title: Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements.
abstract: Cancer derived microarray data sets are routinely produced by various platforms that are either commercially available or manufactured by academic groups. The fundamental difference in their probe selection strategies holds the promise that identical observations produced by more than one platform prove to be more robust when validated by biology. However, cross-platform comparison requires matching corresponding probe sets. We are introducing here sequence-based matching of probes instead of gene identifier-based matching. We analyzed breast cancer cell line derived RNA aliquots using Agilent cDNA and Affymetrix oligonucleotide microarray platforms to assess the advantage of this method. We show, that at different levels of the analysis, including gene expression ratios and difference calls, cross-platform consistency is significantly improved by sequence- based matching. We also present evidence that sequence-based probe matching produces more consistent results when comparing similar biological data sets obtained by different microarray platforms. This strategy allowed a more efficient transfer of classification of breast cancer samples between data sets produced by cDNA microarray and Affymetrix gene-chip platforms.
authors.affiliation: Division of Pulmonary and Critical Care Medicine, Department of Medicine and Pulmonary Bioinformatics, The Lung Biology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Brigham H
authors.initials: BH
authors.lastname: Mecham
authors.forename: Gregory T
authors.initials: GT
authors.lastname: Klus
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Strovel
authors.forename: Meena
authors.initials: M
authors.lastname: Augustus
authors.forename: David
authors.initials: D
authors.lastname: Byrne
authors.forename: Peter
authors.initials: P
authors.lastname: Bozso
authors.forename: Daniel Z
authors.initials: DZ
authors.lastname: Wetmore
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Mariani
authors.forename: Isaac S
authors.initials: IS
authors.lastname: Kohane
authors.forename: Zoltan
authors.initials: Z
authors.lastname: Szallasi
mesh_terms: D001940:Breast / Q000378:metabolism; D001943:Breast Neoplasms / Q000145:classification / Q000235:genetics; D002460:Cell Line; D045744:Cell Line, Tumor; D015342:DNA Probes / Q000235:genetics* / Q000592:standards*; D018076:DNA, Complementary / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods / Q000592:standards; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012334:RNA, Neoplasm / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D015342:DNA Probes; D018076:DNA, Complementary; D012333:RNA, Messenger; D012334:RNA, Neoplasm