A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture
Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality-assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%–3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies.
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Format: | artículo biblioteca |
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John Wiley & Sons
2019-05
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Subjects: | Chimpanzees, Conservation genomics, Faecal samples, Population genomics, Target enrichment, |
Online Access: | http://hdl.handle.net/10261/201293 http://dx.doi.org/10.13039/501100011033 http://dx.doi.org/10.13039/501100004189 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/100000011 http://dx.doi.org/10.13039/501100002809 |
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dig-ibe-es-10261-2012932022-11-07T12:14:24Z A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture White, Lauren C. Fontsere, Claudia Lizano, Esther Hughes, David A. Angedakin, Samuel Arandjelovic, Mimi Granjon, Anne‐Céline Hans, Jörg B. Lester, Jack D. Rabanus-Wallace, M. Timothy Rowney, Carolyn Städele, Veronika Marqués-Bonet, Tomàs Langergraber, Kevin E. Vigilant, Linda Agencia Estatal de Investigación (España) Max Planck Society Ministerio de Ciencia, Innovación y Universidades (España) European Commission Howard Hughes Medical Institute Fundación "la Caixa" Generalitat de Catalunya La Caixa Chimpanzees Conservation genomics Faecal samples Population genomics Target enrichment Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality-assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%–3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies. Funding was provided by the Max Planck Society and the President's Strategic Initiative Fund of ASU. T.M.B. is supported by BFU2017‐86471‐P (MINECO/FEDER, UE), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d'Universitats i Recerca and CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880) and C.F. is supported by a La Caixa PhD Fellowship. 2020-02-20T08:04:36Z 2020-02-20T08:04:36Z 2019-05 2020-02-20T08:04:36Z artículo http://purl.org/coar/resource_type/c_6501 doi: 10.1111/1755-0998.12993 e-issn: 1755-0998 issn: 1755-098X Molecular Ecology Resources 19: 609- 622 (2019) http://hdl.handle.net/10261/201293 10.1111/1755-0998.12993 http://dx.doi.org/10.13039/501100011033 http://dx.doi.org/10.13039/501100004189 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/100000011 http://dx.doi.org/10.13039/501100002809 #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# BFU2017‐86471-P/AEI/10.13039/501100011033 info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/BFU2017-86471-P http://dx.doi.org/10.1111/1755-0998.12993 Sí none John Wiley & Sons |
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Chimpanzees Conservation genomics Faecal samples Population genomics Target enrichment Chimpanzees Conservation genomics Faecal samples Population genomics Target enrichment |
spellingShingle |
Chimpanzees Conservation genomics Faecal samples Population genomics Target enrichment Chimpanzees Conservation genomics Faecal samples Population genomics Target enrichment White, Lauren C. Fontsere, Claudia Lizano, Esther Hughes, David A. Angedakin, Samuel Arandjelovic, Mimi Granjon, Anne‐Céline Hans, Jörg B. Lester, Jack D. Rabanus-Wallace, M. Timothy Rowney, Carolyn Städele, Veronika Marqués-Bonet, Tomàs Langergraber, Kevin E. Vigilant, Linda A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture |
description |
Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality-assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%–3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies. |
author2 |
Agencia Estatal de Investigación (España) |
author_facet |
Agencia Estatal de Investigación (España) White, Lauren C. Fontsere, Claudia Lizano, Esther Hughes, David A. Angedakin, Samuel Arandjelovic, Mimi Granjon, Anne‐Céline Hans, Jörg B. Lester, Jack D. Rabanus-Wallace, M. Timothy Rowney, Carolyn Städele, Veronika Marqués-Bonet, Tomàs Langergraber, Kevin E. Vigilant, Linda |
format |
artículo |
topic_facet |
Chimpanzees Conservation genomics Faecal samples Population genomics Target enrichment |
author |
White, Lauren C. Fontsere, Claudia Lizano, Esther Hughes, David A. Angedakin, Samuel Arandjelovic, Mimi Granjon, Anne‐Céline Hans, Jörg B. Lester, Jack D. Rabanus-Wallace, M. Timothy Rowney, Carolyn Städele, Veronika Marqués-Bonet, Tomàs Langergraber, Kevin E. Vigilant, Linda |
author_sort |
White, Lauren C. |
title |
A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture |
title_short |
A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture |
title_full |
A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture |
title_fullStr |
A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture |
title_full_unstemmed |
A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture |
title_sort |
roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture |
publisher |
John Wiley & Sons |
publishDate |
2019-05 |
url |
http://hdl.handle.net/10261/201293 http://dx.doi.org/10.13039/501100011033 http://dx.doi.org/10.13039/501100004189 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/100000011 http://dx.doi.org/10.13039/501100002809 |
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