Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.
Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.
复制标题
DOI：
10.1186/s12864-020-07229-y
复制
发表时间：
2020-11-30
期刊：
影响因子：
4.4
通讯作者：
Díez-Del-Molino D
中科院分区：
文献类型：
--
作者：
Feuerborn TR;Palkopoulou E;van der Valk T;von Seth J;Munters AR;Pečnerová P;Dehasque M;Ureña I;Ersmark E;Lagerholm VK;Krzewińska M;Rodríguez-Varela R;Götherström A;Dalén L;Díez-Del-Molino D
经过十多年在野外采集、实验室方法和高通量测序方面的发展，污染仍然是古代DNA研究中的一个关键问题。目前，人类和微生物污染的DNA仍然对成本效益高的测序和准确解释古代DNA数据构成挑战。在这里，我们调查是否可以在古代动物群测序数据集中发现人类污染的DNA。我们确定了不同程度的人类污染，即使在序列读数已经被映射到动物群参考基因组之后，这种污染仍然存在。这种污染有可能影响一系列下游分析。我们提出了一种基于竞争作图的快速、简单的方法，该方法允许在丢失真实古代数据的情况下识别和去除古代动物DNA数据中的人类污染。这种方法可能是古代DNA领域的一种重要工具。
After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data. Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses. We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.
登录
查看更多内容
基因组暗物质：基因组映射分数所说明的简读映射的可靠性。
DOI：
10.1093/bioinformatics/bts330
发表时间：
2012-08-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Lee H;Schatz MC
通讯作者：
Schatz MC
影响因子：
64.8
作者：
Lazaridis, Iosif;Patterson, Nick;Mittnik, Alissa;Renaud, Gabriel;Mallick, Swapan;Kirsanow, Karola;Sudmant, Peter H.;Schraiber, Joshua G.;Castellano, Sergi;Lipson, Mark;Berger, Bonnie;Economou, Christos;Bollongino, Ruth;Fu, Qiaomei;Bos, Kirsten I.;Nordenfelt, Susanne;Li, Heng;de Filippo, Cesare;Pruefer, Kay;Sawyer, Susanna;Posth, Cosimo;Haak, Wolfgang;Hallgren, Fredrik;Fornander, Elin;Rohland, Nadin;Delsate, Dominique;Francken, Michael;Guinet, Jean-Michel;Wahl, Joachim;Ayodo, George;Babiker, Hamza A.;Bailliet, Graciela;Balanovska, Elena;Balanovsky, Oleg;Barrantes, Ramiro;Bedoya, Gabriel;Ben-Ami, Haim;Bene, Judit;Berrada, Fouad;Bravi, Claudio M.;Brisighelli, Francesca;Busby, George B. J.;Cali, Francesco;Churnosov, Mikhail;Cole, David E. C.;Corach, Daniel;Damba, Larissa;van Driem, George;Dryomov, Stanislav;Dugoujon, Jean-Michel;Fedorova, Sardana A.;Romero, Irene Gallego;Gubina, Marina;Hammer, Michael;Henn, Brenna M.;Hervig, Tor;Hodoglugil, Ugur;Jha, Aashish R.;Karachanak-Yankova, Sena;Khusainova, Rita;Khusnutdinova, Elza;Kittles, Rick;Kivisild, Toomas;Klitz, William;Kucinskas, Vaidutis;Kushniarevich, Alena;Laredj, Leila;Litvinov, Sergey;Loukidis, Theologos;Mahley, Robert W.;Melegh, Bela;Metspalu, Ene;Molina, Julio;Mountain, Joanna;Nakkalajarvi, Klemetti;Nesheva, Desislava;Nyambo, Thomas;Osipova, Ludmila;Parik, Jueri;Platonov, Fedor;Posukh, Olga;Romano, Valentino;Rothhammer, Francisco;Rudan, Igor;Ruizbakiev, Ruslan;Sahakyan, Hovhannes;Sajantila, Antti;Salas, Antonio;Starikovskaya, Elena B.;Tarekegn, Ayele;Toncheva, Draga;Turdikulova, Shahlo;Uktveryte, Ingrida;Utevska, Olga;Vasquez, Rene;Villena, Mercedes;Voevoda, Mikhail;Winkler, Cheryl A.;Yepiskoposyan, Levon;Zalloua, Pierre;Zemunik, Tatijana;Cooper, Alan;Capelli, Cristian;Thomas, Mark G.;Ruiz-Linares, Andres;Tishkoff, Sarah A.;Singh, Lalji;Thangaraj, Kumarasamy;Villems, Richard;Comas, David;Sukernik, Rem;Metspalu, Mait;Meyer, Matthias;Eichler, Evan E.;Burger, Joachim;Slatkin, Montgomery;Paeaebo, Svante;Kelso, Janet;Reich, David;Krause, Johannes
通讯作者：
Krause, Johannes
影响因子：
--
作者：
Meyer, Matthias;Kircher, Martin
通讯作者：
Kircher, Martin
影响因子：
7.7
作者：
Gamba, Cristina;Hanghoj, Kristian;Orlando, Ludovic
通讯作者：
Orlando, Ludovic
影响因子：
4.9
作者：
Der Sarkissian, C.;Ermini, L.;Orlando, L.
通讯作者：
Orlando, L.