The mutation significance cutoff: gene-level thresholds for variant predictions

被引:243
作者
Itan, Yuval [1 ]
Shang, Lei [1 ]
Boisson, Bertrand [1 ,2 ,3 ]
Ciancanelli, Michael J. [1 ]
Markle, Janet G. [1 ]
Martinez-Barricarte, Ruben [1 ]
Scott, Eric [4 ]
Shah, Ishaan [1 ]
Stenson, Peter D. [5 ]
Gleeson, Joseph [4 ,6 ]
Cooper, David N. [5 ]
Quintana-Murci, Lluis [7 ,8 ]
Zhang, Shen-Ying [1 ,2 ,3 ]
Abel, Laurent [1 ,2 ,3 ]
Casanova, Jean-Laurent [1 ,2 ,3 ,6 ,9 ]
机构
[1] Rockefeller Univ, St Giles Lab Human Genet Infect Dis, Rockefeller Branch, 1230 York Ave, New York, NY 10021 USA
[2] INSERM, U1163, Lab Human Genet Infect Dis, Paris, France
[3] Paris Descartes Univ, Imagine Inst, Paris, France
[4] Univ Calif San Diego, Dept Neurosci, Neurogenet Lab, San Diego, CA 92103 USA
[5] Cardiff Univ, Sch Med, Inst Med Genet, Cardiff CF10 3AX, S Glam, Wales
[6] Howard Hughes Med Inst, New York, NY USA
[7] Inst Pasteur, Human Evolutionary Genet Unit, Paris, France
[8] CNRS, URA 3012, Paris, France
[9] Necker Hosp Sick Children, Pediat Immunol Hematol Unit, Paris, France
关键词
FRAMEWORK;
D O I
10.1038/nmeth.3739
中图分类号
Q5 [生物化学];
学科分类号
070307 [化学生物学];
摘要
引用
收藏
页码:109 / 110
页数:2
相关论文
共 9 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]
A global reference for human genetic variation [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. ;
Wang, Jun ;
Wilson, Richard K. ;
Boerwinkle, Eric ;
Doddapaneni, Harsha ;
Han, Yi ;
Korchina, Viktoriya ;
Kovar, Christie ;
Lee, Sandra ;
Muzny, Donna ;
Reid, Jeffrey G. ;
Zhu, Yiming ;
Chang, Yuqi ;
Feng, Qiang ;
Fang, Xiaodong ;
Guo, Xiaosen ;
Jian, Min ;
Jiang, Hui ;
Jin, Xin ;
Lan, Tianming ;
Li, Guoqing ;
Li, Jingxiang ;
Li, Yingrui ;
Liu, Shengmao ;
Liu, Xiao ;
Lu, Yao ;
Ma, Xuedi ;
Tang, Meifang ;
Wang, Bo .
NATURE, 2015, 526 (7571) :68-+
[3]
The human gene damage index as a gene-level approach to prioritizing exome variants [J].
Itan, Yuval ;
Shang, Lei ;
Boisson, Bertrand ;
Patin, Etienne ;
Bolze, Alexandre ;
Moncada-Velez, Marcela ;
Scott, Eric ;
Ciancanelli, Michael J. ;
Lafaille, Fabien G. ;
Markle, Janet G. ;
Martinez-Barricarte, Ruben ;
de Jong, Sarah Jill ;
Kong, Xiao-Fei ;
Nitschke, Patrick ;
Belkadi, Aziz ;
Bustamante, Jacinta ;
Puel, Anne ;
Boisson-Dupuis, Stephanie ;
Stenson, Peter D. ;
Gleeson, Joseph G. ;
Cooper, David N. ;
Quintana-Murci, Lluis ;
Claverie, Jean-Michel ;
Zhang, Shen-Ying ;
Abel, Laurent ;
Casanova, Jean-Laurent .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (44) :13615-13620
[4]
A general framework for estimating the relative pathogenicity of human genetic variants [J].
Kircher, Martin ;
Witten, Daniela M. ;
Jain, Preti ;
O'Roak, Brian J. ;
Cooper, Gregory M. ;
Shendure, Jay .
NATURE GENETICS, 2014, 46 (03) :310-+
[5]
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm [J].
Kumar, Prateek ;
Henikoff, Steven ;
Ng, Pauline C. .
NATURE PROTOCOLS, 2009, 4 (07) :1073-1082
[6]
ClinVar: public archive of relationships among sequence variation and human phenotype [J].
Landrum, Melissa J. ;
Lee, Jennifer M. ;
Riley, George R. ;
Jang, Wonhee ;
Rubinstein, Wendy S. ;
Church, Deanna M. ;
Maglott, Donna R. .
NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D980-D985
[7]
Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes [J].
Petrovski, Slave ;
Wang, Quanli ;
Heinzen, Erin L. ;
Allen, Andrew S. ;
Goldstein, David B. .
PLOS GENETICS, 2013, 9 (08)
[8]
A framework for the interpretation of de novo mutation in human disease [J].
Samocha, Kaitlin E. ;
Robinson, Elise B. ;
Sanders, Stephan J. ;
Stevens, Christine ;
Sabo, Aniko ;
McGrath, Lauren M. ;
Kosmicki, Jack A. ;
Rehnstrom, Karola ;
Mallick, Swapan ;
Kirby, Andrew ;
Wall, Dennis P. ;
MacArthur, Daniel G. ;
Gabriel, Stacey B. ;
DePristo, Mark ;
Purcell, Shaun M. ;
Palotie, Aarno ;
Boerwinkle, Eric ;
Buxbaum, Joseph D. ;
Cook, Edwin H., Jr. ;
Gibbs, Richard A. ;
Schellenberg, Gerard D. ;
Sutcliffe, James S. ;
Devlin, Bernie ;
Roeder, Kathryn ;
Neale, Benjamin M. ;
Daly, Mark J. .
NATURE GENETICS, 2014, 46 (09) :944-+
[9]
The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine [J].
Stenson, Peter D. ;
Mort, Matthew ;
Ball, Edward V. ;
Shaw, Katy ;
Phillips, Andrew D. ;
Cooper, David N. .
HUMAN GENETICS, 2014, 133 (01) :1-9