scholarly journals Comparing Two Automated Methods of DNA Extraction from Degraded Skeletal Remains

2021 ◽  
Vol 09 (02) ◽  
pp. 24-30
Author(s):  
Linda Rubinstein
Keyword(s):  
Dna Extraction ◽  
Skeletal Remains ◽  
Automated Methods

scholarly journals Comparing two automated methods of DNA extraction from degraded skeletal remains

2020 ◽  
Author(s):  
Linda Rubinstein
Keyword(s):  
Dna Extraction ◽  
Extraction Methods ◽  
Positive Control ◽  
Skeletal Remains ◽  
Variable Environment ◽  
Dna Profile ◽  
Preparation Step ◽  
Dna Profiles ◽  
Skeletal Samples ◽  
Automated Methods

AbstractDNA extraction from degraded skeletal samples is often particularly challenging. The difficulty derives from the fact that variable environment has significant effect on DNA preservation. During the years 2002-2015 unidentified degraded skeletal remains were accumulated at our institute, National Institute of Forensic Medicine (NIFM), most of them with none or partial DNA profile.As new methods rapidly emerge, we revisited the samples with partial DNA profiles. We have chosen to use these samples to compare two automated methods: Prepfiler Express BTA (Applied Biosystems) and QIAcube (Quiagen), in hope of acquiring a more complete DNA profile and eventually even make new identifications. In both methods a preparation step is required, after which the samples undergo automatic DNA extraction.The two protocols are based on different extraction methods. Fresh or non-problematic bone samples as the positive control gave the same results in both methods. In the degraded skeletal samples, the results were significantly better using the QIAcube method.

scholarly journals Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments

2018 ◽  
Vol 166 (4) ◽  
pp. 824-836 ◽  
Author(s):  
Maria A. Nieves-Colón ◽  
Andrew T. Ozga ◽  
William J. Pestle ◽  
Andrea Cucina ◽  
Vera Tiesler ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Ancient Dna ◽  
Skeletal Remains ◽  
Tropical Environments

Evaluation Of A Powder-Free DNA Extraction Method For Skeletal Remains

2018 ◽  
Vol 63 (6) ◽  
pp. 1819-1823 ◽  
Author(s):  
Michelle Harrel ◽  
Carrie Mayes ◽  
David Gangitano ◽  
Sheree Hughes-Stamm
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Skeletal Remains ◽  
Free Dna ◽  
Dna Extraction Method

Human DNA extraction from highly degraded skeletal remains: How to find a suitable method?

2020 ◽  
Vol 41 (24) ◽  
pp. 2149-2158
Author(s):  
Diana C. Vinueza‐Espinosa ◽  
Cristina Santos ◽  
Cristina Martínez‐Labarga ◽  
Assumpció Malgosa
Keyword(s):  
Dna Extraction ◽  
Skeletal Remains ◽  
Suitable Method ◽  
Human Dna

Simple and highly effective DNA extraction methods from old skeletal remains using silica columns

2010 ◽  
Vol 4 (5) ◽  
pp. 275-280 ◽  
Author(s):  
Hwan Young Lee ◽  
Myung Jin Park ◽  
Na Young Kim ◽  
Jeong Eun Sim ◽  
Woo Ick Yang ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Extraction Methods ◽  
Skeletal Remains ◽  
Highly Effective ◽  
Dna Extraction Methods

scholarly journals Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments

2017 ◽  
Author(s):  
Maria A. Nieves-Colón ◽  
Andrew T. Ozga ◽  
William J. Pestle ◽  
Andrea Cucina ◽  
Vera Tiesler ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Ancient Dna ◽  
Extraction Methods ◽  
Optimal Choice ◽  
Skeletal Remains ◽  
Tissue Type ◽  
Dna Fragments ◽  
Illumina Hiseq ◽  
Tropical Environments ◽  
Significant Difference

ABSTRACTObjectivesThe tropics harbor a large part of the world’s biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semitropical sites in Tanzania, Mexico, and Puerto Rico (N=12).Materials and MethodsAll samples were extracted twice, built into double-stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step.ResultsNo significant difference was found in overall ancient DNA yields or post-mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality-filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments.DiscussionBoth methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future.

scholarly journals Optimization of DNA extraction protocol using skeletal remains found in Sri Lanka

2019 ◽  
Vol 3 (2) ◽  
pp. 16
Author(s):  
K. M. Chandimal ◽  
S. G. Yasawardene ◽  
Ruwan J. Illeperuma
Keyword(s):  
Sri Lanka ◽  
Dna Extraction ◽  
Skeletal Remains ◽  
Extraction Protocol

scholarly journals A method for the temperature-controlled extraction of DNA from ancient bones

BioTechniques ◽  
2021 ◽  
Author(s):  
Elena Essel ◽  
Petra Korlević ◽  
Matthias Meyer
Keyword(s):  
Dna Extraction ◽  
Sequence Data ◽  
Skeletal Remains ◽  
Exogenous Dna ◽  
Significant Challenge ◽  
Sodium Phosphate Buffer ◽  
Fold Enrichment ◽  
Complete Destruction ◽  
Genome Wide ◽  
Temperature Controlled

Contamination with microbial and other exogenous DNA poses a significant challenge in the generation of genome-wide sequence data from ancient skeletal remains. Here we describe a method for separating ancient DNA into multiple fractions during DNA extraction by sequential temperature-controlled release of DNA into sodium phosphate buffer. An evaluation of the effectiveness of the method using a set of three ancient bones resulted in between 1.6- and 32-fold enrichment of endogenous DNA compared with regular DNA extraction. For two bones, the method outperformed previous methods of decontaminating ancient bones, including hypochlorite treatment, which resulted in near-complete destruction of DNA in the worst-preserved sample. This extraction method expands the spectrum of methods available for depleting contaminant DNA from ancient skeletal remains.

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