title: Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
abstract: The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols, and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated.
authors.affiliation: Department of Genetics, Stanford University Medical Center, Stanford, California 94305, USA.
authors.forename: David S
authors.initials: DS
authors.lastname: Johnson
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: D Benjamin
authors.initials: DB
authors.lastname: Gordon
authors.forename: Arindam
authors.initials: A
authors.lastname: Bhattacharjee
authors.forename: Bo
authors.initials: B
authors.lastname: Curry
authors.forename: Jayati
authors.initials: J
authors.lastname: Ghosh
authors.forename: Leonardo
authors.initials: L
authors.lastname: Brizuela
authors.forename: Jason S
authors.initials: JS
authors.lastname: Carroll
authors.forename: Myles
authors.initials: M
authors.lastname: Brown
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
authors.forename: Christoph M
authors.initials: CM
authors.lastname: Koch
authors.forename: Ian
authors.initials: I
authors.lastname: Dunham
authors.forename: Mark
authors.initials: M
authors.lastname: Bieda
authors.forename: Xiaoqin
authors.initials: X
authors.lastname: Xu
authors.forename: Peggy J
authors.initials: PJ
authors.lastname: Farnham
authors.forename: Philipp
authors.initials: P
authors.lastname: Kapranov
authors.forename: David A
authors.initials: DA
authors.lastname: Nix
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
authors.forename: Xinmin
authors.initials: X
authors.lastname: Zhang
authors.forename: Heather
authors.initials: H
authors.lastname: Holster
authors.forename: Nan
authors.initials: N
authors.lastname: Jiang
authors.forename: Roland D
authors.initials: RD
authors.lastname: Green
authors.forename: Jun S
authors.initials: JS
authors.lastname: Song
authors.forename: Scott A
authors.initials: SA
authors.lastname: McCuine
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Anton
authors.forename: Loan
authors.initials: L
authors.lastname: Nguyen
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Trinklein
authors.forename: Zhen
authors.initials: Z
authors.lastname: Ye
authors.forename: Keith
authors.initials: K
authors.lastname: Ching
authors.forename: David
authors.initials: D
authors.lastname: Hawkins
authors.forename: Bing
authors.initials: B
authors.lastname: Ren
authors.forename: Peter C
authors.initials: PC
authors.lastname: Scacheri
authors.forename: Joel
authors.initials: J
authors.lastname: Rozowsky
authors.forename: Alexander
authors.initials: A
authors.lastname: Karpikov
authors.forename: Ghia
authors.initials: G
authors.lastname: Euskirchen
authors.forename: Sherman
authors.initials: S
authors.lastname: Weissman
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: Annie
authors.initials: A
authors.lastname: Yang
authors.forename: Zarmik
authors.initials: Z
authors.lastname: Moqtaderi
authors.forename: Heather
authors.initials: H
authors.lastname: Hirsch
authors.forename: Hennady P
authors.initials: HP
authors.lastname: Shulha
authors.forename: Yutao
authors.initials: Y
authors.lastname: Fu
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
authors.forename: Kevin
authors.initials: K
authors.lastname: Struhl
authors.forename: Richard M
authors.initials: RM
authors.lastname: Myers
authors.forename: Jason D
authors.initials: JD
authors.lastname: Lieb
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002869:Chromosome Aberrations; D004247:DNA / Q000737:chemistry; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes; D016133:Polymerase Chain Reaction; D012372:ROC Curve; D015203:Reproducibility of Results; D020080:Tandem Repeat Sequences
chemical_list: D015345:Oligonucleotide Probes; D004247:DNA