Functional annotation of noncoding sequence variants

被引：399

作者：

Ritchie, Graham R. S. ^{[1
,2
]}

Dunham, Ian ^{[1
]}

Zeggini, Eleftheria ^{[2
]}

Flicek, Paul ^{[1
,2
]}

机构：

[1] European Bioinformat Inst, European Mol Biol Lab, Cambridge, England

[2] Wellcome Trust Sanger Inst, Cambridge, England

来源：

NATURE METHODS | 2014年 / 11卷 / 03期

基金：

英国惠康基金;

关键词：

DATABASE;

D O I：

10.1038/nmeth.2832

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Identifying functionally relevant variants against the background of ubiquitous genetic variation is a major challenge in human genetics. For variants in protein-coding regions, our understanding of the genetic code and splicing allows us to identify likely candidates, but interpreting variants outside genic regions is more difficult. Here we present genome-wide annotation of variants (GWAVA), a tool that supports prioritization of noncoding variants by integrating various genomic and epigenomic annotations.

引用

页码：294 / U351

页数：6

共 23 条

[1] A method and server for predicting damaging missense mutations [J].

Adzhubei, Ivan A. ;

Schmidt, Steffen ;

Peshkin, Leonid ;

Ramensky, Vasily E. ;

Gerasimova, Anna ;

Bork, Peer ;

Kondrashov, Alexey S. ;

Sunyaev, Shamil R. .

NATURE METHODS, 2010, 7 (04) :248-249

[2] An integrated map of genetic variation from 1,092 human genomes [J].

Altshuler, David M. ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Donnelly, Peter ;

Eichler, Evan E. ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Green, Eric D. ;

Hurles, Matthew E. ;

Knoppers, Bartha M. ;

Korbel, Jan O. ;

Lander, Eric S. ;

Lee, Charles ;

Lehrach, Hans ;

Mardis, Elaine R. ;

Marth, Gabor T. ;

McVean, Gil A. ;

Nickerson, Deborah A. ;

Schmidt, Jeanette P. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Dinh, Huyen ;

Kovar, Christie ;

Lee, Sandra ;

Lewis, Lora ;

Muzny, Donna ;

Reid, Jeff ;

Wang, Min ;

Wang, Jun ;

Fang, Xiaodong ;

Guo, Xiaosen ;

Jian, Min ;

Jiang, Hui ;

Jin, Xin ;

Li, Guoqing ;

Li, Jingxiang ;

Li, Yingrui ;

Li, Zhuo ;

Liu, Xiao ;

Lu, Yao ;

Ma, Xuedi ;

Su, Zhe ;

Tai, Shuaishuai ;

Tang, Meifang .

NATURE, 2012, 491 (7422) :56-65

[3] The NIH Roadmap Epigenomics Mapping Consortium [J].

Bernstein, Bradley E. ;

Stamatoyannopoulos, John A. ;

Costello, Joseph F. ;

Ren, Bing ;

Milosavljevic, Aleksandar ;

Meissner, Alexander ;

Kellis, Manolis ;

Marra, Marco A. ;

Beaudet, Arthur L. ;

Ecker, Joseph R. ;

Farnham, Peggy J. ;

Hirst, Martin ;

Lander, Eric S. ;

Mikkelsen, Tarjei S. ;

Thomson, James A. .

NATURE BIOTECHNOLOGY, 2010, 28 (10) :1045-1048

[4] Random forests [J].

Breiman, L .

MACHINE LEARNING, 2001, 45 (01) :5-32

[5] Modernizing Reference Genome Assemblies [J].

Church, Deanna M. ;

Schneider, Valerie A. ;

Graves, Tina ;

Auger, Katherine ;

Cunningham, Fiona ;

Bouk, Nathan ;

Chen, Hsiu-Chuan ;

Agarwala, Richa ;

McLaren, William M. ;

Ritchie, Graham R. S. ;

Albracht, Derek ;

Kremitzki, Milinn ;

Rock, Susan ;

Kotkiewicz, Holland ;

Kremitzki, Colin ;

Wollam, Aye ;

Trani, Lee ;

Fulton, Lucinda ;

Fulton, Robert ;

Matthews, Lucy ;

Whitehead, Siobhan ;

Chow, Will ;

Torrance, James ;

Dunn, Matthew ;

Harden, Glenn ;

Threadgold, Glen ;

Wood, Jonathan ;

Collins, Joanna ;

Heath, Paul ;

Griffiths, Guy ;

Pelan, Sarah ;

Grafham, Darren ;

Eichler, Evan E. ;

Weinstock, George ;

Mardis, Elaine R. ;

Wilson, Richard K. ;

Howe, Kerstin ;

Flicek, Paul ;

Hubbard, Tim .

PLOS BIOLOGY, 2011, 9 (07)

[6] Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data [J].

Cooper, Gregory M. ;

Shendure, Jay .

NATURE REVIEWS GENETICS, 2011, 12 (09) :628-640

[7] Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP plus [J].

Davydov, Eugene V. ;

Goode, David L. ;

Sirota, Marina ;

Cooper, Gregory M. ;

Sidow, Arend ;

Batzoglou, Serafim .

PLOS COMPUTATIONAL BIOLOGY, 2010, 6 (12)

[8] An integrated encyclopedia of DNA elements in the human genome [J].

Dunham, Ian ;

Kundaje, Anshul ;

Aldred, Shelley F. ;

Collins, Patrick J. ;

Davis, CarrieA. ;

Doyle, Francis ;

Epstein, Charles B. ;

Frietze, Seth ;

Harrow, Jennifer ;

Kaul, Rajinder ;

Khatun, Jainab ;

Lajoie, Bryan R. ;

Landt, Stephen G. ;

Lee, Bum-Kyu ;

Pauli, Florencia ;

Rosenbloom, Kate R. ;

Sabo, Peter ;

Safi, Alexias ;

Sanyal, Amartya ;

Shoresh, Noam ;

Simon, Jeremy M. ;

Song, Lingyun ;

Trinklein, Nathan D. ;

Altshuler, Robert C. ;

Birney, Ewan ;

Brown, James B. ;

Cheng, Chao ;

Djebali, Sarah ;

Dong, Xianjun ;

Dunham, Ian ;

Ernst, Jason ;

Furey, Terrence S. ;

Gerstein, Mark ;

Giardine, Belinda ;

Greven, Melissa ;

Hardison, Ross C. ;

Harris, Robert S. ;

Herrero, Javier ;

Hoffman, Michael M. ;

Iyer, Sowmya ;

Kellis, Manolis ;

Khatun, Jainab ;

Kheradpour, Pouya ;

Kundaje, Anshul ;

Lassmann, Timo ;

Li, Qunhua ;

Lin, Xinying ;

Marinov, Georgi K. ;

Merkel, Angelika ;

Mortazavi, Ali .

NATURE, 2012, 489 (7414) :57-74

[9] ChromHMM: automating chromatin-state discovery and characterization [J].

Ernst, Jason ;

Kellis, Manolis .

NATURE METHODS, 2012, 9 (03) :215-216

[10] Ensembl 2013 [J].

Flicek, Paul ;

Ahmed, Ikhlak ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Brent, Simon ;

Carvalho-Silva, Denise ;

Clapham, Peter ;

Coates, Guy ;

Fairley, Susan ;

Fitzgerald, Stephen ;

Gil, Laurent ;

Garcia-Giron, Carlos ;

Gordon, Leo ;

Hourlier, Thibaut ;

Hunt, Sarah ;

Juettemann, Thomas ;

Kaehaeri, Andreas K. ;

Keenan, Stephen ;

Komorowska, Monika ;

Kulesha, Eugene ;

Longden, Ian ;

Maurel, Thomas ;

McLaren, William M. ;

Muffato, Matthieu ;

Nag, Rishi ;

Overduin, Bert ;

Pignatelli, Miguel ;

Pritchard, Bethan ;

Pritchard, Emily ;

Riat, Harpreet Singh ;

Ritchie, Graham R. S. ;

Ruffier, Magali ;

Schuster, Michael ;

Sheppard, Daniel ;

Sobral, Daniel ;

Taylor, Kieron ;

Thormann, Anja ;

Trevanion, Stephen ;

White, Simon ;

Wilder, Steven P. ;

Aken, Bronwen L. ;

Birney, Ewan ;

Cunningham, Fiona ;

Dunham, Ian ;

Harrow, Jennifer ;

Herrero, Javier ;

Hubbard, Tim J. P. ;

Johnson, Nathan ;

Kinsella, Rhoda .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D48-D55

← 1 2 3 →