Sequencing technology does not eliminate biological variability

被引:140
作者
Hansen, Kasper D. [1 ]
Wu, Zhijin [2 ]
Irizarry, Rafael A. [1 ]
Leek, Jeffrey T. [1 ]
机构
[1] Johns Hopkins Bloomberg Sch Publ Hlth, Dept Biostat, Baltimore, MD USA
[2] Brown Univ, Dept Community Hlth, Biostat Sect, Providence, RI 02912 USA
关键词
GENE-EXPRESSION; RNA-SEQ; REPRODUCIBILITY; IMPACT;
D O I
10.1038/nbt.1910
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
引用
收藏
页码:572 / 573
页数:3
相关论文
共 16 条
[1]   Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments [J].
Bullard, James H. ;
Purdom, Elizabeth ;
Hansen, Kasper D. ;
Dudoit, Sandrine .
BMC BIOINFORMATICS, 2010, 11
[2]   Genetic Analysis of Human Traits In Vitro: Drug Response and Gene Expression in Lymphoblastoid Cell Lines [J].
Choy, Edwin ;
Yelensky, Roman ;
Bonakdar, Sasha ;
Plenge, Robert M. ;
Saxena, Richa ;
De Jager, Philip L. ;
Shaw, Stanley Y. ;
Wolfish, Cara S. ;
Slavik, Jacqueline M. ;
Cotsapas, Chris ;
Rivas, Manuel ;
Dermitzakis, Emmanouil T. ;
Cahir-McFarland, Ellen ;
Kieff, Elliott ;
Hafler, David ;
Daly, Mark J. ;
Altshuler, David .
PLOS GENETICS, 2008, 4 (11)
[3]   Fundamentals of experimental design for cDNA microarrays [J].
Churchill, GA .
NATURE GENETICS, 2002, 32 (Suppl 4) :490-495
[4]   Stochastic gene expression in a single cell [J].
Elowitz, MB ;
Levine, AJ ;
Siggia, ED ;
Swain, PS .
SCIENCE, 2002, 297 (5584) :1183-1186
[5]   Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring [J].
Golub, TR ;
Slonim, DK ;
Tamayo, P ;
Huard, C ;
Gaasenbeek, M ;
Mesirov, JP ;
Coller, H ;
Loh, ML ;
Downing, JR ;
Caligiuri, MA ;
Bloomfield, CD ;
Lander, ES .
SCIENCE, 1999, 286 (5439) :531-537
[6]   Multiple-laboratory comparison of microarray platforms [J].
Irizarry, RA ;
Warren, D ;
Spencer, F ;
Kim, IF ;
Biswal, S ;
Frank, BC ;
Gabrielson, E ;
Garcia, JGN ;
Geoghegan, J ;
Germino, G ;
Griffin, C ;
Hilmer, SC ;
Hoffman, E ;
Jedlicka, AE ;
Kawasaki, E ;
Martínez-Murillo, F ;
Morsberger, L ;
Lee, H ;
Petersen, D ;
Quackenbush, J ;
Scott, A ;
Wilson, M ;
Yang, YQ ;
Ye, SQ ;
Yu, W .
NATURE METHODS, 2005, 2 (05) :345-349
[7]   Tackling the widespread and critical impact of batch effects in high-throughput data [J].
Leek, Jeffrey T. ;
Scharpf, Robert B. ;
Bravo, Hector Corrada ;
Simcha, David ;
Langmead, Benjamin ;
Johnson, W. Evan ;
Geman, Donald ;
Baggerly, Keith ;
Irizarry, Rafael A. .
NATURE REVIEWS GENETICS, 2010, 11 (10) :733-739
[8]   RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays [J].
Marioni, John C. ;
Mason, Christopher E. ;
Mane, Shrikant M. ;
Stephens, Matthew ;
Gilad, Yoav .
GENOME RESEARCH, 2008, 18 (09) :1509-1517
[9]   Transcriptome genetics using second generation sequencing in a Caucasian population [J].
Montgomery, Stephen B. ;
Sammeth, Micha ;
Gutierrez-Arcelus, Maria ;
Lach, Radoslaw P. ;
Ingle, Catherine ;
Nisbett, James ;
Guigo, Roderic ;
Dermitzakis, Emmanouil T. .
NATURE, 2010, 464 (7289) :773-U151
[10]   Mapping and quantifying mammalian transcriptomes by RNA-Seq [J].
Mortazavi, Ali ;
Williams, Brian A. ;
McCue, Kenneth ;
Schaeffer, Lorian ;
Wold, Barbara .
NATURE METHODS, 2008, 5 (07) :621-628