Relative performance of two DNA extraction and library preparation methods on archaeological human teeth samples
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 q...
Main Authors: | , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Taylor & Francis Group
2017-01-01
|
Series: | Science and Technology of Archaeological Research |
Subjects: | |
Online Access: | http://dx.doi.org/10.1080/20548923.2017.1388551 |
id |
doaj-c48ff8a955f44364bcade07b2bc5743b |
---|---|
record_format |
Article |
spelling |
doaj-c48ff8a955f44364bcade07b2bc5743b2020-11-24T22:16:36ZengTaylor & Francis GroupScience and Technology of Archaeological Research2054-89232017-01-0131808810.1080/20548923.2017.13885511388551Relative performance of two DNA extraction and library preparation methods on archaeological human teeth samplesMarcela Sandoval-Velasco0Inge K. C. Lundstrøm1Nathan Wales2María C. Ávila-Arcos3Hannes Schroeder4M. Thomas P. Gilbert5University of CopenhagenUniversity of CopenhagenUniversity of CopenhagenNational Autonomous University of MexicoUniversity of CopenhagenUniversity of CopenhagenDNA 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.http://dx.doi.org/10.1080/20548923.2017.1388551Ancient DNADNA extractionDNA library preparationMethod comparison |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Marcela Sandoval-Velasco Inge K. C. Lundstrøm Nathan Wales María C. Ávila-Arcos Hannes Schroeder M. Thomas P. Gilbert |
spellingShingle |
Marcela Sandoval-Velasco Inge K. C. Lundstrøm Nathan Wales María C. Ávila-Arcos Hannes Schroeder M. Thomas P. Gilbert Relative performance of two DNA extraction and library preparation methods on archaeological human teeth samples Science and Technology of Archaeological Research Ancient DNA DNA extraction DNA library preparation Method comparison |
author_facet |
Marcela Sandoval-Velasco Inge K. C. Lundstrøm Nathan Wales María C. Ávila-Arcos Hannes Schroeder M. Thomas P. Gilbert |
author_sort |
Marcela Sandoval-Velasco |
title |
Relative performance of two DNA extraction and library preparation methods on archaeological human teeth samples |
title_short |
Relative performance of two DNA extraction and library preparation methods on archaeological human teeth samples |
title_full |
Relative performance of two DNA extraction and library preparation methods on archaeological human teeth samples |
title_fullStr |
Relative performance of two DNA extraction and library preparation methods on archaeological human teeth samples |
title_full_unstemmed |
Relative performance of two DNA extraction and library preparation methods on archaeological human teeth samples |
title_sort |
relative performance of two dna extraction and library preparation methods on archaeological human teeth samples |
publisher |
Taylor & Francis Group |
series |
Science and Technology of Archaeological Research |
issn |
2054-8923 |
publishDate |
2017-01-01 |
description |
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. |
topic |
Ancient DNA DNA extraction DNA library preparation Method comparison |
url |
http://dx.doi.org/10.1080/20548923.2017.1388551 |
work_keys_str_mv |
AT marcelasandovalvelasco relativeperformanceoftwodnaextractionandlibrarypreparationmethodsonarchaeologicalhumanteethsamples AT ingekclundstrøm relativeperformanceoftwodnaextractionandlibrarypreparationmethodsonarchaeologicalhumanteethsamples AT nathanwales relativeperformanceoftwodnaextractionandlibrarypreparationmethodsonarchaeologicalhumanteethsamples AT mariacavilaarcos relativeperformanceoftwodnaextractionandlibrarypreparationmethodsonarchaeologicalhumanteethsamples AT hannesschroeder relativeperformanceoftwodnaextractionandlibrarypreparationmethodsonarchaeologicalhumanteethsamples AT mthomaspgilbert relativeperformanceoftwodnaextractionandlibrarypreparationmethodsonarchaeologicalhumanteethsamples |
_version_ |
1725788911172583424 |