title: Use of a mixed tissue RNA design for performance assessments on multiple microarray formats.
abstract: The comparability and reliability of data generated using microarray technology would be enhanced by use of a common set of standards that allow accuracy, reproducibility and dynamic range assessments on multiple formats. We designed and tested a complex biological reagent for performance measurements on three commercial oligonucleotide array formats that differ in probe design and signal measurement methodology. The reagent is a set of two mixtures with different proportions of RNA for each of four rat tissues (brain, liver, kidney and testes). The design provides four known ratio measurements of >200 reference probes, which were chosen for their tissue-selectivity, dynamic range coverage and alignment to the same exemplar transcript sequence across all three platforms. The data generated from testing three biological replicates of the reagent at eight laboratories on three array formats provides a benchmark set for both laboratory and data processing performance assessments. Close agreement with target ratios adjusted for sample complexity was achieved on all platforms and low variance was observed among platforms, replicates and sites. The mixed tissue design produces a reagent with known gene expression changes within a complex sample and can serve as a paradigm for performance standards for microarrays that target other species.
authors.affiliation: Center for Drug Evaluation and Research, US FDA, Silver Spring, MD 20993, USA. karol.thompson@fda.hhs.gov
authors.forename: Karol L
authors.initials: KL
authors.lastname: Thompson
authors.forename: Barry A
authors.initials: BA
authors.lastname: Rosenzweig
authors.forename: P Scott
authors.initials: PS
authors.lastname: Pine
authors.forename: Jacques
authors.initials: J
authors.lastname: Retief
authors.forename: Yaron
authors.initials: Y
authors.lastname: Turpaz
authors.forename: Cynthia A
authors.initials: CA
authors.lastname: Afshari
authors.forename: Hisham K
authors.initials: HK
authors.lastname: Hamadeh
authors.forename: Michael A
authors.initials: MA
authors.lastname: Damore
authors.forename: Michael
authors.initials: M
authors.lastname: Boedigheimer
authors.forename: Eric
authors.initials: E
authors.lastname: Blomme
authors.forename: Rita
authors.initials: R
authors.lastname: Ciurlionis
authors.forename: Jeffrey F
authors.initials: JF
authors.lastname: Waring
authors.forename: James C
authors.initials: JC
authors.lastname: Fuscoe
authors.forename: Richard
authors.initials: R
authors.lastname: Paules
authors.forename: Charles J
authors.initials: CJ
authors.lastname: Tucker
authors.forename: Thomas
authors.initials: T
authors.lastname: Fare
authors.forename: Ernest M
authors.initials: EM
authors.lastname: Coffey
authors.forename: Yudong
authors.initials: Y
authors.lastname: He
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Collins
authors.forename: Kurt
authors.initials: K
authors.lastname: Jarnagin
authors.forename: Susan
authors.initials: S
authors.lastname: Fujimoto
authors.forename: Brigitte
authors.initials: B
authors.lastname: Ganter
authors.forename: Gretchen
authors.initials: G
authors.lastname: Kiser
authors.forename: Tamma
authors.initials: T
authors.lastname: Kaysser-Kranich
authors.forename: Joseph
authors.initials: J
authors.lastname: Sina
authors.forename: Frank D
authors.initials: FD
authors.lastname: Sistare
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods / Q000592:standards*; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000592:standards*; D015345:Oligonucleotide Probes; D012333:RNA, Messenger / Q000378:metabolism / Q000592:standards*; D051381:Rats; D017207:Rats, Sprague-Dawley; D012015:Reference Standards; D015203:Reproducibility of Results; D014018:Tissue Distribution
chemical_list: D015345:Oligonucleotide Probes; D012333:RNA, Messenger