Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
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.
Johnson
David S
DS
Department of Genetics, Stanford University Medical Center, Stanford, California 94305, USA.
Li
Wei
W
Gordon
D Benjamin
DB
Bhattacharjee
Arindam
A
Curry
Bo
B
Ghosh
Jayati
J
Brizuela
Leonardo
L
Carroll
Jason S
JS
Brown
Myles
M
Flicek
Paul
P
Koch
Christoph M
CM
Dunham
Ian
I
Bieda
Mark
M
Xu
Xiaoqin
X
Farnham
Peggy J
PJ
Kapranov
Philipp
P
Nix
David A
DA
Gingeras
Thomas R
TR
Zhang
Xinmin
X
Holster
Heather
H
Jiang
Nan
N
Green
Roland D
RD
Song
Jun S
JS
McCuine
Scott A
SA
Anton
Elizabeth
E
Nguyen
Loan
L
Trinklein
Nathan D
ND
Ye
Zhen
Z
Ching
Keith
K
Hawkins
David
D
Ren
Bing
B
Scacheri
Peter C
PC
Rozowsky
Joel
J
Karpikov
Alexander
A
Euskirchen
Ghia
G
Weissman
Sherman
S
Gerstein
Mark
M
Snyder
Michael
M
Yang
Annie
A
Moqtaderi
Zarmik
Z
Hirsch
Heather
H
Shulha
Hennady P
HP
Fu
Yutao
Y
Weng
Zhiping
Z
Struhl
Kevin
K
Myers
Richard M
RM
Lieb
Jason D
JD
Liu
X Shirley
XS
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
D015345:Oligonucleotide Probes; D004247:DNA