Computational challenges in the analysis of ancient DNA

被引：90

作者：

Pruefer, Kay ^{[1
]}

Stenzel, Udo ^{[1
]}

Hofreiter, Michael ^{[1
,2
]}

Paeaebo, Svante ^{[1
]}

Kelso, Janet ^{[1
]}

Green, Richard E. ^{[1
]}

机构：

[1] Max Planck Inst Evolutionary Anthropol, D-04103 Leipzig, Germany

[2] Univ York, Dept Biol, York YO10 5YW, N Yorkshire, England

来源：

GENOME BIOLOGY | 2010年 / 11卷 / 05期

关键词：

MITOCHONDRIAL GENOME; NEANDERTHAL GENOME; SEQUENCE; EVOLUTION; MAMMOTH; MOUSE; BLAST; AMPLIFICATION; ALIGNMENTS; PHYLOGENY;

D O I：

10.1186/gb-2010-11-5-r47

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.

引用

页数：15

共 53 条

[31] Initial sequencing and analysis of the human genome [J].

Lander, ES ;

Int Human Genome Sequencing Consortium ;

Linton, LM ;

Birren, B ;

Nusbaum, C ;

Zody, MC ;

Baldwin, J ;

Devon, K ;

Dewar, K ;

Doyle, M ;

FitzHugh, W ;

Funke, R ;

Gage, D ;

Harris, K ;

Heaford, A ;

Howland, J ;

Kann, L ;

Lehoczky, J ;

LeVine, R ;

McEwan, P ;

McKernan, K ;

Meldrim, J ;

Mesirov, JP ;

Miranda, C ;

Morris, W ;

Naylor, J ;

Raymond, C ;

Rosetti, M ;

Santos, R ;

Sheridan, A ;

Sougnez, C ;

Stange-Thomann, N ;

Stojanovic, N ;

Subramanian, A ;

Wyman, D ;

Rogers, J ;

Sulston, J ;

Ainscough, R ;

Beck, S ;

Bentley, D ;

Burton, J ;

Clee, C ;

Carter, N ;

Coulson, A ;

Deadman, R ;

Deloukas, P ;

Dunham, A ;

Dunham, I ;

Durbin, R ;

French, L .

NATURE, 2001, 409 (6822) :860-921

[32] Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome [J].

Margulies, Elliott H. ;

Cooper, Gregory M. ;

Asimenos, George ;

Thomas, Daryl J. ;

Dewey, Colin N. ;

Siepel, Adam ;

Birney, Ewan ;

Keefe, Damian ;

Schwartz, Ariel S. ;

Hou, Minmei ;

Taylor, James ;

Nikolaev, Sergey ;

Montoya-Burgos, Juan I. ;

Loytynoja, Ari ;

Whelan, Simon ;

Pardi, Fabio ;

Massingham, Tim ;

Brown, James B. ;

Bickel, Peter ;

Holmes, Ian ;

Mullikin, James C. ;

Ureta-Vidal, Abel ;

Paten, Benedict ;

Stone, Eric A. ;

Rosenbloom, Kate R. ;

Kent, W. James ;

Antonarakis, Stylianos E. ;

Batzoglou, Serafim ;

Goldman, Nick ;

Hardison, Ross ;

Haussler, David ;

Miller, Webb ;

Pachter, Lior ;

Green, Eric D. ;

Sidow, Arend .

GENOME RESEARCH, 2007, 17 (06) :760-774

[33] Genome sequencing in microfabricated high-density picolitre reactors [J].

Margulies, M ;

Egholm, M ;

Altman, WE ;

Attiya, S ;

Bader, JS ;

Bemben, LA ;

Berka, J ;

Braverman, MS ;

Chen, YJ ;

Chen, ZT ;

Dewell, SB ;

Du, L ;

Fierro, JM ;

Gomes, XV ;

Godwin, BC ;

He, W ;

Helgesen, S ;

Ho, CH ;

Irzyk, GP ;

Jando, SC ;

Alenquer, MLI ;

Jarvie, TP ;

Jirage, KB ;

Kim, JB ;

Knight, JR ;

Lanza, JR ;

Leamon, JH ;

Lefkowitz, SM ;

Lei, M ;

Li, J ;

Lohman, KL ;

Lu, H ;

Makhijani, VB ;

McDade, KE ;

McKenna, MP ;

Myers, EW ;

Nickerson, E ;

Nobile, JR ;

Plant, R ;

Puc, BP ;

Ronan, MT ;

Roth, GT ;

Sarkis, GJ ;

Simons, JF ;

Simpson, JW ;

Srinivasan, M ;

Tartaro, KR ;

Tomasz, A ;

Vogt, KA ;

Volkmer, GA .

NATURE, 2005, 437 (7057) :376-380

[34] Optimization of 454 sequencing library preparation from small amounts of DNA permits sequence determination of both DNA strands [J].

Maricic, Tomislav ;

Paeaebo, Svante .

BIOTECHNIQUES, 2009, 46 (01) :51-+

[35] Sequencing the nuclear genome of the extinct woolly mammoth [J].

Miller, Webb ;

Drautz, Daniela I. ;

Ratan, Aakrosh ;

Pusey, Barbara ;

Qi, Ji ;

Lesk, Arthur M. ;

Tomsho, Lynn P. ;

Packard, Michael D. ;

Zhao, Fangqing ;

Sher, Andrei ;

Tikhonov, Alexei ;

Raney, Brian ;

Patterson, Nick ;

Lindblad-Toh, Kerstin ;

Lander, Eric S. ;

Knight, James R. ;

Irzyk, Gerard P. ;

Fredrikson, Karin M. ;

Harkins, Timothy T. ;

Sheridan, Sharon ;

Pringle, Tom ;

Schuster, Stephan C. .

NATURE, 2008, 456 (7220) :387-U51

[36] Sequencing and analysis of Neanderthal genomic DNA [J].

Noonan, James P. ;

Coop, Graham ;

Kudaravalli, Sridhar ;

Smith, Doug ;

Krause, Johannes ;

Alessi, Joe ;

Platt, Darren ;

Paabo, Svante ;

Pritchard, Jonathan K. ;

Rubin, Edward M. .

SCIENCE, 2006, 314 (5802) :1113-1118

[37] Genomic sequencing of Pleistocene cave bears [J].

Noonan, JP ;

Hofreiter, M ;

Smith, D ;

Priest, JR ;

Rohland, N ;

Rabeder, G ;

Krause, J ;

Detter, JC ;

Pääbo, S ;

Rubin, EM .

SCIENCE, 2005, 309 (5734) :597-600

[38] Genetic analyses from ancient DNA [J].

Pääbo, S ;

Poinar, H ;

Serre, D ;

Jaenicke-Després, V ;

Hebler, J ;

Rohland, N ;

Kuch, M ;

Krause, J ;

Vigilant, L ;

Hofreiter, M .

ANNUAL REVIEW OF GENETICS, 2004, 38 :645-679

[39] Zerg: a very fast BLAST parser library [J].

Paquola, ACM ;

Machado, AA ;

Reis, EM ;

da Silva, AM ;

Verjovski-Almeida, S .

BIOINFORMATICS, 2003, 19 (08) :1035-1036

[40] IMPROVED TOOLS FOR BIOLOGICAL SEQUENCE COMPARISON [J].

PEARSON, WR ;

LIPMAN, DJ .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1988, 85 (08) :2444-2448

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