A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

Nucleic Acids Research
Nuno L Barbosa-MoraisSimon Tavaré

Abstract

Illumina BeadArrays are among the most popular and reliable platforms for gene expression profiling. However, little external scrutiny has been given to the design, selection and annotation of BeadArray probes, which is a fundamental issue in data quality and interpretation. Here we present a pipeline for the complete genomic and transcriptomic re-annotation of Illumina probe sequences, also applicable to other platforms, with its output available through a Web interface and incorporated into Bioconductor packages. We have identified several problems with the design of individual probes and we show the benefits of probe re-annotation on the analysis of BeadArray gene expression data sets. We discuss the importance of aspects such as probe coverage of individual transcripts, alternative messenger RNA splicing, single-nucleotide polymorphisms, repeat sequences, RNA degradation biases and probes targeting genomic regions with no known transcription. We conclude that many of the Illumina probes have unreliable original annotation and that our re-annotation allows analyses to focus on the good quality probes, which form the majority, and also to expand the scope of biological information that can be extracted.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jan 31, 2002·Trends in Genetics : TIG·Ben LehnerChristopher M Sanderson
Apr 5, 2002·Genome Research·W James Kent
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Mar 18, 2003·Nature Biotechnology·Rodrigo YelinGalit Rotman
Feb 13, 2004·Bioinformatics·Laurent GautierRafael A Irizarry
Aug 18, 2004·BMC Bioinformatics·Laurent GautierSteen Knudsen
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Oct 29, 2004·The American Journal of Pathology·Marina BibikovaJian-Bing Fan
Apr 20, 2005·Genome Research·Sudheer DossAldons J Lusis
Jul 8, 2005·Applied and Environmental Microbiology·Zhili HeJizhong Zhou
Aug 20, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Zhijin Wu, Rafael A Irizarry
Dec 20, 2005·PLoS Genetics·Barbara E StrangerEmmanouil T Dermitzakis
Feb 28, 2006·Bioinformatics·Fan HsuDavid Haussler
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Jun 6, 2006·BMC Bioinformatics·Michał J Okoniewski, Crispin J Miller
Nov 14, 2006·Nucleic Acids Research·Tanya BarrettRon Edgar
Feb 10, 2007·BMC Bioinformatics·Rickard Sandberg, Ola Larsson
Feb 10, 2007·Science·Barbara E StrangerEmmanouil T Dermitzakis
Mar 22, 2007·BioTechniques·Michał J OkoniewskiCrispin J Miller
May 15, 2007·Bioinformatics·Sean Davis, Paul S Meltzer
Jun 15, 2007·Nucleic Acids Research·Dmitriy SkvortsovSimon Tavaré
Jun 26, 2007·Bioinformatics·Mark J DunningSimon Tavaré
Sep 18, 2007·Nature Genetics·Harald H H GöringJohn Blangero
Sep 20, 2007·PloS One·Hendrik J M de JongeArja ter Elst
Oct 19, 2007·Nature·UNKNOWN International HapMap ConsortiumJohn Stewart
Nov 7, 2007·Nucleic Acids Research·Elspeth A BrufordEwan Birney
Nov 17, 2007·BMC Bioinformatics·Mark D Robinson, Terence P Speed
Dec 13, 2007·Nucleic Acids Research·Dennis A BensonDavid L Wheeler
Dec 19, 2007·Nucleic Acids Research·D KarolchikW J Kent
Jan 8, 2008·Nucleic Acids Research·Simon M LinWarren A Kibbe
Feb 8, 2008·BMC Bioinformatics·Mark J DunningMatthew E Ritchie
Feb 27, 2008·BMC Bioinformatics·Danny A BittonCrispin J Miller
Mar 28, 2008·PloS One·Lieven ThorrezFrans Schuit
Aug 20, 2008·BMC Research Notes·Mark J DunningAndy G Lynch

❮ Previous
Next ❯

Citations

Oct 9, 2013·Molecular and Cellular Biochemistry·Neeta AdhikariJennifer L Hall
Aug 19, 2011·European Journal of Human Genetics : EJHG·Jessica BeckerJohannes Schumacher
Jun 14, 2012·European Journal of Human Genetics : EJHG·Divya MehtaHolger Prokisch
Nov 23, 2013·Nature Communications·Daniah TrabzuniUNKNOWN North American Brain Expression Consortium
Mar 10, 2012·Human Molecular Genetics·Chris WallaceStefan Blankenberg
Apr 9, 2013·Human Molecular Genetics·Mete CivelekAldons J Lusis
Feb 26, 2013·Nucleic Acids Research·Adaikalavan RamasamyMichael E Weale
Jun 15, 2013·Nucleic Acids Research·Jianguo XiaRobert E W Hancock
Jun 11, 2011·Genome Research·Toshinori HinouePeter W Laird
May 23, 2012·Genome Research·Suhaida A SelamatIte A Laird-Offringa
Sep 2, 2010·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Wencai MaRichard E Davis
May 25, 2011·Circulation. Cardiovascular Genetics·Philipp S WildStefan Blankenberg
Aug 16, 2013·The Journal of Clinical Investigation·Derek E ByersMichael J Holtzman
Oct 18, 2011·BMC Genomics·M Aleksi KallioEija I Korpelainen
Sep 11, 2012·BMC Cancer·Carole M TactacanUNKNOWN Australian Pancreratic Genome Initiative
Dec 7, 2011·PLoS Computational Biology·Matthew E RitchieAndy G Lynch
Feb 6, 2013·PLoS Genetics·Sophie GarnierDavid-Alexandre Trégouët
Aug 23, 2012·PloS One·Andy G LynchChristina Curtis
Oct 3, 2012·PloS One·Nicolas GrelicheDavid-Alexandre Trégouët
Jan 28, 2014·Nature·Maria A ChristophorouTony Kouzarides
Sep 1, 2014·Nature Neuroscience·Adaikalavan RamasamyMichael E Weale
Oct 5, 2012·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Marcelo P CobaSeth G N Grant
Sep 13, 2012·Nature Communications·Alejandra BrunaCarlos Caldas

❮ Previous
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Datasets Mentioned

BETA
GPL2507
GSE13733
AK024373

Methods Mentioned

BETA
chip

Software Mentioned

RepeatMasker
Bioconductor
Perl script
PluriNet
BeadArrays
limma
Ensembl
illuminaHumanv3
Perl
MySQL

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