Relative performance of two DNA extraction and library preparation methods on archaeological human teeth samples

TY - JOUR

T1 - Relative performance of two DNA extraction and library preparation methods on archaeological human teeth samples

AU - Sandoval-Velasco, Marcela

AU - Lundstrøm, Inge K.C.

AU - Wales, Nathan

AU - Ávila-Arcos, María C.

AU - Schroeder, Hannes

AU - Gilbert, M. Thomas P.

N1 - Funding Information: We would like to thank Gordon Turner-Walker, Elizabeth Peacock, Jon Anders Risvaag and Birgitte Skar of the Norwegian University of Science and Technology (Trondheim, Norway) for supplying the samples, and the staff of the Danish National High-Throughput DNA Sequencing Center for technical assistance and sequencing. We acknowledge the following funding sources: Marie Curie grants EUROTAST FP7-PEOPLE-2010 MC ITN, Danish Council for Independent Research grants 10-081390 and DNRF94, and Lundbeck Foundation grant R52-A506. Special thanks to José Victor Moreno-Mayar and José Samaniego for assistance during data analysis. Publisher Copyright: © 2017, © 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

PY - 2017/11/1

Y1 - 2017/11/1

N2 - DNA extraction and library preparation are crucial steps in any ancient DNA study. Although palaeogenomic researchers are facing a growing choice of DNA extraction and sequencing library preparation methods, how their performance varies with DNA preservation remains unclear. To help elucidate this question, we compared the performance of two common DNA extraction and Illumina library preparation methods on a set of archaeological human samples, considered to contain ancient DNA of intermediate to good preservation (5–50% endogenous DNA). Results indicate that while the levels of contamination and endogenous DNA recovered are comparable for both silica-in-solution and silica-column based extractions, the ability of the former to accommodate larger starting quantities of sample material confers notable benefits with regards to library complexity, and furthermore seems to aid with the recovery of shorter endogenous DNA molecules. While our observations gained from comparing the single-stranded with double-stranded DNA library construction methods largely replicate earlier observations, the combination of our data with previously published datasets demonstrate that the benefits gained using single-stranded methods are inversely proportional to the endogenous DNA content in the ancient sample.

AB - DNA extraction and library preparation are crucial steps in any ancient DNA study. Although palaeogenomic researchers are facing a growing choice of DNA extraction and sequencing library preparation methods, how their performance varies with DNA preservation remains unclear. To help elucidate this question, we compared the performance of two common DNA extraction and Illumina library preparation methods on a set of archaeological human samples, considered to contain ancient DNA of intermediate to good preservation (5–50% endogenous DNA). Results indicate that while the levels of contamination and endogenous DNA recovered are comparable for both silica-in-solution and silica-column based extractions, the ability of the former to accommodate larger starting quantities of sample material confers notable benefits with regards to library complexity, and furthermore seems to aid with the recovery of shorter endogenous DNA molecules. While our observations gained from comparing the single-stranded with double-stranded DNA library construction methods largely replicate earlier observations, the combination of our data with previously published datasets demonstrate that the benefits gained using single-stranded methods are inversely proportional to the endogenous DNA content in the ancient sample.

KW - Ancient DNA

KW - DNA extraction

KW - DNA library preparation

KW - Method comparison

UR - http://www.scopus.com/inward/record.url?scp=85057156219&partnerID=8YFLogxK

U2 - 10.1080/20548923.2017.1388551

DO - 10.1080/20548923.2017.1388551

M3 - Article

AN - SCOPUS:85057156219

SN - 2054-8923

VL - 3

SP - 80

EP - 88

JO - Science and Technology of Archaeological Research

JF - Science and Technology of Archaeological Research

IS - 1

ER -