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Childebayeva A, Zavala EI. Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics. iScience 2023; 26:108066. [PMID: 37927550 PMCID: PMC10622734 DOI: 10.1016/j.isci.2023.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | - Elena I. Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, University of Oregon, Eugene, OR, USA
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Zupanič Pajnič I, Zupanc T, Leskovar T, Črešnar M, Fattorini P. Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach. Genes (Basel) 2022; 13:genes13081432. [PMID: 36011343 PMCID: PMC9407562 DOI: 10.3390/genes13081432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Tamara Leskovar
- Department of Archaeology, Faculty of Arts, University of Ljubljana, Zavetiška 5, 1000 Ljubljana, Slovenia
| | - Matija Črešnar
- Department of Archaeology, Faculty of Arts, University of Ljubljana, Zavetiška 5, 1000 Ljubljana, Slovenia
| | - Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Strada per Fiume 447, 34149 Trieste, Italy
- Correspondence: ; Tel.: +39-040-399-3265
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Brzobohatá K, Drozdová E, Smutný J, Zeman T, Beňuš R. Comparison of Suitability of the Most Common Ancient DNA Quantification Methods. Genet Test Mol Biomarkers 2017; 21:265-271. [DOI: 10.1089/gtmb.2016.0197] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Kristýna Brzobohatá
- Laboratory of Biological and Molecular Anthropology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Eva Drozdová
- Laboratory of Biological and Molecular Anthropology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Smutný
- Biovendor, Laboratory Medicine, Brno, Czech Republic
| | - Tomáš Zeman
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Radoslav Beňuš
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
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Fattorini P, Previderé C, Carboni I, Marrubini G, Sorçaburu-Cigliero S, Grignani P, Bertoglio B, Vatta P, Ricci U. Performance of the ForenSeqTMDNA Signature Prep kit on highly degraded samples. Electrophoresis 2017; 38:1163-1174. [DOI: 10.1002/elps.201600290] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 12/16/2016] [Accepted: 01/02/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Paolo Fattorini
- Department of Medicine; Surgery and Health; University of Trieste; Trieste Italy
| | - Carlo Previderé
- Department of Public Health; Experimental and Forensic Medicine; Section of Legal Medicine and Forensic Sciences; University of Pavia; Pavia Italy
| | | | | | | | - Pierangela Grignani
- Department of Public Health; Experimental and Forensic Medicine; Section of Legal Medicine and Forensic Sciences; University of Pavia; Pavia Italy
| | - Barbara Bertoglio
- Department of Public Health; Experimental and Forensic Medicine; Section of Legal Medicine and Forensic Sciences; University of Pavia; Pavia Italy
| | - Paolo Vatta
- Scuola Internazionale Superiore di Studi Avanzati (SISSA); Functional and Structural Genomics sector; Trieste Italy
| | - Ugo Ricci
- SOD Diagnostica Genetica, A.O-U Careggi; Firenze Italy
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Surveying the repair of ancient DNA from bones via high-throughput sequencing. Biotechniques 2015; 59:19-25. [PMID: 26156780 DOI: 10.2144/000114307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/05/2015] [Indexed: 11/23/2022] Open
Abstract
DNA damage in the form of abasic sites, chemically altered nucleotides, and strand fragmentation is the foremost limitation in obtaining genetic information from many ancient samples. Upon cell death, DNA continues to endure various chemical attacks such as hydrolysis and oxidation, but repair pathways found in vivo no longer operate. By incubating degraded DNA with specific enzyme combinations adopted from these pathways, it is possible to reverse some of the post-mortem nucleic acid damage prior to downstream analyses such as library preparation, targeted enrichment, and high-throughput sequencing. Here, we evaluate the performance of two available repair protocols on previously characterized DNA extracts from four mammoths. Both methods use endonucleases and glycosylases along with a DNA polymerase-ligase combination. PreCR Repair Mix increases the number of molecules converted to sequencing libraries, leading to an increase in endogenous content and a decrease in cytosine-to-thymine transitions due to cytosine deamination. However, the effects of Nelson Repair Mix on repair of DNA damage remain inconclusive.
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Dovgerd AP, Zharkov DO. Application of repair enzymes to improve the quality of degraded DNA templates for PCR amplification. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814030053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hybridization capture reveals evolution and conservation across the entire Koala retrovirus genome. PLoS One 2014; 9:e95633. [PMID: 24752422 PMCID: PMC3994108 DOI: 10.1371/journal.pone.0095633] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/28/2014] [Indexed: 11/19/2022] Open
Abstract
The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin.
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Preamplification procedure for the analysis of ancient DNA samples. ScientificWorldJournal 2013; 2013:734676. [PMID: 24187523 PMCID: PMC3800654 DOI: 10.1155/2013/734676] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/02/2013] [Indexed: 11/18/2022] Open
Abstract
In ancient DNA studies the low amount of endogenous DNA represents a limiting factor that often hampers the result achievement. In this study we extracted the DNA from nine human skeletal remains of different ages found in the Byzantine cemetery of Abdera Halkidiki and in the medieval cemetery of St. Spiridion in Rhodes (Greece). Real-time quantitative polymerase chain reaction (qPCR) was used to detect in the extracts the presence of PCR inhibitors and to estimate the DNA content. As mitochondrial DNA was detected in all samples, amplification of nuclear targets, as amelogenin and the polymorphism M470V of the transmembrane conductance regulator gene, yielded positive results in one case only. In an effort to improve amplification success, we applied, for the first time in ancient DNA, a preamplification strategy based on TaqMan PreAmp Master Mix. A comparison between results obtained from nonpreamplified and preamplified samples is reported. Our data, even if preliminary, show that the TaqMan PreAmp procedure may improve the sensitivity of qPCR analysis.
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Harder M, Renneberg R, Meyer P, Krause-Kyora B, von Wurmb-Schwark N. STR-typing of ancient skeletal remains: which multiplex-PCR kit is the best? Croat Med J 2013; 53:416-22. [PMID: 23100203 PMCID: PMC3494155 DOI: 10.3325/cmj.2012.53.416] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Aim To comparatively test nine commercially available short tandem repeat (STR)-multiplex kits (PowerPlex 16, 16HS, ES, ESI17, ESX17, S5 [all Promega]; AmpFiSTR Identifiler, NGM and SEfiler [all Applied Biosystems]) for their efficiency and applicability to analyze ancient and thus highly degraded DNA samples. Methods Fifteen human skeletal remains from the late medieval age were obtained and analyzed using the nine polymerase chain reaction assays with slightly modified protocols. Data were systematically compared to find the most meaningful and sensitive assay. Results The ESI, ESX, and NGM kits showed the best overall results regarding amplification success, detection rate, identification of heterozygous alleles, sex determination, and reproducibility of the obtained data. Conclusion Since application of these three kits enables the employment of different primer sequences for all the investigated amplicons, a combined application is recommended for best possible and – most importantly – reliable genetic analysis of ancient skeletal material or otherwise highly degraded samples, eg, from forensic cases.
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Affiliation(s)
- Melanie Harder
- Institute of Legal Medicine, University Hospital Schleswig-Holstein, Campus Kiel, Arnold-Heller-Strasse 12, Kiel, Germany
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Budimlija ZM, Caragine TA. Interpretation guidelines for multilocus STR forensic profiles from low template DNA samples. Methods Mol Biol 2012; 830:199-211. [PMID: 22139662 DOI: 10.1007/978-1-61779-461-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Low template (LT) DNA testing is a more sensitive method of PCR DNA typing which tests lower quantities of DNA compared to traditional PCR DNA protocols. Methods applied in this testing involve amplification or postamplification efforts to increase detection sensitivity. Establishing the interpretation rules of the results obtained is condition sine qua non for successful incorporation of this valuable technique into forensic casework. Here we describe a successfully optimized and validated approach to interpretation of LT-DNA samples.
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Affiliation(s)
- Zoran M Budimlija
- Department of Forensic Biology, New York City Office of Chief Medical Examiner, New York, NY, USA
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Speller CF, Nicholas GP, Yang DY. Feather barbs as a good source of mtDNA for bird species identification in forensic wildlife investigations. INVESTIGATIVE GENETICS 2011; 2:16. [PMID: 21794178 PMCID: PMC3199791 DOI: 10.1186/2041-2223-2-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 07/28/2011] [Indexed: 12/01/2022]
Abstract
Background The ability to accurately identify bird species is crucial for wildlife law enforcement and bird-strike investigations. However, such identifications may be challenging when only partial or damaged feathers are available for analysis. Results By applying vigorous contamination controls and sensitive PCR amplification protocols, we found that it was feasible to obtain accurate mitochondrial (mt)DNA-based species identification with as few as two feather barbs. This minimally destructive DNA approach was successfully used and tested on a variety of bird species, including North American wild turkey (Meleagris gallopavo), Canada goose (Branta canadensis), blue heron (Ardea herodias) and pygmy owl (Glaucidium californicum). The mtDNA was successfully obtained from 'fresh' feathers, historic museum specimens and archaeological samples, demonstrating the sensitivity and versatility of this technique. Conclusions By applying appropriate contamination controls, sufficient quantities of mtDNA can be reliably recovered and analyzed from feather barbs. This previously overlooked substrate provides new opportunities for accurate DNA species identification when minimal feather samples are available for forensic analysis.
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Affiliation(s)
- Camilla F Speller
- Centre for Forensic Research, Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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Winters M, Barta JL, Monroe C, Kemp BM. To clone or not to clone: method analysis for retrieving consensus sequences in ancient DNA samples. PLoS One 2011; 6:e21247. [PMID: 21738625 PMCID: PMC3124491 DOI: 10.1371/journal.pone.0021247] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 05/24/2011] [Indexed: 01/06/2023] Open
Abstract
The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from "modern" DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be "gold standards" in the field, including cloning aDNA amplicons as opposed to directly sequencing them. However, no standardized protocol has emerged regarding the necessary number of clones to sequence, how a consensus sequence is most appropriately derived, or how results should be reported in the literature. In addition, there has been no systematic demonstration of the degree to which direct sequences are affected by damage or whether direct sequencing would provide disparate results from a consensus of clones.To address this issue, a comparative study was designed to examine both cloned and direct sequences amplified from ∼3,500 year-old ancient northern fur seal DNA extracts. Majority rules and the Consensus Confidence Program were used to generate consensus sequences for each individual from the cloned sequences, which exhibited damage at 31 of 139 base pairs across all clones. In no instance did the consensus of clones differ from the direct sequence. This study demonstrates that, when appropriate, cloning need not be the default method, but instead, should be used as a measure of authentication on a case-by-case basis, especially when this practice adds time and cost to studies where it may be superfluous.
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Affiliation(s)
- Misa Winters
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Jodi Lynn Barta
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
| | - Cara Monroe
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, University of California-Santa Barbara, Santa Barbara, California, United States of America
| | - Brian M. Kemp
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
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Tsangaras K, Greenwood AD. Museums and disease: using tissue archive and museum samples to study pathogens. Ann Anat 2011; 194:58-73. [PMID: 21641784 DOI: 10.1016/j.aanat.2011.04.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 04/06/2011] [Accepted: 04/06/2011] [Indexed: 11/28/2022]
Abstract
Molecular studies of archival and fossil samples have traditionally focused on the nucleic acids derived from the host species. However, there has recently been an increase in ancient DNA research on the identification and characterization of infectious agents within the hosts. The study of pathogens from the past provides great opportunities for discovering the causes of historical infection events, characterizing host-microorganism co-evolution and directly investigating the evolution of specific pathogens. Several research teams have been able to isolate and characterize a variety of different bacterial, parasite and viral microorganisms. However, this emerging field is not without obstacles. The diagenetic processes that make ancient DNA research generally difficult are also impediments to ancient pathogen research and perhaps more so given that their DNA may represent an even rarer proportion of the remaining nucleic acids in a fossil sample than host DNA. However, studies performed under controlled conditions and following stringent ancient DNA protocols can and have yielded reliable and often surprising results. This article reviews the advantages, problems, and failures of ancient microbiological research.
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Naidoo T, Schlebusch CM, Makkan H, Patel P, Mahabeer R, Erasmus JC, Soodyall H. Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations. INVESTIGATIVE GENETICS 2010; 1:6. [PMID: 21092339 PMCID: PMC2988483 DOI: 10.1186/2041-2223-1-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 09/01/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND The ability of the Y chromosome to retain a record of its evolution has seen it become an essential tool of molecular anthropology. In the last few years, however, it has also found use in forensic genetics, providing information on the geographic origin of individuals. This has been aided by the development of efficient screening methods and an increased knowledge of geographic distribution. In this study, we describe the development of single base extension assays used to resolve 61 Y chromosome haplogroups, mainly within haplogroups A, B and E, found in Africa. RESULTS Seven multiplex assays, which incorporated 60 Y chromosome markers, were developed. These resolved Y chromosomes to 61 terminal branches of the major African haplogroups A, B and E, while also including a few Eurasian haplogroups found occasionally in African males. Following its validation, the assays were used to screen 683 individuals from Southern Africa, including south eastern Bantu speakers (BAN), Khoe-San (KS) and South African Whites (SAW). Of the 61 haplogroups that the assays collectively resolved, 26 were found in the 683 samples. While haplogroup sharing was common between the BAN and KS, the frequencies of these haplogroups varied appreciably. Both groups showed low levels of assimilation of Eurasian haplogroups and only two individuals in the SAW clearly had Y chromosomes of African ancestry. CONCLUSIONS The use of these single base extension assays in screening increased haplogroup resolution and sampling throughput, while saving time and DNA. Their use, together with the screening of short tandem repeat markers would considerably improve resolution, thus refining the geographic ancestry of individuals.
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Affiliation(s)
- Thijessen Naidoo
- Human Genomic Diversity and Disease Research Unit, Division of Human Genetics, School of Pathology, University of the Witwatersrand and the National Health Laboratory Services, Johannesburg, South Africa.
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Rohland N, Siedel H, Hofreiter M. A rapid column-based ancient DNA extraction method for increased sample throughput. Mol Ecol Resour 2009; 10:677-83. [PMID: 21565072 DOI: 10.1111/j.1755-0998.2009.02824.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Genetic analyses using museum specimens and ancient DNA from fossil samples are becoming increasingly important in phylogenetic and especially population genetic studies. Recent progress in ancient DNA sequencing technologies has substantially increased DNA sequence yields and, in combination with barcoding methods, has enabled large-scale studies using any type of DNA. Moreover, more and more studies now use nuclear DNA sequences in addition to mitochondrial ones. Unfortunately, nuclear DNA is, due to its much lower copy number in living cells compared to mitochondrial DNA, much more difficult to obtain from low-quality samples. Therefore, a DNA extraction method that optimizes DNA yields from low-quality samples and at the same time allows processing many samples within a short time frame is immediately required. In fact, the major bottleneck in the analysis process using samples containing low amounts of degraded DNA now lies in the extraction of samples, as column-based methods using commercial kits are fast but have proven to give very low yields, while more efficient methods are generally very time-consuming. Here, we present a method that combines the high DNA yield of batch-based silica extraction with the time-efficiency of column-based methods. Our results on Pleistocene cave bear samples show that DNA yields are quantitatively comparable, and in fact even slightly better than with silica batch extraction, while at the same time the number of samples that can conveniently be processed in parallel increases and both bench time and costs decrease using this method. Thus, this method is suited for harvesting the power of high-throughput sequencing using the DNA preserved in the millions of paleontological and museums specimens.
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Affiliation(s)
- Nadin Rohland
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA Department of Biology, University of York, YO10 5YW, York, UK
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Matheson CD, Marion TE, Hayter S, Esau N, Fratpietro R, Vernon KK. Technical note: Removal of metal ion inhibition encountered during DNA extraction and amplification of copper-preserved archaeological bone using size exclusion chromatography. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 140:384-91. [DOI: 10.1002/ajpa.21106] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Pegard A, Miquel C, Valentini A, Coissac E, Bouvier F, François D, Taberlet P, Engel E, Pompanon F. Universal DNA-based methods for assessing the diet of grazing livestock and wildlife from feces. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:5700-5706. [PMID: 19566081 DOI: 10.1021/jf803680c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Because of the demand for controlling livestock diets, two methods that characterize the DNA of plants present in feces were developed. After DNA extraction from fecal samples, a short fragment of the chloroplastic trnL intron was amplified by PCR using a universal primer pair for plants. The first method generates a signature that is the electrophoretic migration pattern of the PCR product. The second method consists of sequencing several hundred DNA fragments from the PCR product through pyrosequencing. These methods were validated with a blind analysis of feces from concentrate- and pasture-fed lambs. The signature method allowed differentiation of the two diets and confirmed the presence of concentrate in one of them. The pyrosequencing method allowed the identification of up to 25 taxa in a diet. These methods are complementary to the chemical methods already used. They could be applied to the control of diets and the study of food preferences.
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Affiliation(s)
- Anthony Pegard
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble Cedex 9, France
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von Wurmb-Schwark N, Heinrich A, Freudenberg M, Gebühr M, Schwark T. The impact of DNA contamination of bone samples in forensic case analysis and anthropological research. Leg Med (Tokyo) 2008; 10:125-30. [DOI: 10.1016/j.legalmed.2007.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 09/10/2007] [Accepted: 10/03/2007] [Indexed: 10/22/2022]
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Performance evaluation of thermal cyclers for PCR in a rapid cycling condition. Biotechniques 2008; 44:495-6, 498, 500 passim. [DOI: 10.2144/000112705] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The performance of thermal cyclers for polymerase chain reactions (PCR) is of great concern in terms of the reliability of PCR-based assays, particularly when rapid cycling conditions are applied to small volume reactions. In this work, the precision of the temperature controls during rapid thermal cycling was measured in 19 commercial thermal cyclers of 8 different models. The temperatures of test solutions in specific locations in each thermal block were simultaneously monitored at 1 s intervals during thermal cycling. A temperature-sensitive multiplex PCR was run in parallel to assess undesirable PCR results caused by poor temperature control. Under the given conditions (20 s of annealing time and 20 µL reaction volume), a majority of the tested instruments showed prominent curving, undershooting, and/or overshooting in their temperature profiles, which substantially influenced the results of the temperature-sensitive multiplex PCR. Variations between wells were also observed in most instruments. It is strongly hoped that these problems will be addressed by manufacturers and that they will make substantial improvements in the precision and efficiency of thermal cyclers. In the meantime, users of thermal cyclers might be able to avoid unexpected poor outcomes of sensitive PCR-based assays by designing their PCR protocols with these findings in mind.
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Salas A, Bandelt HJ, Macaulay V, Richards MB. Phylogeographic investigations: the role of trees in forensic genetics. Forensic Sci Int 2006; 168:1-13. [PMID: 16814504 DOI: 10.1016/j.forsciint.2006.05.037] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Revised: 05/19/2006] [Accepted: 05/21/2006] [Indexed: 11/16/2022]
Abstract
The human mitochondrial DNA (mtDNA) genome is commonly analyzed in various disciplines, such as population, medical, and forensic genetics, but conceptual and scientific exchange between them is still limited. Here we review several aspects of the mtDNA phylogeny that are particularly--but not exclusively--of interest to the forensic community. Among the issues that arise, we emphasize the importance of integrating evolutionary concepts into the forensic routine. We also discuss topics such as mtDNA mutation-rate heterogeneity and the weight of evidence, ethnic affiliations of mtDNA profiles, and the abuse of reference databases. Finally, we show the usefulness of coding-region variation in a forensic context.
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Affiliation(s)
- A Salas
- Unidad de Genética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, 15782 Galicia, Spain.
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Kemp BM, Smith DG. Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Sci Int 2005; 154:53-61. [PMID: 16182949 DOI: 10.1016/j.forsciint.2004.11.017] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2004] [Revised: 11/24/2004] [Accepted: 11/26/2004] [Indexed: 11/22/2022]
Abstract
The extraction of DNA from archaeological or forensic skeletal remains can provide quite powerful data for analysis, but is plagued by a unique set of methodological problems. One of the most important methodological problems to overcome in such analyses is the presence of modern contamination on the surfaces of bones and teeth, which can lead to false positives and erroneous results unless it is removed before DNA extraction is initiated. Ancient DNA (aDNA) researchers and forensic scientists have employed a number of techniques to minimize such contamination. One such technique is the use of bleach (sodium hypochlorite--NaOCl) to "destroy" contaminating DNA. However, a consensus on the optimum concentration of sodium hypochlorite to be used and the amount of time the bone or tooth should be exposed to it has not emerged. The present study systematically approaches the issue by introducing contamination to ancient bones (from approximately 500 BP) and determining which of several sodium hypochlorite treatments best eliminates surface contamination. The elimination of surface contamination from bone requires immersion in at least 3.0% (w/v) sodium hypochlorite (approximately equal parts of commercial bleach and water) for at least 15 min. Endogenous DNA proved to be quite stable to even extreme sodium hypochlorite treatments (6% for 21 h), suggesting that DNA adsorbs to hydroxyapatite in the bone and that this process facilitates the preservation of DNA in ancient skeletal remains.
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Affiliation(s)
- Brian M Kemp
- Department of Anthropology, University of California, Davis, CA 95616, USA.
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Yang I, Kim YH, Byun JY, Park SR. Use of multiplex polymerase chain reactions to indicate the accuracy of the annealing temperature of thermal cycling. Anal Biochem 2005; 338:192-200. [PMID: 15745739 DOI: 10.1016/j.ab.2004.09.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Indexed: 10/25/2022]
Abstract
A condition for multiplex polymerase chain reactions (PCRs) of which outcomes sensitively indicate the actual annealing temperature of thermal cycling is reported. The multiplex reaction was designed to produce four different amplicons of 200, 300, 400, and 480 bp. However, the degree of amplification of each amplicon sensitively responds to a small change in the annealing temperature, by which one can predict the actual annealing temperature of thermal cycling. Deviations between the actual and the designated annealing temperatures as small as 0.5 degrees C were manifested by the banding patterns of the multiplex PCRs in simple agarose gel electrophoresis. For prediction of temperatures in a more objective manner, capillary electrophoresis was also applied to obtain numerical expressions of the relative intensities of the amplicons. By optimizing the multiplex PCR conditions, where concentrations of buffer, dNTPs, and primer pairs were major factors, satisfactory sensitivity and reproducibility of the band patterning were achieved. Blind tests demonstrated the accuracy of the prediction of actual annealing temperatures within +/-0.5 degrees C. The multiplex PCR approach will be further refined and tested for realization of an easily accessible alternative to a physical temperature measurement device in testing the performance of thermal cyclers for PCR.
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Affiliation(s)
- Inchul Yang
- Division of Chemical Metrology and Materials Evaluation, Korea Research Institute of Standards and Science, 1 Doryong-dong, Yuseong-gu, Daejeon 305-340, Republic of Korea
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Affiliation(s)
- T A Brettell
- Office of Forensic Sciences, New Jersey State Police, New Jersey Forensic Science and Technology Complex, 1200 Negron Road, Horizon Center, Hamilton, New Jersey 08691, USA
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