel J. Turner verfasserin aut David Yu Zhang verfasserin aut In Genome Biology BMC, 2014 22(2021), 1, Seite 17 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:22 year:2021 number:1 pages:17 https://doi.org/10.1186/s13059-021-02449-1 kostenfrei https://doaj.org/article/4bf551b9432b4350a7d2d7853a93be54 kostenfrei https://doi.org/10.1186/s13059-021-02449-1 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 22 2021 1 17
spelling	10.1186/s13059-021-02449-1 doi (DE-627)DOAJ07684224X (DE-599)DOAJ4bf551b9432b4350a7d2d7853a93be54 DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Deepak Thirunavukarasu verfasserin aut Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Nanopore Sequencing Cancer Mutation detection Biology (General) Genetics Lauren Y. Cheng verfasserin aut Ping Song verfasserin aut Sherry X. Chen verfasserin aut Mitesh J. Borad verfasserin aut Lawrence Kwong verfasserin aut Phillip James verfasserin aut Daniel J. Turner verfasserin aut David Yu Zhang verfasserin aut In Genome Biology BMC, 2014 22(2021), 1, Seite 17 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:22 year:2021 number:1 pages:17 https://doi.org/10.1186/s13059-021-02449-1 kostenfrei https://doaj.org/article/4bf551b9432b4350a7d2d7853a93be54 kostenfrei https://doi.org/10.1186/s13059-021-02449-1 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 22 2021 1 17
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allfieldsSound	10.1186/s13059-021-02449-1 doi (DE-627)DOAJ07684224X (DE-599)DOAJ4bf551b9432b4350a7d2d7853a93be54 DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Deepak Thirunavukarasu verfasserin aut Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Nanopore Sequencing Cancer Mutation detection Biology (General) Genetics Lauren Y. Cheng verfasserin aut Ping Song verfasserin aut Sherry X. Chen verfasserin aut Mitesh J. Borad verfasserin aut Lawrence Kwong verfasserin aut Phillip James verfasserin aut Daniel J. Turner verfasserin aut David Yu Zhang verfasserin aut In Genome Biology BMC, 2014 22(2021), 1, Seite 17 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:22 year:2021 number:1 pages:17 https://doi.org/10.1186/s13059-021-02449-1 kostenfrei https://doaj.org/article/4bf551b9432b4350a7d2d7853a93be54 kostenfrei https://doi.org/10.1186/s13059-021-02449-1 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 22 2021 1 17
language	English
source	In Genome Biology 22(2021), 1, Seite 17 volume:22 year:2021 number:1 pages:17
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authorswithroles_txt_mv	Deepak Thirunavukarasu @@aut@@ Lauren Y. Cheng @@aut@@ Ping Song @@aut@@ Sherry X. Chen @@aut@@ Mitesh J. Borad @@aut@@ Lawrence Kwong @@aut@@ Phillip James @@aut@@ Daniel J. Turner @@aut@@ David Yu Zhang @@aut@@
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callnumber-first	Q - Science
author	Deepak Thirunavukarasu
spellingShingle	Deepak Thirunavukarasu misc QH301-705.5 misc QH426-470 misc Nanopore Sequencing misc Cancer misc Mutation detection misc Biology (General) misc Genetics Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection
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topic_title	QH301-705.5 QH426-470 Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection Nanopore Sequencing Cancer Mutation detection
topic	misc QH301-705.5 misc QH426-470 misc Nanopore Sequencing misc Cancer misc Mutation detection misc Biology (General) misc Genetics
topic_unstemmed	misc QH301-705.5 misc QH426-470 misc Nanopore Sequencing misc Cancer misc Mutation detection misc Biology (General) misc Genetics
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title	Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection
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title_full	Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection
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title_sort	oncogene concatenated enriched amplicon nanopore sequencing for rapid, accurate, and affordable somatic mutation detection
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title_auth	Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection
abstract	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.
abstractGer	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.
abstract_unstemmed	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.
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title_short	Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection
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Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection

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