Current trend of annotating single nucleotide variation in humans--A case study on SNVrap.
作者： Mulin Jun Li , Junwen Wang
DOI: 10.1016/J.YMETH.2014.10.003
关键词:
摘要: As high throughput methods, such as whole genome genotyping arrays, exome sequencing (WES) and (WGS), have detected huge amounts of genetic variants associated with human diseases, function annotation these is an indispensable step in understanding disease etiology. Large-scale functional genomics projects, The ENCODE Project Roadmap Epigenomics Project, provide genome-wide profiling elements across different cell types tissues. With the urgent demands for identification disease-causal variants, comprehensive easy-to-use tool highly demand. Here we review discuss current progress trend variant field. Furthermore, introduce a web portal annotating variants. We use gene-based features latest datasets to annotate single nucleotide variation (SNVs) human, at scale. further apply several prediction algorithms SNVs that might affect biological processes, including transcriptional gene regulation, alternative splicing, post-transcriptional translation post-translational modifications. SNVrap freely available http://jjwanglab.org/snvrap.
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P Makrythanasis, SE Antonarakis, Pathogenic variants in non‐protein‐coding sequences Clinical Genetics. ,vol. 84, pp. 422- 428 ,(2013) , 10.1111/CGE.12272
M. Kasowski, F. Grubert, C. Heffelfinger, M. Hariharan, A. Asabere, S. M. Waszak, L. Habegger, J. Rozowsky, M. Shi, A. E. Urban, M. Y. Hong, K. J. Karczewski, W. Huber, S. M. Weissman, M. B. Gerstein, J. O. Korbel, M. Snyder, Variation in Transcription Factor Binding Among Humans Science. ,vol. 328, pp. 232- 235 ,(2010) , 10.1126/SCIENCE.1183621
Iñigo Olalde, Morten E. Allentoft, Federico Sánchez-Quinto, Gabriel Santpere, Charleston W. K. Chiang, Michael DeGiorgio, Javier Prado-Martinez, Juan Antonio Rodríguez, Simon Rasmussen, Javier Quilez, Oscar Ramírez, Urko M. Marigorta, Marcos Fernández-Callejo, María Encina Prada, Julio Manuel Vidal Encinas, Rasmus Nielsen, Mihai G. Netea, John Novembre, Richard A. Sturm, Pardis Sabeti, Tomàs Marquès-Bonet, Arcadi Navarro, Eske Willerslev, Carles Lalueza-Fox, Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European Nature. ,vol. 507, pp. 225- 228 ,(2014) , 10.1038/NATURE12960
Robert E Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T Maurano, Eric Haugen, Nathan C Sheffield, Andrew B Stergachis, Hao Wang, Benjamin Vernot, Kavita Garg, Sam John, Richard Sandstrom, Daniel Bates, Lisa Boatman, Theresa K Canfield, Morgan Diegel, Douglas Dunn, Abigail K Ebersol, Tristan Frum, Erika Giste, Audra K Johnson, Ericka M Johnson, Tanya Kutyavin, Bryan Lajoie, Bum-Kyu Lee, Kristen Lee, Darin London, Dimitra Lotakis, Shane Neph, Fidencio Neri, Eric D Nguyen, Hongzhu Qu, Alex P Reynolds, Vaughn Roach, Alexias Safi, Minerva E Sanchez, Amartya Sanyal, Anthony Shafer, Jeremy M Simon, Lingyun Song, Shinny Vong, Molly Weaver, Yongqi Yan, Zhancheng Zhang, Zhuzhu Zhang, Boris Lenhard, Muneesh Tewari, Michael O Dorschner, R Scott Hansen, Patrick A Navas, George Stamatoyannopoulos, Vishwanath R Iyer, Jason D Lieb, Shamil R Sunyaev, Joshua M Akey, Peter J Sabo, Rajinder Kaul, Terrence S Furey, Job Dekker, Gregory E Crawford, John A Stamatoyannopoulos, None, The accessible chromatin landscape of the human genome Nature. ,vol. 489, pp. 75- 82 ,(2012) , 10.1038/NATURE11232
Luisa Luna, Veslemøy Rolseth, Gunn A Hildrestrand, Marit Otterlei, Francoise Dantzer, Magnar Bjørås, Erling Seeberg, Dynamic relocalization of hOGG1 during the cell cycle is disrupted in cells harbouring the hOGG1-Cys326 polymorphic variant. Nucleic Acids Research. ,vol. 33, pp. 1813- 1824 ,(2005) , 10.1093/NAR/GKI325
Sarah B. Ng, Emily H. Turner, Peggy D. Robertson, Steven D. Flygare, Abigail W. Bigham, Choli Lee, Tristan Shaffer, Michelle Wong, Arindam Bhattacharjee, Evan E. Eichler, Michael Bamshad, Deborah A. Nickerson, Jay Shendure, Targeted capture and massively parallel sequencing of 12 human exomes Nature. ,vol. 461, pp. 272- 276 ,(2009) , 10.1038/NATURE08250
Mulin Jun Li, Panwen Wang, Xiaorong Liu, Ee Lyn Lim, Zhangyong Wang, Meredith Yeager, Maria P. Wong, Pak Chung Sham, Stephen J. Chanock, Junwen Wang, GWASdb: a database for human genetic variants identified by genome-wide association studies Nucleic Acids Research. ,vol. 40, pp. 1047- 1054 ,(2012) , 10.1093/NAR/GKR1182
Ian Tomlinson, Kimmo Palin, Esko Ukkonen, Auli Karhu, Jussi Taipale, Lauri A Aaltonen, Sari Tuupanen, Mikko Turunen, Rainer Lehtonen, Outi Hallikas, Sakari Vanharanta, Teemu Kivioja, Mikael Björklund, Gonghong Wei, Jian Yan, Iina Niittymäki, Jukka-Pekka Mecklin, Heikki Järvinen, Ari Ristimäki, Mariachiara Di-Bernardo, Phil East, Luis Carvajal-Carmona, Richard S Houlston, The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling Nature Genetics. ,vol. 41, pp. 885- 890 ,(2009) , 10.1038/NG.406
Chanika Phornphutkul, Yair Anikster, Marjan Huizing, Paula Braun, Chaya Brodie, Janice Y. Chou, William A. Gahl, The promoter of a lysosomal membrane transporter gene, CTNS, binds Sp-1, shares sequences with the promoter of an adjacent gene, CARKL, and causes cystinosis if mutated in a critical region. American Journal of Human Genetics. ,vol. 69, pp. 712- 721 ,(2001) , 10.1086/323484
Tomoaki Niimi, Mitsuru Munakata, Catherine L. Keck-Waggoner, Nicholas C. Popescu, Roy C. Levitt, Michie Hisada, Shioko Kimura, A polymorphism in the human UGRP1 gene promoter that regulates transcription is associated with an increased risk of asthma. American Journal of Human Genetics. ,vol. 70, pp. 718- 725 ,(2002) , 10.1086/339272