Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs
作者： A. Van Geystelen , R. Decorte , M.H.D. Larmuseau
DOI: 10.1016/J.FSIGEN.2013.03.010
关键词: Computational biology 、 Phylogenetic tree 、 Biology 、 False positive paradox 、 Set (abstract data type) 、 Tree (data structure) 、 Haplogroup 、 Whole genome sequencing 、 Genome 、 Phylogenetic network 、 Genetics
摘要: The Y-chromosomal phylogenetic tree has a wide variety of important forensic applications and therefore it needs to be state-of-the-art. Nevertheless, since the last 'official' published many publications reported additional lineages other topologies. Therefore, is difficult for scientists interpret those reports use an up-to-date corresponding nomenclature in their daily work. Whole genome sequencing (WGS) data useful verify optimise current haploid markers. AMY-tree software first open access program which analyses WGS applications. Here, all information collected correctness this checked based on large analysis 747 samples with AMY-tree. obtained result one peer-reviewed Y-SNPs without observed recurrent ambiguous mutations. results showed that currently only genomes limited set (sub-)haplogroups available newly projects are false positives, even high coverage methods. This study demonstrates usefulness process checking quality present accentuates difficulties enlarge
core.ac.uk
elsevier.com
sci-hub.se 参考文章(49)
John M Butler, Advanced Topics in Forensic DNA Typing: Methodology ,(2011)
Simona Fornarino, Maria Pala, Vincenza Battaglia, Ramona Maranta, Alessandro Achilli, Guido Modiano, Antonio Torroni, Ornella Semino, Silvana A Santachiara-Benerecetti, Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation BMC Evolutionary Biology. ,vol. 9, pp. 154- 154 ,(2009) , 10.1186/1471-2148-9-154
Lynn M. Sims, Dennis Garvey, Jack Ballantyne, Improved resolution haplogroup G phylogeny in the Y chromosome, revealed by a set of newly characterized SNPs. PLOS ONE. ,vol. 4, ,(2009) , 10.1371/JOURNAL.PONE.0005792
R. Drmanac, A. B. Sparks, M. J. Callow, A. L. Halpern, N. L. Burns, B. G. Kermani, P. Carnevali, I. Nazarenko, G. B. Nilsen, G. Yeung, F. Dahl, A. Fernandez, B. Staker, K. P. Pant, J. Baccash, A. P. Borcherding, A. Brownley, R. Cedeno, L. Chen, D. Chernikoff, A. Cheung, R. Chirita, B. Curson, J. C. Ebert, C. R. Hacker, R. Hartlage, B. Hauser, S. Huang, Y. Jiang, V. Karpinchyk, M. Koenig, C. Kong, T. Landers, C. Le, J. Liu, C. E. McBride, M. Morenzoni, R. E. Morey, K. Mutch, H. Perazich, K. Perry, B. A. Peters, J. Peterson, C. L. Pethiyagoda, K. Pothuraju, C. Richter, A. M. Rosenbaum, S. Roy, J. Shafto, U. Sharanhovich, K. W. Shannon, C. G. Sheppy, M. Sun, J. V. Thakuria, A. Tran, D. Vu, A. W. Zaranek, X. Wu, S. Drmanac, A. R. Oliphant, W. C. Banyai, B. Martin, D. G. Ballinger, G. M. Church, C. A. Reid, Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays Science. ,vol. 327, pp. 78- 81 ,(2010) , 10.1126/SCIENCE.1181498
Beniamino Trombetta, Fulvio Cruciani, Daniele Sellitto, Rosaria Scozzari, A New Topology of the Human Y Chromosome Haplogroup E1b1 (E-P2) Revealed through the Use of Newly Characterized Binary Polymorphisms PLoS ONE. ,vol. 6, pp. e16073- ,(2011) , 10.1371/JOURNAL.PONE.0016073
Jonathan M. Rothberg, Wolfgang Hinz, Todd M. Rearick, Jonathan Schultz, William Mileski, Mel Davey, John H. Leamon, Kim Johnson, Mark J. Milgrew, Matthew Edwards, Jeremy Hoon, Jan F. Simons, David Marran, Jason W. Myers, John F. Davidson, Annika Branting, John R. Nobile, Bernard P. Puc, David Light, Travis A. Clark, Martin Huber, Jeffrey T. Branciforte, Isaac B. Stoner, Simon E. Cawley, Michael Lyons, Yutao Fu, Nils Homer, Marina Sedova, Xin Miao, Brian Reed, Jeffrey Sabina, Erika Feierstein, Michelle Schorn, Mohammad Alanjary, Eileen Dimalanta, Devin Dressman, Rachel Kasinskas, Tanya Sokolsky, Jacqueline A. Fidanza, Eugeni Namsaraev, Kevin J. McKernan, Alan Williams, G. Thomas Roth, James Bustillo, An integrated semiconductor device enabling non-optical genome sequencing Nature. ,vol. 475, pp. 348- 352 ,(2011) , 10.1038/NATURE10242
Shi Yan, Chuan-Chao Wang, Hui Li, Shi-Lin Li, Li Jin, Theodore G Schurr, Fabricio R Santos, Lluis Quintana-Murci, Jaume Bertranpetit, David Comas, Chris Tyler-Smith, Pierre A Zalloua, Elena Balanovska, Oleg Balanovsky, R John Mitchell, Himla Soodyall, Ramasamy Pitchappan, Alan Cooper, Lisa Matisoo-Smith, Ajay K Royyuru, Daniel E Platt, Laxmi Parida, Jason Blue-Smith, David F Soria Hernanz, R Spencer Wells, None, An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4 European Journal of Human Genetics. ,vol. 19, pp. 1018- 1018 ,(2011) , 10.1038/EJHG.2011.64
Lai-Ping Wong, Rick Twee-Hee Ong, Wan-Ting Poh, Xuanyao Liu, Peng Chen, Ruoying Li, Kevin Koi-Yau Lam, Nisha Esakimuthu Pillai, Kar-Seng Sim, Haiyan Xu, Ngak-Leng Sim, Shu-Mei Teo, Jia-Nee Foo, Linda Wei-Lin Tan, Yenly Lim, Seok-Hwee Koo, Linda Seo-Hwee Gan, Ching-Yu Cheng, Sharon Wee, Eric Peng-Huat Yap, Pauline Crystal Ng, Wei-Yen Lim, Richie Soong, Markus Rene Wenk, Tin Aung, Tien-Yin Wong, Chiea-Chuen Khor, Peter Little, Kee-Seng Chia, Yik-Ying Teo, Deep whole-genome sequencing of 100 southeast Asian Malays. American Journal of Human Genetics. ,vol. 92, pp. 52- 66 ,(2013) , 10.1016/J.AJHG.2012.12.005
Sascha Willuweit, Lutz Roewer, Y chromosome haplotype reference database (YHRD): update. Forensic Science International-genetics. ,vol. 1, pp. 83- 87 ,(2007) , 10.1016/J.FSIGEN.2007.01.017
Jun Wang, Wei Wang, Ruiqiang Li, Yingrui Li, Geng Tian, Laurie Goodman, Wei Fan, Junqing Zhang, Jun Li, Juanbin Zhang, Yiran Guo, Binxiao Feng, Heng Li, Yao Lu, Xiaodong Fang, Huiqing Liang, Zhenglin Du, Dong Li, Yiqing Zhao, Yujie Hu, Zhenzhen Yang, Hancheng Zheng, Ines Hellmann, Michael Inouye, John Pool, Xin Yi, Jing Zhao, Jinjie Duan, Yan Zhou, Junjie Qin, Lijia Ma, Guoqing Li, Zhentao Yang, Guojie Zhang, Bin Yang, Chang Yu, Fang Liang, Wenjie Li, Shaochuan Li, Dawei Li, Peixiang Ni, Jue Ruan, Qibin Li, Hongmei Zhu, Dongyuan Liu, Zhike Lu, Ning Li, Guangwu Guo, Jianguo Zhang, Jia Ye, Lin Fang, Qin Hao, Quan Chen, Yu Liang, Yeyang Su, A San, Cuo Ping, Shuang Yang, Fang Chen, Li Li, Ke Zhou, Hongkun Zheng, Yuanyuan Ren, Ling Yang, Yang Gao, Guohua Yang, Zhuo Li, Xiaoli Feng, Karsten Kristiansen, Gane Ka-Shu Wong, Rasmus Nielsen, Richard Durbin, Lars Bolund, Xiuqing Zhang, Songgang Li, Huanming Yang, Jian Wang, None, The diploid genome sequence of an Asian individual. Nature. ,vol. 456, pp. 60- 65 ,(2008) , 10.1038/NATURE07484