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The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing

Targeted capture massively parallel sequencing is increasingly being used in clinical settings, and as costs continue to decline, use of this technology may become routine in health care. However, a limited amount of tissue has often been a challenge in meeting quality requirements. To offer a pract...

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Autores principales: Chung, Jongsuk, Son, Dae-Soon, Jeon, Hyo-Jeong, Kim, Kyoung-Mee, Park, Gahee, Ryu, Gyu Ha, Park, Woong-Yang, Park, Donghyun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4879621/
https://www.ncbi.nlm.nih.gov/pubmed/27220682
http://dx.doi.org/10.1038/srep26732
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author Chung, Jongsuk
Son, Dae-Soon
Jeon, Hyo-Jeong
Kim, Kyoung-Mee
Park, Gahee
Ryu, Gyu Ha
Park, Woong-Yang
Park, Donghyun
author_facet Chung, Jongsuk
Son, Dae-Soon
Jeon, Hyo-Jeong
Kim, Kyoung-Mee
Park, Gahee
Ryu, Gyu Ha
Park, Woong-Yang
Park, Donghyun
author_sort Chung, Jongsuk
collection PubMed
description Targeted capture massively parallel sequencing is increasingly being used in clinical settings, and as costs continue to decline, use of this technology may become routine in health care. However, a limited amount of tissue has often been a challenge in meeting quality requirements. To offer a practical guideline for the minimum amount of input DNA for targeted sequencing, we optimized and evaluated the performance of targeted sequencing depending on the input DNA amount. First, using various amounts of input DNA, we compared commercially available library construction kits and selected Agilent’s SureSelect-XT and KAPA Biosystems’ Hyper Prep kits as the kits most compatible with targeted deep sequencing using Agilent’s SureSelect custom capture. Then, we optimized the adapter ligation conditions of the Hyper Prep kit to improve library construction efficiency and adapted multiplexed hybrid selection to reduce the cost of sequencing. In this study, we systematically evaluated the performance of the optimized protocol depending on the amount of input DNA, ranging from 6.25 to 200 ng, suggesting the minimal input DNA amounts based on coverage depths required for specific applications.
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spelling pubmed-48796212016-06-07 The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing Chung, Jongsuk Son, Dae-Soon Jeon, Hyo-Jeong Kim, Kyoung-Mee Park, Gahee Ryu, Gyu Ha Park, Woong-Yang Park, Donghyun Sci Rep Article Targeted capture massively parallel sequencing is increasingly being used in clinical settings, and as costs continue to decline, use of this technology may become routine in health care. However, a limited amount of tissue has often been a challenge in meeting quality requirements. To offer a practical guideline for the minimum amount of input DNA for targeted sequencing, we optimized and evaluated the performance of targeted sequencing depending on the input DNA amount. First, using various amounts of input DNA, we compared commercially available library construction kits and selected Agilent’s SureSelect-XT and KAPA Biosystems’ Hyper Prep kits as the kits most compatible with targeted deep sequencing using Agilent’s SureSelect custom capture. Then, we optimized the adapter ligation conditions of the Hyper Prep kit to improve library construction efficiency and adapted multiplexed hybrid selection to reduce the cost of sequencing. In this study, we systematically evaluated the performance of the optimized protocol depending on the amount of input DNA, ranging from 6.25 to 200 ng, suggesting the minimal input DNA amounts based on coverage depths required for specific applications. Nature Publishing Group 2016-05-25 /pmc/articles/PMC4879621/ /pubmed/27220682 http://dx.doi.org/10.1038/srep26732 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Chung, Jongsuk
Son, Dae-Soon
Jeon, Hyo-Jeong
Kim, Kyoung-Mee
Park, Gahee
Ryu, Gyu Ha
Park, Woong-Yang
Park, Donghyun
The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing
title The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing
title_full The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing
title_fullStr The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing
title_full_unstemmed The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing
title_short The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing
title_sort minimal amount of starting dna for agilent’s hybrid capture-based targeted massively parallel sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4879621/
https://www.ncbi.nlm.nih.gov/pubmed/27220682
http://dx.doi.org/10.1038/srep26732
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