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A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features

Standard units of measurement are required for the quantitative description of nature; however, few standard units have been established for genomics to date. Here, we have developed a synthetic DNA ladder that defines a quantitative standard unit that can measure DNA sequence abundance within a nex...

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Autores principales: Reis, Andre L. M., Deveson, Ira W., Wong, Ted, Madala, Bindu Swapna, Barker, Chris, Blackburn, James, Marcellin, Esteban, Mercer, Tim R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7367866/
https://www.ncbi.nlm.nih.gov/pubmed/32681090
http://dx.doi.org/10.1038/s41467-020-17445-5
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author Reis, Andre L. M.
Deveson, Ira W.
Wong, Ted
Madala, Bindu Swapna
Barker, Chris
Blackburn, James
Marcellin, Esteban
Mercer, Tim R.
author_facet Reis, Andre L. M.
Deveson, Ira W.
Wong, Ted
Madala, Bindu Swapna
Barker, Chris
Blackburn, James
Marcellin, Esteban
Mercer, Tim R.
author_sort Reis, Andre L. M.
collection PubMed
description Standard units of measurement are required for the quantitative description of nature; however, few standard units have been established for genomics to date. Here, we have developed a synthetic DNA ladder that defines a quantitative standard unit that can measure DNA sequence abundance within a next-generation sequencing library. The ladder can be spiked into a DNA sample, and act as an internal scale that measures quantitative genetics features. Unlike previous spike-ins, the ladder is encoded within a single molecule, and can be equivalently and independently synthesized by different laboratories. We show how the ladder can measure diverse quantitative features, including human genetic variation and microbial abundance, and also estimate uncertainty due to technical variation and improve normalization between libraries. This ladder provides an independent quantitative unit that can be used with any organism, application or technology, thereby providing a common metric by which genomes can be measured.
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spelling pubmed-73678662020-07-21 A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features Reis, Andre L. M. Deveson, Ira W. Wong, Ted Madala, Bindu Swapna Barker, Chris Blackburn, James Marcellin, Esteban Mercer, Tim R. Nat Commun Article Standard units of measurement are required for the quantitative description of nature; however, few standard units have been established for genomics to date. Here, we have developed a synthetic DNA ladder that defines a quantitative standard unit that can measure DNA sequence abundance within a next-generation sequencing library. The ladder can be spiked into a DNA sample, and act as an internal scale that measures quantitative genetics features. Unlike previous spike-ins, the ladder is encoded within a single molecule, and can be equivalently and independently synthesized by different laboratories. We show how the ladder can measure diverse quantitative features, including human genetic variation and microbial abundance, and also estimate uncertainty due to technical variation and improve normalization between libraries. This ladder provides an independent quantitative unit that can be used with any organism, application or technology, thereby providing a common metric by which genomes can be measured. Nature Publishing Group UK 2020-07-17 /pmc/articles/PMC7367866/ /pubmed/32681090 http://dx.doi.org/10.1038/s41467-020-17445-5 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Reis, Andre L. M.
Deveson, Ira W.
Wong, Ted
Madala, Bindu Swapna
Barker, Chris
Blackburn, James
Marcellin, Esteban
Mercer, Tim R.
A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features
title A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features
title_full A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features
title_fullStr A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features
title_full_unstemmed A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features
title_short A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features
title_sort universal and independent synthetic dna ladder for the quantitative measurement of genomic features
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7367866/
https://www.ncbi.nlm.nih.gov/pubmed/32681090
http://dx.doi.org/10.1038/s41467-020-17445-5
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