Progress in forensic bone DNA analysis: lessons learned from ancient DNA

Ancient DNA: do it right or not at all.

Science. 289 (): 1139

A molecular handle on the Neanderthals.

Nature. 388: 225-226Dabney J. Meyer M. Pääbo S.

Ancient DNA damage.

Cold Spring Harbor perspectives in biology. 5a012567Mitchell D. Willerslev E. Hansen A.

Damage and repair of ancient DNA.

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. 571: 265-276Ambers A.D. Churchill J.D. King J.L. Stoljarova M. Gill-King H. Assidi M. Abu-Elmagd M. Buhmeida A. Al-Qahtani M. Budowle B.

More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing.

BMC genomics. 17: 21-30Ambers A. Votrubova J. Vanek D. Sajantila A. Budowle B.

Improved Y-STR typing for disaster victim identification, missing persons investigations, and historical human skeletal remains.

International journal of legal medicine. 132: 1545-1553Ambers A. Gill-King H. Dirkmaat D. Benjamin R. King J. Budowle B.

Autosomal and Y-STR analysis of degraded DNA from the 120-year-old skeletal remains of Ezekiel Harper. Forensic Science.

International: Genetics. 9: 33-41Malmström H. Storå J. Dalén L. Holmlund G. Götherström A.

Extensive human DNA contamination in extracts from ancient dog bones and teeth.

Molecular biology and evolution. 22: 2040-2047Bouwman A.S. Chilvers E.R. Brown K.A. Brown T.A.

Brief communication: identification of the authentic ancient DNA sequence in a human bone contaminated with modern DNA.

American Journal of Physical Anthropology: The Official Publication of the American Association of Physical Anthropologists. 131: 428-431Votrubova-Dubska J. Vanek D. Zikmund J. Mestek O. Urbanova V. Brzobohata H. Brestovansky P.

Efficient removal of a PCR inhibitory agent (vivianite) found on excavated bones.

Forensic science international. 261: 8-13

Ancient DNA extraction from bones and teeth.

Nature protocols. 2: 1756-1762Montiel R. Malgosa A. Subirà E. Overcoming P.C.R.

inhibitors in ancient DNA extracts from teeth.

J Ancient Biomol. 1: 221-225Hagelberg E. Sykes B. Hedges R.

Ancient bone DNA amplified.

Nature. 342: 485Pääbo S. Gifford J.A. Wilson A.C.

Mitochondrial DNA sequences from a 7000-year old brain.

Nucleic acids research. 16: 9775-9787Hochmeister M.N. Dirnhofer R. Borer U. Budowle B. Jung J. Comey C.T.

PCR-based typing of DNA extracted from cigarette butts.

International Journal of Legal Medicine. 104: 229-233Hochmeister M.N. Budowle B. Borer U.V. Eggmann U. Comey C.T. Dirnhofer R.

Typing of deoxyribonucleic acid (DNA) extracted from compact bone from human remains.

Journal of Forensic Science. 36: 1649-1661Kistler L. Ware R. Smith O. Collins M. Allaby R.G.

A new model for ancient DNA decay based on paleogenomic meta-analysis.

Nucleic Acids Research. 45: 6310-6320

Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification.

Proceedings of the National Academy of Sciences. 86: 1939-1943Rollo F. Venanzi F.M. Amici A.

Nucleic acids in mummified plant seeds: biochemistry and molecular genetics of pre-Columbian maize.

Genetics Research. 58: 193-201Dabney J. Knapp M. Glocke I. Gansauge M.-T. Weihmann A. Nickel B. Valdiosera C. García N. Pääbo S. Arsuaga J.L. Meyer M.

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.

Proceedings of the National Academy of Sciences. 110: 15758-15763

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth.

Genome research. 27: 1230-1237Hansen A.J. Mitchell D.L. Wiuf C. Paniker L. Brand T.B. Binladen J. Gilichinsky D.A. Rønn R. Willerslev E.

Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments.

Genetics. 173: 1175-1179Heyn P. Stenzel U. Briggs A.W. Kircher M. Hofreiter M. Meyer M.

Road blocks on paleogenomes—polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA.

Nucleic acids research. 38 (): 161Vanek D. Saskova L. Koch H.

Kinship and Y-chromosome analysis of 7th century human remains: novel DNA extraction and typing procedure for ancient material.

Croatian medical journal. 50: 286-295Yahya P. Gaudieri S. Franklin D.

DNA analysis of human skeletal remains associated with the Batavia mutiny of 1629.

Records of the Western Australian Museum. 26: 98Haak W. Brandt G. de Jong H.N. Meyer C. Ganslmeier R. Heyd V. Hawkesworth C. Pike A.W. Meller H. Alt K.W.

Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age.

Proceedings of the National Academy of Sciences. 105: 18226-18231Lassen C. Hummel S. Herrmann B.

[Molecular sex determination in skeletal remains of premature and newborn infants of the Aegerten, Switzerland, burial field].

Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur. 55: 183-191

Molecular sex identification of juvenile skeletal remains from an Irish medieval population using ancient DNA analysis.

Journal of Archaeological Science. 62: 27-38Bouakaze C. Keyser C. Crubézy E. Montagnon D. Ludes B.

Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis.

International journal of legal medicine. 123: 315-325Draus-Barini J. Walsh S. Pośpiech E. Kupiec T. Głąb H. Branicki W. Kayser M.

Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains.

Investigative genetics. 4: 3Zink A. Grabner W. Reischl U. Wolf H. Nerlich A.

Molecular study on human tuberculosis in three geographically distinct and time delineated populations from ancient Egypt.

Epidemiology & Infection. 130: 239-249

Massive migrations? The impact of recent aDNA studies on our view of third millennium Europe.

European Journal of Archaeology. 21: 159-191

Osteomorphology and osteometry versus aDNA in taxonomic identification of fragmentary sheep and sheep/goat bones from archaeological deposits: Blydefontein Shelter, Karoo, South Africa.

Southern African Humanities. : 28Shin D.H. Oh C.S. Lee H.J. Chai J.Y. Lee S.J. Hong D.-W. Lee S.D. Seo M.

Ancient DNA analysis on Clonorchis sinensis eggs remained in samples from medieval Korean mummy.

Journal of Archaeological Science. 40: 211-216Panagiotakopulu E. Buckland P.C.

Forensic archaeoentomology—an insect fauna from a burial in York Minster.

Forensic Science International. 221: 125-130Spencer P. Schmidt D. Hummel S.

Identification of historical specimens and wildlife seizures originating from highly degraded sources of kangaroos and other macropods.

Forensic Science, Medicine, and Pathology. 6: 225-232Götherström A. Anderung C. Hellborg L. Elburg R. Smith C. Bradley D.G. Ellegren H.

Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe.

Proceedings of the Royal Society B: Biological Sciences. 272: 2345-2351Dorado G. Fraile I.R. Sánchez-Cañete F.J.S. Luque F. Jiménez I. Gálvez M. et al.

Ancient DNA to decipher the domestication of dog.

Archaeobios. 3: 127-132Nelson‐Chorney H.T. Davis C.S. Poesch M.S. Vinebrooke R.D. Carli C.M. Taylor M.K.

Environmental DNA in lake sediment reveals biogeography of native genetic diversity.

Frontiers in Ecology and the Environment. 17: 313-318Oswald J.A. Allen J.M. Witt K.E. Folk R.A. Albury N.A. Steadman D.W. Guralnick R.P.

Ancient DNA from a 2,500-year-old Caribbean fossil places an extinct bird (Caracara creightoni) in a phylogenetic context.

Molecular phylogenetics and evolution. 140106576Dittmar K. SMd Souza Araújo A.

Challenges of phylogenetic analyses of aDNA sequences.

Memorias do Instituto Oswaldo Cruz. 101: 9-13Karanth K.P. Delefosse T. Rakotosamimanana B. Parsons T.J. Yoder A.D.

Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates.

Proceedings of the National Academy of Sciences. 102: 5090-5095Devault A.M. McLoughlin K. Jaing C. Gardner S. Porter T.M. Enk J.M. Thissen J. Allen J. Borucki M. DeWitte S.N. Dhody A.N. Poinar H.N.

Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array.

Scientific reports. 4: 1-8

The search for a sequencing thoroughbred.

Nature Biotechnology. 23: 1333-1335Mohammadi A. Ghorbani Alvanegh A. Khafaei M. Habibi Azarian S. Naderi M. Kiyani E. et al.

A new and efficient method for DNA extraction from human skeletal remains usable in DNA typing.

Journal of Applied Biotechnology Reports. 4: 609-614Hines D.Z. Vennemeyer M. Amory S. Huel R.L. Hanson I. Katzmarzyk C. et al.

Prioritized sampling of bone and teeth for DNA analysis in commingled cases.

Commingled Human Remains. Elsevier, : 275-305Milos A. Selmanović A. Smajlović L. Huel R.L. Katzmarzyk C. Rizvić A. Parsons T.J.

Success rates of nuclear short tandem repeat typing from different skeletal elements.

Croatian medical journal. 48: 486-493Charlton S. Booth T. Barnes I.

The problem with petrous? A consideration of the potential biases in the utilization of pars petrosa for ancient DNA analysis.

World archaeology. 51: 574-585Gaudio D. Fernandes D.M. Schmidt R. Cheronet O. Mazzarelli D. Mattia M. O'Keeffe T. Feeney R. Cattaneo C. Pinhasi R.

Genome-wide DNA from degraded petrous bones and the assessment of sex and probable geographic origins of forensic cases.

Scientific reports. 9: 1-11Pilli E. Vai S. Caruso M.G. D’Errico G. Berti A. Caramelli D.

Neither femur nor tooth: Petrous bone for identifying archaeological bone samples via forensic approach.

Forensic science international. 283: 144-149Hansen H.B. Damgaard P.B. Margaryan A. Stenderup J. Lynnerup N. Willerslev E. Allentoft M.E.

Comparing ancient DNA preservation in petrous bone and tooth cementum.

PloS one. 120170940Pinhasi R. Fernandes D. Sirak K. Novak M. Connell S. Alpaslan-Roodenberg S. Gerritsen F. Moiseyev V. Gromov A. Raczky P. Anders A. Pietrusewsky M. Rollefson G. Jovanovic M. Trinhhoang H. Bar-Oz G. Oxenham M. Matsumura H. Hofreiter M.

Optimal ancient DNA yields from the inner ear part of the human petrous bone.

PloS one. 100129102Edson S.M. Christensen A.F. Barritt S.M. Meehan A. Leney M.D. Finelli L.N.

Sampling of the cranium for mitochondrial DNA analysis of human skeletal remains.

Forensic Science International: Genetics Supplement Series. 2: 269-270Chipangura N. Silika K.K.

Contested archaeological approaches to mass grave exhumations in Zimbabwe.

Journal of Conflict Archaeology. 14: 163-180Mansour H. Krebs O. Sperhake J.P. Augustin C. Koehne T. Amling M. Püschel K.

Cementum as a source of DNA in challenging forensic cases.

Journal of Forensic and Legal Medicine. 54: 76-81Higgins D. Kaidonis J. Townsend G. Hughes T. Austin J.J.

Targeted sampling of cementum for recovery of nuclear DNA from human teeth and the impact of common decontamination measures.

Investigative genetics. 4: 1-8Mann A.E. Sabin S. Ziesemer K. Vågene Å.J. Schroeder H. Ozga A.T. Sankaranarayanan K. Hofman C.A. Fellows Yates J.A. Salazar-García D.C. Frohlich B. Aldenderfer M. Hoogland M. Read C. Milner G.R. Stone A.C. Lewis CM Jr Krause J. Hofman C. Bos K.I. Warinner C.

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin.

Scientific reports. 8: 1-15Parker C. Rohrlach A.B. Friederich S. Nagel S. Meyer M. Krause J. Bos K.I. Haak W.

A systematic investigation of human DNA preservation in medieval skeletons.

Scientific reports. 10: 1-16Alberti F. Gonzalez J. Paijmans J. Basler N. Preick M. Henneberger K. Trinks A. Rabeder G. Conard N.J. Münzel S.C. Joger U. Fritsch G. Hildebrandt T. Hofreiter M. Barlow A.

Optimized DNA sampling of ancient bones using Computed Tomography scans.

Molecular ecology resources. 18: 1196-1208Kontopoulos I. Penkman K. Mullin V.E. Winkelbach L. Unterländer M. Scheu A. Kreutzer S. Hansen H.B. Margaryan A. Teasdale M.D. Gehlen B. Street M. Lynnerup N. Liritzis I. Sampson A. Papageorgopoulou C. Allentoft M.E. Burger J. Bradley D.G. Collins M.J.

Screening archaeological bone for palaeogenetic and palaeoproteomic studies.

PloS one. 150235146

Teeth as a source of DNA for forensic identification of human remains: a review.

Science & Justice. 53: 433-441Higgins D. Kaidonis J. Townsend G. Hughes T. Austin J.J.

Targeted sampling of cementum for recovery of nuclear DNA from human teeth and the impact of common decontamination measures.

Investigative genetics. 4: 18Gilbert M.T. Willerslev E. Hansen A.J. Barnes I. Rudbeck L. Lynnerup N. Cooper A.

Distribution patterns of postmortem damage in human mitochondrial DNA.

The American Journal of Human Genetics. 72: 32-47

Examination of DNA yield rates for different skeletal elements at increasing post mortem intervals. Forensic Science.

International: Genetics. 8: 55-63Sirak K.A. Fernandes D.M. Cheronet O. Novak M. Gamarra B. Balassa T. Bernert Z. Cséki A. Dani J. Gallina J.Z. Kocsis-Buruzs G. Kővári I. László O. Pap I. Patay R. Petkes Z. Szenthe G. Szeniczey T. Hajdu T. Pinhasi R.

A minimally-invasive method for sampling human petrous bones from the cranial base for ancient DNA analysis.

BioTechniques. 62: 283-289Austin R.M. Sholts S.B. Williams L. Kistler L. Hofman C.A.

Opinion: To curate the molecular past, museums need a carefully considered set of best practices.

Proceedings of the National Academy of Sciences. 116: 1471-1474

de León M.S.P. , Koesbardiati T. , Weissmann J.D. , Milella M. , Reyna-Blanco C.S. , Suwa G. , et al. Human bony labyrinth is an indicator of population history and dispersal from Africa. Proceedings of the National Academy of Sciences. 2018 ;115(16):4128-4133.

Norén A. Lynnerup N. Czarnetzki A. Graw M.

Lateral angle: a method for sexing using the petrous bone.

American Journal of Physical Anthropology: The Official Publication of the American Association of Physical Anthropologists. 128: 318-323Masotti S. Pasini A. Gualdi-Russo E.

Sex determination in cremated human remains using the lateral angle of the pars petrosa ossis temporalis: is old age a limiting factor? Forensic.

Science, Medicine and Pathology. 15: 392-398Jørkov M.L.S. Heinemeier J. Lynnerup N.

The petrous bone—A new sampling site for identifying early dietary patterns in stable isotopic studies.

American journal of physical anthropology. 138: 199-209Krenz‐Niedbała M. Łukasik S.

Skeletal evidence for otitis media in mediaeval and Post-Mediaeval children from poland, central europe.

International Journal of Osteoarchaeology. 27: 375-386

Chronic otitis media sequelae in skeletal material from medieval Denmark.

The Laryngoscope. 111: 114-118Homøe P. Lynnerup N. Skovgaard L. Rasmussen N.

Estimation of otitis media in ancient populations: A study of past and present Greenlandic Inuit.

The Journal of Laryngology & Otology. 110: 1114-1119

The labyrinth of human variation.

Proceedings of the National Academy of Sciences. 115: 3992-3994

Balancing analytical goals and anthropological stewardship in the midst of the paleogenomics revolution.

World Archaeology. 51: 560-573Pálsdóttir A.H. Bläuer A. Rannamäe E. Boessenkool S. Hallsson J.H.

Not a limitless resource: ethics and guidelines for destructive sampling of archaeofaunal remains.

Royal Society Open Science. 6191059Makarewicz C. Marom N. Bar-Oz G.

Palaeobiology: Ensure equal access to ancient DNA.

Nature. 548: 158

Bioarchaeological ethics: a historical perspective on the value of human remains.

Biological anthropology of the human skeleton. 3: 40

Nanibaa'A G, Bolnick DA, Raff JA, Walker A, et al. Advancing the ethics of paleogenomics.

Science. 360: 384-385

Anthropological Applications of Ancient DNA: Problems and Prospects.

American Antiquity. 71: 365-380

Ancient DNA comes of age, but still has some teenage problems.

South African Journal of Science. 113: 1-2Vanek D. Budowle B. Dubska-Votrubova J. Ambers A. Frolik J. Pospisek M. Al Afeefi A.A. Al Hosani K.I. Allen M. Al Naimi K.S. Al Salafi D. Al Tayyari W. Arguetaa W. Bottinelli M. Bus M.M. Cemper-Kiesslich J. Cepil O. De Cock G. Desmyter S. El Amri H. El Ossmani H. Galdies R. Grün S. Guidet F. Hoefges A. Iancu C.B. Lotz P. Maresca A. Nagy M. Novotny J. Rachid H. Rothe J. Stenersen M. Stephenson M. Stevanovitch A. Strien J. Sumita D.R. Vella J. Zander J.

Results of a collaborative study on DNA identification of aged bone samples.

Croatian medical journal. 58: 203-213Imaizumi K. Taniguchi K. Ogawa Y.

DNA survival and physical and histological properties of heat-induced alterations in burnt bones.

International journal of legal medicine. 128: 439-446Sawyer S. Krause J. Guschanski K. Savolainen V. Pääbo S.

Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA.

PloS one. 7: 34131Loreille O.M. Diegoli T.M. Irwin J.A. Coble M.D. Parsons T.J.

High efficiency DNA extraction from bone by total demineralization. Forensic Science.

International: Genetics. 1: 191-195Seo S.B. Zhang A. Kim H.Y. Yi J.A. Lee H.Y. Shin D.H. Lee S.D.

Efficiency of total demineralization and ion-exchange column for DNA extraction from bone.

American Journal of Physical Anthropology: The Official Publication of the American Association of Physical Anthropologists. 141: 158-162Amory S. Huel R. Bilić A. Loreille O. Parsons T.J.

Automatable full demineralization DNA extraction procedure from degraded skeletal remains. Forensic Science.

International: Genetics. 6: 398-406Rohland N. Siedel H. Hofreiter M.

A rapid column-based ancient DNA extraction method for increased sample throughput.

Molecular ecology resources. 10: 677-683Poinar H.N. Schwarz C. Qi J. Shapiro B. MacPhee R.D. Buigues B. Tikhonov A. Huson D.H. Tomsho L.P. Auch A. Rampp M. Miller W. Schuster S.C.

Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.

science. 311: 392-394Meyer M. Arsuaga J.-L. de Filippo C. Nagel S. Aximu-Petri A. Nickel B. Martínez I. Gracia A. Bermúdez de Castro J.M. Carbonell E. Viola B. Kelso J. Prüfer K. Pääbo S.

Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins.

Nature. 531: 504-507Meyer M. Fu Q. Aximu-Petri A. Glocke I. Nickel B. Arsuaga J.-L. Martínez I. Gracia A. de Castro J.M. Carbonell E. Pääbo S.

A mitochondrial genome sequence of a hominin from Sima de los Huesos.

Nature. 505: 403-406Barlow A. Fortes G.G. Dalén L. Pinhasi R. Gasparyan B. Rabeder G. Frischauf C. Paijmans J.L.A. Hofreiter M.

Massive influence of DNA isolation and library preparation approaches on palaeogenomic sequencing data.

BioRxiv. 075911Dolle D.D. Liu Z. Cotten M. Simpson J.T. Iqbal Z. Durbin R. McCarthy S.A. Keane T.M.

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.

Genome research. 27: 300-309

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.

Bioinformatics. 27: 764-770Dayama G. Emery S.B. Kidd J.M. Mills R.E.

The genomic landscape of polymorphic human nuclear mitochondrial insertions.

Nucleic acids research. 42: 12640-12649Balciuniene J. Balciunas D.

A nuclear mtDNA concatemer (mega-NUMT) could mimic paternal inheritance of mitochondrial genome.

Frontiers in genetics. 10: 518Lutz-Bonengel S. Niederstätter H. Naue J. Koziel R. Yang F. Sänger T. Huber G. Berger C. Pflugradt R. Strobl C. Xavier C. Volleth M. Weiß S.C. Irwin J.A. Romsos E.L. Vallone P.M. Ratzinger G. Schmuth M. Jansen-Dürr P. Liehr T. Lichter P. Parsons T.J. Pollak S. Parson W.

Evidence for multi-copy Mega-NUMTs in the human genome.

Nucleic Acids Research. 49: 1517-1531Wei W. Pagnamenta A.T. Gleadall N. Sanchis-Juan A. Stephens J. Broxholme J. Tuna S. Odhams C.A. Fratter C. Turro E. Caulfield M.J. Taylor J.C. Rahman S. Chinnery P.F.

Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA in humans.

Nature communications. 11: 1-11Cihlar J.C. Strobl C. Lagacé R. Muenzler M. Parson W. Budowle B.

Distinguishing mitochondrial DNA and NUMT sequences amplified with the precision ID mtDNA whole genome panel.

Mitochondrion. 55: 122-133

Extraction of highly degraded DNA from ancient bones and teeth. Ancient.

DNA. Springer, : 25-29Gutaker R.M. Reiter E. Furtwängler A. Schuenemann V.J. Burbano H.A.

Extraction of ultrashort DNA molecules from her

留言 (0)

沒有登入
gif