Abundant human DNA contamination identified in non-primate genome databases.
Abundant human DNA contamination identified in non-primate genome databases.
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DOI：
10.1371/journal.pone.0016410
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发表时间：
2011-02-16
期刊：
影响因子：
3.7
通讯作者：
O'Neill RJ
中科院分区：
文献类型：
--
作者：
Longo MS;O'Neill MJ;O'Neill RJ
在使用人类重复元素对NCBI数据库进行常规筛选的过程中，我们发现在广泛的门范围内核苷酸同一性的水平是不太可能的。为了确定包含DNA序列、基因组组装和痕迹档案读取的数据库是否被人类序列污染，我们对非人类物种中的人类起源序列进行了深入搜索。使用灵长类特有的氨基酸AluY，我们从NCBI、Ensambl、JGI和UCSC中筛选了2749个非灵长类公共数据库，发现492个数据库被人类序列污染。这些物种代表了从细菌(蜡状芽孢杆菌)到植物(Z.Mays)到鱼类(D.rerio)的各种物种，其中包括从大多数门中发现的例子。在数据库和序列类型中识别如此广泛的人类序列污染值得测序界在未来的测序工作中谨慎行事，例如人类重新测序。我们讨论了这可能引发的问题，并提供了数据，让我们深入了解这可能是如何发生的。
During routine screens of the NCBI databases using human repetitive elements we discovered an unlikely level of nucleotide identity across a broad range of phyla. To ascertain whether databases containing DNA sequences, genome assemblies and trace archive reads were contaminated with human sequences, we performed an in depth search for sequences of human origin in non-human species. Using a primate specific SINE, AluY, we screened 2,749 non-primate public databases from NCBI, Ensembl, JGI, and UCSC and have found 492 to be contaminated with human sequence. These represent species ranging from bacteria (B. cereus) to plants (Z. mays) to fish (D. rerio) with examples found from most phyla. The identification of such extensive contamination of human sequence across databases and sequence types warrants caution among the sequencing community in future sequencing efforts, such as human re-sequencing. We discuss issues this may raise as well as present data that gives insight as to how this may be occurring.
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影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
5.8
作者：
Waterhouse, Andrew M.;Procter, James B.;Barton, Geoffrey J.
通讯作者：
Barton, Geoffrey J.
影响因子：
56.9
作者：
Poinar, HN;Schwarz, C;Schuster, SC
通讯作者：
Schuster, SC
影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.
影响因子：
64.8
作者：
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Keira;Cox, Tony;Eberle, Michael;James, Terena;Kahn, Scott;Murray, Lisa;Ye, Kai;De La Vega, Francisco M.;Fu, Yutao;Hyland, Fiona C. L.;Manning, Jonathan M.;McLaughlin, Stephen F.;Peckham, Heather E.;Sakarya, Onur;Sun, Yongming A.;Tsung, Eric F.;Batzer, Mark A.;Konkel, Miriam K.;Walker, Jerilyn A.;Sudbrak, Ralf;Albrecht, Marcus W.;Amstislavskiy, Vyacheslav S.;Herwig, Ralf;Parkhomchuk, Dimitri V.;Sherry, Stephen T.;Agarwala, Richa;Khouri, Hodam.;Morgulis, Aleksandr O.;Paschall, Justin E.;Phan, Lon D.;Rotmistrovsky, Kirill E.;Sanders, Robert D.;Shumway, Martin F.;Xiao, Chunlin;McVean, Gil A.;Auton, Adam;Iqbal, Zamin;Lunter, Gerton;Marchini, Jonathan L.;Moutsianas, Loukas;Myers, Simon;Tumian, Afidalina;Desany, Brian;Knight, James;Winer, Roger;Craig, David W.;Beckstrom-Sternberg, Steve M.;Christoforides, Alexis;Kurdoglu, Ahmet A.;Pearson, Johnv.;Sinari, Shripad A.;Tembe, Waibhav D.;Haussler, David;Hinrichs, Angie S.;Katzman, Sol J.;Kern, Andrew;Kuhn, Robert M.;Przeworski, Molly;Hernandez, Ryan D.;Howie, Bryan;Kelley, Joanna L.;Melton, S. Cord;Abecasis, Goncalo R.;Li, Yun;Anderson, Paul;Blackwell, Tom;Chen, Wei;Cookson, William O.;Ding, Jun;Kang, Hyun Min;Lathrop, Mark;Liang, Liming;Moffatt, Miriam F.;Scheet, Paul;Sidore, Carlo;Snyder, Matthew;Zhan, Xiaowei;Zoellner, Sebastian;Awadalla, Philip;Casals, Ferran;Idaghdour, Youssef;Keebler, John;Stone, Eric A.;Zilversmit, Martine;Jorde, Lynn;Xing, Jinchuan;Eichler, Evan E.;Aksay, Gozde;Alkan, Can;Hajirasouliha, Iman;Hormozdiari, Fereydoun;Kidd, Jeffrey M.;Sahinalp, S. Cenk;Sudmant, Peter H.;Mardis, Elaine R.;Chen, Ken;Chinwalla, Asif;Ding, Li;Koboldt, Daniel C.;McLellan, Mike D.;Dooling, David;Weinstock, George;Wallis, John W.;Wendl, Michael C.;Zhang, Qunyuan;Durbin, Richard M.;Albers, Cornelis A.;Ayub, Qasim;Balasubramaniam, Senduran;Barrett, Jeffrey C.;Carter, David M.;Chen, Yuan;Conrad, Donald F.;Danecek, Petr;Dermitzakis, Emmanouil T.;Hu, Min;Huang, Ni;Hurles, Matt E.;Jin, Hanjun;Jostins, Luke;Keane, Thomas M.;Keane, Thomas M.;Le, Si Quang;Lindsay, Sarah;Long, Quan;MacArthur, Daniel G.;Montgomery, Stephen B.;Parts, Leopold;Stalker, James;Tyler-Smith, Chris;Walter, Klaudia;Zhang, Yujun;Gerstein, Mark B.;Snyder, Michael;Abyzov, Alexej;Abyzov, Alexej;Balasubramanian, Suganthi;Bjornson, Robert;Du, Jiang;Grubert, Fabian;Habegger, Lukas;Haraksingh, Rajini;Jee, Justin;Khurana, Ekta;Lam, Hugo Y. K.;Leng, Jing;Mu, Xinmeng Jasmine;Urban, Alexander E.;Zhang, Zhengdong;Li, Yingrui;Luo, Ruibang;Marth, Gabor T.;Garrison, Erik P.;Kural, Deniz;Quinlan, Aaron R.;Stewart, Chip;Stromberg, Michael P.;Ward, Alistair N.;Wu, Jiantao;Lee, Charles;Mills, Ryan E.;Shi, Xinghua;McCarroll, Steven A.;Banks, Eric;DePristo, Mark A.;Handsaker, Robert E.;Hartl, Chris;Korn, Joshua M.;Li, Heng;Nemesh, James C.;Sebat, Jonathan;Makarov, Vladimir;Ye, Kenny;Yoon, Seungtai C.;Degenhardt, Jeremiah;Kaganovich, Mark;Clarke, Laura;Smith, Richard E.;Zheng-Bradley, Xiangqun;Korbel, Jan O.;Humphray, Sean;Cheetham, R. Keira;Eberle, Michael;Kahn, Scott;Murray, Lisa;Ye, Kai;De la Vega, Francisco M.;Fu, Yutao;Peckham, Heather E.;Sun, Yongming A.;Batzer, Mark A.;Konkel, Miriam K.;Xiao, Chunlin;Iqbal, Zamin;Desany, Brian;Blackwell, Tom;Snyder, Matthew;Xing, Jinchuan;Eichler, Evan E.;Aksay, Gozde;Alkan, Can;Hajirasouliha, Iman;Hormozdiari, Fereydoun;Kidd, Jeffrey M.;Chen, Ken;Chinwalla, Asif;Ding, Li;McLellan, Mike D.;Wallis, John W.;Hurles, Matt E.;Conrad, Donald F.;Walter, Klaudia;Zhang, Yujun;Gerstein, Mark B.;Snyder, Michael;Abyzov, Alexej;Du, Jiang;Grubert, Fabian;Haraksingh, Rajini;Jee, Justin;Khurana, Ekta;Lam, Hugo Y. K.;Leng, Jing;Mu, Xinmeng Jasmine;Urban, Alexander E.;Zhang, Zhengdong;Gibbs, Richard A.;Bainbridge, Matthew;Challis, Danny;Coafra, Cristian;Dinh, Huyen;Kovar, Christie;Lee, Sandy;Muzny, Donna;Nazareth, Lynne;Reid, Jeff;Sabo, Aniko;Yu, Fuli;Yu, Jin;Marth, Gabor T.;Garrison, Erik P.;Indap, Amit;Leong, Wen Fung;Quinlan, Aaron R.;Stewart, Chip;Ward, Alistair N.;Wu, Jiantao;Cibulskis, Kristian;Fennell, Tim J.;Gabriel, Stacey B.;Garimella, Kiran V.;Hartl, Chris;Shefler, Erica;Sougnez, Carrie L.;Wilkinson, Jane;Clark, Andrew G.;Gravel, Simon;Grubert, Fabian;Clarke, Laura;Flicek, Paul;Smith, Richard E.;Zheng-Bradley, Xiangqun;Sherry, Stephen T.;Khouri, Hoda M.;Paschall, Justin E.;Shumway, Martin F.;Xiao, Chunlin;McVean, Gil A.;Katzman, Sol J.;Abecasis, Goncalo R.;Blackwell, Tom;Mardis, Elaine R.;Dooling, David;Fulton, Lucinda;Fulton, Robert;Koboldt, Daniel C.;Durbin, Richard M.;Balasubramaniam, Senduran;Coffey, Allison;Keane, Thomas M.;MacArthur, Daniel G.;Palotie, Aarno;Scott, Carol;Stalker, James;Tyler-Smith, Chris;Gerstein, Mark B.;Balasubramanian, Suganthi;Chakravarti, Aravinda;Knoppers, Bartha M.;Peltonen, Leena;Abecasis, Goncalo R.;Bustamante, Carlos D.;Gharani, Neda;Gibbs, Richard A.;Jorde, Lynn;Kaye, Jane S.;Kent, Alastair;Li, Taosha;McGuire, Amy L.;McVean, Gil A.;Ossorio, Pilar N.;Rotimi, Charles N.;Su, Yeyang;Toji, Lorraine H.;Tyler-Smith, Chris;Brooks, Lisa D.;Felsenfeld, Adam L.;McEwen, Jean E.;Abdallah, Assya;Juenger, Christopher R.;Clemm, Nicholas C.;Collins, Francis S.;Duncanson, Audrey;Green, Eric D.;Guyer, Mark S.;Peterson, Jane L.;Schafer, Alan J.;Abecasis, Goncalo R.;Altshuler, David L.;Auton, Adam;Brooks, Lisa D.;Durbin, Richard M.;Gibbs, Richard A.;Hurles, Matt E.;McVean, Gil A.
通讯作者：
McVean, Gil A.