TY  - GEN
A1  - Basler, Nikolas
A1  - Xenikoudakis, Georgios
A1  - Westbury, Michael V.
A1  - Song, Lingfeng
A1  - Sheng, Guilian
A1  - Barlow, Axel
T1  - Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone
T2  - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
N2  - Objective:  A key challenge in ancient DNA research is massive microbial DNA contamination from the deposition site which accumulates post mortem in the study organism’s remains. Two simple and cost-effective methods to enrich the relative endogenous fraction of DNA in ancient samples involve treatment of sample powder with either bleach or Proteinase K pre-digestion prior to DNA extraction. Both approaches have yielded promising but vary-ing results in other studies. Here, we contribute data on the performance of these methods using a comprehensive and systematic series of experiments applied to a single ancient bone fragment from a giant panda (Ailuropoda melanoleuca).Results:  Bleach and pre-digestion treatments increased the endogenous DNA content up to ninefold. However, the absolute amount of DNA retrieved was dramatically reduced by all treatments. We also observed reduced DNA damage patterns in pre-treated libraries compared to untreated ones, resulting in longer mean fragment lengths and reduced thymine over-representation at fragment ends. Guanine–cytosine (GC) contents of both mapped and total reads are consistent between treatments and conform to general expectations, indicating no obvious biasing effect of the applied methods. Our results therefore confirm the value of bleach and pre-digestion as tools in palaeog-enomic studies, providing sufficient material is available.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 715 
KW  - ancient DNA (aDNA)
KW  - bleach
KW  - pre-digestion
KW  - endogenous content
KW  - palaeogenomics
KW  - paleogenomics
KW  - next generation sequencing (NGS)
KW  - giant panda
KW  - Ailuropoda melanoleuca
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-428151
SN  - 1866-8372
IS  - 715
ER  - 
TY  - JOUR
A1  - Alberti, Federica
A1  - Gonzalez, Javier
A1  - Paijmans, Johanna L. A.
A1  - Basler, Nikolas
A1  - Preick, Michaela
A1  - Henneberger, Kirstin
A1  - Trinks, Alexandra
A1  - Rabeder, Gernot
A1  - Conard, Nicholas J.
A1  - Muenzel, Susanne C.
A1  - Joger, Ulrich
A1  - Fritsch, Guido
A1  - Hildebrandt, Thomas
A1  - Hofreiter, Michael
A1  - Barlow, Axel
T1  - Optimized DNA sampling of ancient bones using Computed Tomography scans
JF  - Molecular ecology resources
N2  - The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.
KW  - ancient DNA
KW  - computer tomography
KW  - palaeogenomics
KW  - paleogenetics
KW  - petrous bone
Y1  - 2018
U6  - https://doi.org/10.1111/1755-0998.12911
SN  - 1755-098X
SN  - 1755-0998
VL  - 18
IS  - 6
SP  - 1196
EP  - 1208
PB  - Wiley
CY  - Hoboken
ER  -