title: Microarray-based RNA profiling of breast cancer: batch effect removal improves cross-platform consistency.
abstract: Microarray is a powerful technique used extensively for gene expression analysis. Different technologies are available, but lack of standardization makes it challenging to compare and integrate data. Furthermore, batch-related biases within datasets are common but often not tackled. We have analyzed the same 234 breast cancers on two different microarray platforms. One dataset contained known batch-effects associated with the fabrication procedure used. The aim was to assess the significance of correcting for systematic batch-effects when integrating data from different platforms. We here demonstrate the importance of detecting batch-effects and how tools, such as ComBat, can be used to successfully overcome such systematic variations in order to unmask essential biological signals. Batch adjustment was found to be particularly valuable in the detection of more delicate differences in gene expression. Furthermore, our results show that prober adjustment is essential for integration of gene expression data obtained from multiple sources. We show that high-variance genes are highly reproducibly expressed across platforms making them particularly well suited as biomarkers and for building gene signatures, exemplified by prediction of estrogen-receptor status and molecular subtypes. In conclusion, the study emphasizes the importance of utilizing proper batch adjustment methods when integrating data across different batches and platforms.
authors.affiliation: Department of Clinical Genetics, Odense University Hospital, Sdr. Boulevard 29, 5000 Odense C, Denmark ; Human Genetics, Institute of Clinical Research, University of Southern Denmark, Winsløwvej 19, 5000 Odense C, Denmark.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Larsen
authors.affiliation: Department of Clinical Genetics, Odense University Hospital, Sdr. Boulevard 29, 5000 Odense C, Denmark ; Human Genetics, Institute of Clinical Research, University of Southern Denmark, Winsløwvej 19, 5000 Odense C, Denmark.
authors.forename: Mads
authors.initials: M
authors.lastname: Thomassen
authors.affiliation: Human Genetics, Institute of Clinical Research, University of Southern Denmark, Winsløwvej 19, 5000 Odense C, Denmark ; Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9B, 5000 Odense C, Denmark.
authors.forename: Qihua
authors.initials: Q
authors.lastname: Tan
authors.affiliation: Department of Clinical Genetics, Odense University Hospital, Sdr. Boulevard 29, 5000 Odense C, Denmark ; Human Genetics, Institute of Clinical Research, University of Southern Denmark, Winsløwvej 19, 5000 Odense C, Denmark.
authors.forename: Kristina P
authors.initials: KP
authors.lastname: Sørensen
authors.affiliation: Department of Clinical Genetics, Odense University Hospital, Sdr. Boulevard 29, 5000 Odense C, Denmark ; Human Genetics, Institute of Clinical Research, University of Southern Denmark, Winsløwvej 19, 5000 Odense C, Denmark.
authors.forename: Torben A
authors.identifier: 0000-0002-2460-6483
authors.initials: TA
authors.lastname: Kruse
mesh_terms: D014408:Biomarkers, Tumor / Q000096:biosynthesis*; D001943:Breast Neoplasms / Q000145:classification / Q000235:genetics* / Q000473:pathology; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D009363:Neoplasm Proteins / Q000096:biosynthesis; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D057089:Pathology, Molecular; D012313:RNA / Q000096:biosynthesis*
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D012313:RNA
references.citation: Biostatistics. 2007 Jan;8(1):118-27
references.pmid: 16632515
references.citation: Biochem Biophys Res Commun. 2006 Jun 16;344(4):1111-20
references.pmid: 16647037
references.citation: BMC Bioinformatics. 2002 Aug 23;3:22
references.pmid: 12194703
references.citation: Nature. 2000 Aug 17;406(6797):747-52
references.pmid: 10963602
references.citation: Bioinformatics. 2004 Jan 1;20(1):105-14
references.pmid: 14693816
references.citation: Environ Mol Mutagen. 2007 Jun;48(5):380-94
references.pmid: 17370338
references.citation: Bioinformatics. 2007 Oct 15;23(20):2700-7
references.pmid: 17720982
references.citation: BMC Bioinformatics. 2011 Mar 17;12:77
references.pmid: 21414208
references.citation: Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10869-74
references.pmid: 11553815
references.citation: Pharmacogenomics J. 2010 Aug;10(4):278-91
references.pmid: 20676067
references.citation: Nucleic Acids Res. 2000 Nov 15;28(22):4552-7
references.pmid: 11071945
references.citation: Clin Cancer Res. 2004 Aug 15;10(16):5508-17
references.pmid: 15328190
references.citation: BMC Bioinformatics. 2006 Sep 06;7 Suppl 2:S17
references.pmid: 17118138
references.citation: Nucleic Acids Res. 2003 Oct 1;31(19):5676-84
references.pmid: 14500831
references.citation: Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8418-23
references.pmid: 12829800
references.citation: BMC Med Genomics. 2014 Jan 31;7:9
references.pmid: 24479546
references.citation: PLoS One. 2013 May 21;8(5):e64268
references.pmid: 23704984
references.citation: J Pathol. 2010 Aug;221(4):452-61
references.pmid: 20593485
references.citation: PLoS One. 2011 Feb 28;6(2):e17238
references.pmid: 21386892
references.citation: Nucleic Acids Res. 2002 Feb 15;30(4):e15
references.pmid: 11842121
references.citation: PLoS One. 2010 Dec 01;5(12):e15031
references.pmid: 21152022
references.citation: J Clin Oncol. 2009 Mar 10;27(8):1160-7
references.pmid: 19204204
references.citation: Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10101-6
references.pmid: 10963673
references.citation: BMC Bioinformatics. 2005 Jul 15;6 Suppl 2:S12
references.pmid: 16026597
references.citation: BMC Genomics. 2006 Apr 27;7:96
references.pmid: 16643655
references.citation: Pharmacogenomics J. 2010 Aug;10(4):247-57
references.pmid: 20676064
references.citation: Nat Biotechnol. 2006 Jul;24(7):832-40
references.pmid: 16823376