Experimental conditions improving in-solution target enrichment for ancient DNA

Diana I. Cruz-Dávalos; Bastien Llamas; Charleen Gaunitz; Antoine Alphonse Fages; Cristina Gamba; Julien Soubrier; Pablo Librado Sanz; Andaine Seguin-Orlando; Mélanie Pruvost; Ahmed H. Alfarhan; Saleh A. Alquraishi; Khaled A. S. Al-Rasheid; Amelie Scheu; Norbert Beneke; Arne Ludwig; Alan Cooper; Eske Willerslev; Ludovic Antoine Alexandre Orlando

doi:10.1111/1755-0998.12595

Experimental conditions improving in-solution target enrichment for ancient DNA

Diana I. Cruz-Dávalos, Bastien Llamas, Charleen Gaunitz, Antoine Alphonse Fages, Cristina Gamba, Julien Soubrier, Pablo Librado Sanz, Andaine Seguin-Orlando, Mélanie Pruvost, Ahmed H. Alfarhan, Saleh A. Alquraishi, Khaled A. S. Al-Rasheid, Amelie Scheu, Norbert Beneke, Arne Ludwig, Alan Cooper, Eske Willerslev, Ludovic Antoine Alexandre Orlando

35 Citationer (Scopus)

Abstract

High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods represent cost-effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in-solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self-annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.

Originalsprog	Engelsk
Tidsskrift	Molecular Ecology Resources
Vol/bind	17
Udgave nummer	3
Sider (fra-til)	508-522
Antal sider	15
ISSN	1755-098X
DOI	https://doi.org/10.1111/1755-0998.12595
Status	Udgivet - maj 2017

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10.1111/1755-0998.12595

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Cruz-Dávalos, D. I., Llamas, B., Gaunitz, C., Fages, A. A., Gamba, C., Soubrier, J., Sanz, P. L., Seguin-Orlando, A., Pruvost, M., Alfarhan, A. H., Alquraishi, S. A., Al-Rasheid, K. A. S., Scheu, A., Beneke, N., Ludwig, A., Cooper, A., Willerslev, E., & Orlando, L. A. A. (2017). Experimental conditions improving in-solution target enrichment for ancient DNA. Molecular Ecology Resources, 17(3), 508-522. https://doi.org/10.1111/1755-0998.12595

Cruz-Dávalos, DI, Llamas, B, Gaunitz, C, Fages, AA, Gamba, C, Soubrier, J, Sanz, PL, Seguin-Orlando, A, Pruvost, M, Alfarhan, AH, Alquraishi, SA, Al-Rasheid, KAS, Scheu, A, Beneke, N, Ludwig, A, Cooper, A, Willerslev, E & Orlando, LAA 2017, 'Experimental conditions improving in-solution target enrichment for ancient DNA', Molecular Ecology Resources, bind 17, nr. 3, s. 508-522. https://doi.org/10.1111/1755-0998.12595

@article{3d3e803b7d44454b9e28fe12e1f89b96,

title = "Experimental conditions improving in-solution target enrichment for ancient DNA",

abstract = "High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods represent cost-effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in-solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self-annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.",

author = "Cruz-D{\'a}valos, {Diana I.} and Bastien Llamas and Charleen Gaunitz and Fages, {Antoine Alphonse} and Cristina Gamba and Julien Soubrier and Sanz, {Pablo Librado} and Andaine Seguin-Orlando and M{\'e}lanie Pruvost and Alfarhan, {Ahmed H.} and Alquraishi, {Saleh A.} and Al-Rasheid, {Khaled A. S.} and Amelie Scheu and Norbert Beneke and Arne Ludwig and Alan Cooper and Eske Willerslev and Orlando, {Ludovic Antoine Alexandre}",

note = "{\textcopyright} 2016 John Wiley & Sons Ltd.",

year = "2017",

month = may,

doi = "10.1111/1755-0998.12595",

language = "English",

volume = "17",

pages = "508--522",

journal = "Molecular Ecology",

issn = "0962-1083",

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number = "3",

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TY - JOUR

T1 - Experimental conditions improving in-solution target enrichment for ancient DNA

AU - Cruz-Dávalos, Diana I.

AU - Llamas, Bastien

AU - Gaunitz, Charleen

AU - Fages, Antoine Alphonse

AU - Gamba, Cristina

AU - Soubrier, Julien

AU - Sanz, Pablo Librado

AU - Seguin-Orlando, Andaine

AU - Pruvost, Mélanie

AU - Alfarhan, Ahmed H.

AU - Alquraishi, Saleh A.

AU - Al-Rasheid, Khaled A. S.

AU - Scheu, Amelie

AU - Beneke, Norbert

AU - Ludwig, Arne

AU - Cooper, Alan

AU - Willerslev, Eske

AU - Orlando, Ludovic Antoine Alexandre

PY - 2017/5

Y1 - 2017/5

N2 - High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods represent cost-effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in-solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self-annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.

AB - High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods represent cost-effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in-solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self-annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.

U2 - 10.1111/1755-0998.12595

DO - 10.1111/1755-0998.12595

M3 - Journal article

C2 - 27566552

SN - 0962-1083

VL - 17

SP - 508

EP - 522

JO - Molecular Ecology

JF - Molecular Ecology

IS - 3

ER -

Experimental conditions improving in-solution target enrichment for ancient DNA

Abstract

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