The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules

Abstract Accurate quantification of biomolecules in system-wide measurements is in high demand, especially for systems with limited sample amounts such as single cells. Because of this, digital quantification of nucleic acid molecules using molecular barcodes has been developed, making, e.g., transc...

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Autores principales:	Taisaku Ogawa, Kirill Kryukov, Tadashi Imanishi, Katsuyuki Shiroguchi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/174ff9a22ba6468c8716e68dd0232a99
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spelling	oai:doaj.org-article:174ff9a22ba6468c8716e68dd0232a992021-12-02T15:06:08ZThe efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules10.1038/s41598-017-13529-32045-2322https://doaj.org/article/174ff9a22ba6468c8716e68dd0232a992017-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-13529-3https://doaj.org/toc/2045-2322Abstract Accurate quantification of biomolecules in system-wide measurements is in high demand, especially for systems with limited sample amounts such as single cells. Because of this, digital quantification of nucleic acid molecules using molecular barcodes has been developed, making, e.g., transcriptome analysis highly reproducible and quantitative. This counting scheme was shown to work using sequence-restricted barcodes, and non-sequence-restricted (random-base) barcodes that may provide a much higher dynamic range at significantly lower cost have been widely used. However, the efficacy of random-base barcodes is significantly affected by base changes due to amplification and/or sequencing errors and has not been investigated experimentally or quantitatively. Here, we show experimentally that random-base barcodes enable absolute and digital quantification of DNA molecules with high dynamic range (from one to more than 104, potentially up to 1015 molecules) conditional on our barcode design and variety, a certain range of sequencing depths, and computational analyses. Moreover, we quantitatively show further functional advantages of the molecular barcodes: the molecular barcodes enable one to find contaminants and misidentifications of target sequences. Our scheme here may be generally used to confirm that the digital quantification works in each platform.Taisaku OgawaKirill KryukovTadashi ImanishiKatsuyuki ShiroguchiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Taisaku Ogawa Kirill Kryukov Tadashi Imanishi Katsuyuki Shiroguchi The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules
description	Abstract Accurate quantification of biomolecules in system-wide measurements is in high demand, especially for systems with limited sample amounts such as single cells. Because of this, digital quantification of nucleic acid molecules using molecular barcodes has been developed, making, e.g., transcriptome analysis highly reproducible and quantitative. This counting scheme was shown to work using sequence-restricted barcodes, and non-sequence-restricted (random-base) barcodes that may provide a much higher dynamic range at significantly lower cost have been widely used. However, the efficacy of random-base barcodes is significantly affected by base changes due to amplification and/or sequencing errors and has not been investigated experimentally or quantitatively. Here, we show experimentally that random-base barcodes enable absolute and digital quantification of DNA molecules with high dynamic range (from one to more than 104, potentially up to 1015 molecules) conditional on our barcode design and variety, a certain range of sequencing depths, and computational analyses. Moreover, we quantitatively show further functional advantages of the molecular barcodes: the molecular barcodes enable one to find contaminants and misidentifications of target sequences. Our scheme here may be generally used to confirm that the digital quantification works in each platform.
format	article
author	Taisaku Ogawa Kirill Kryukov Tadashi Imanishi Katsuyuki Shiroguchi
author_facet	Taisaku Ogawa Kirill Kryukov Tadashi Imanishi Katsuyuki Shiroguchi
author_sort	Taisaku Ogawa
title	The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules
title_short	The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules
title_full	The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules
title_fullStr	The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules
title_full_unstemmed	The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules
title_sort	efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/174ff9a22ba6468c8716e68dd0232a99
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The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules

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