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Mol Ecol Resour. 2017 May;17(3):508-522. doi: 10.1111/1755-0998.12595. Epub 2016 Sep 18.

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

Author information

1
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.
2
Undergraduate Program on Genomic Sciences, Universidad Nacional Autónoma de México, Av. Universidad s/n, 62210, Cuernavaca, Mexico.
3
Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
4
Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier, 31000, Toulouse, France.
5
National High-Throughput DNA Sequencing Center, University of Copenhagen, Øster Farimagsgade 2D, 1353K, Copenhagen, Denmark.
6
Institut Jacques Monod, UMR7592 CNRS, Université Paris 7, 75205, Paris cédex 13, France.
7
Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
8
Palaeogenetics Group, Johannes Gutenberg-University, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany.
9
Smurfit Institute of Genetics, Trinity College Dublin, Dublin, 2, Ireland.
10
Naturwissenschaftliches Referat an der Zentrale, Deutsches Archäologisches Institut, Im Dol 2-6, 14195, Berlin, Germany.
11
Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany.

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.

KEYWORDS:

ancient DNA; capture; enrichment; in-solution

PMID:
27566552
DOI:
10.1111/1755-0998.12595
[Indexed for MEDLINE]

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