Molecular sampling at logarithmic rates for next-generation sequencing.

Next-generation sequencing is a cutting edge technology, but to quantify a dynamic range of abundances for different RNA or DNA species requires increasing sampling depth to levels that can be prohibitively expensive due to physical limits on molecular throughput of sequencers. To overcome this prob...

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Autores principales:	Caroline Horn, Julia Salzman
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2019
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/d5491ee8787e49ebbb7b74662c8f7bff
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spelling	oai:doaj.org-article:d5491ee8787e49ebbb7b74662c8f7bff2021-12-02T19:58:10ZMolecular sampling at logarithmic rates for next-generation sequencing.1553-734X1553-735810.1371/journal.pcbi.1007537https://doaj.org/article/d5491ee8787e49ebbb7b74662c8f7bff2019-12-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1007537https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Next-generation sequencing is a cutting edge technology, but to quantify a dynamic range of abundances for different RNA or DNA species requires increasing sampling depth to levels that can be prohibitively expensive due to physical limits on molecular throughput of sequencers. To overcome this problem, we introduce a new general sampling theory which uses biophysical principles to functionally encode the abundance of a species before sampling, SeQUential depletIon and enriCHment (SQUICH). In theory and simulation, SQUICH enables sampling at a logarithmic rate to achieve the same precision as attained with conventional sequencing. A simple proof of principle experimental implementation of SQUICH in a controlled complex system of ~262,000 oligonucleotides already reduces sequencing depth by a factor of 10. SQUICH lays the groundwork for a general solution to a fundamental problem in molecular sampling and enables a new generation of efficient, precise molecular measurement at logarithmic or better sampling depth.Caroline HornJulia SalzmanPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 15, Iss 12, p e1007537 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Caroline Horn Julia Salzman Molecular sampling at logarithmic rates for next-generation sequencing.
description	Next-generation sequencing is a cutting edge technology, but to quantify a dynamic range of abundances for different RNA or DNA species requires increasing sampling depth to levels that can be prohibitively expensive due to physical limits on molecular throughput of sequencers. To overcome this problem, we introduce a new general sampling theory which uses biophysical principles to functionally encode the abundance of a species before sampling, SeQUential depletIon and enriCHment (SQUICH). In theory and simulation, SQUICH enables sampling at a logarithmic rate to achieve the same precision as attained with conventional sequencing. A simple proof of principle experimental implementation of SQUICH in a controlled complex system of ~262,000 oligonucleotides already reduces sequencing depth by a factor of 10. SQUICH lays the groundwork for a general solution to a fundamental problem in molecular sampling and enables a new generation of efficient, precise molecular measurement at logarithmic or better sampling depth.
format	article
author	Caroline Horn Julia Salzman
author_facet	Caroline Horn Julia Salzman
author_sort	Caroline Horn
title	Molecular sampling at logarithmic rates for next-generation sequencing.
title_short	Molecular sampling at logarithmic rates for next-generation sequencing.
title_full	Molecular sampling at logarithmic rates for next-generation sequencing.
title_fullStr	Molecular sampling at logarithmic rates for next-generation sequencing.
title_full_unstemmed	Molecular sampling at logarithmic rates for next-generation sequencing.
title_sort	molecular sampling at logarithmic rates for next-generation sequencing.
publisher	Public Library of Science (PLoS)
publishDate	2019
url	https://doaj.org/article/d5491ee8787e49ebbb7b74662c8f7bff
work_keys_str_mv	AT carolinehorn molecularsamplingatlogarithmicratesfornextgenerationsequencing AT juliasalzman molecularsamplingatlogarithmicratesfornextgenerationsequencing
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Molecular sampling at logarithmic rates for next-generation sequencing.

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