BIOINFORMATICS APPLICATIONS NOTE
Vol. 27 no. 15 2011, pages 2144–2146
False positive peaks in ChIP-seq and other sequencing-based
functional assays caused by unannotated high copy number
Joseph K. Pickrell1,∗,†, Daniel J. Gaffney1,2,∗,†, Yoav Gilad1,∗
and Jonathan K. Pritchard1,2,∗
1Department of Human Genetics and2Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637,
Associate Editor: Alex Bateman
Advance Access publication June 19, 2011
DNase-seq and MNase-seq have become important tools for
genome annotation. In these assays, short sequence reads enriched
for loci of interest are mapped to a reference genome to determine
their origin. Here, we consider whether false positive peak calls
can be caused by particular type of error in the reference genome:
multicopy sequences which have been incorrectly assembled and
collapsed into a single copy.
Results: Using sequencing data from the 1000 Genomes Project,
we systematically scanned the human genome for regions of high
sequencing depth. These regions are highly enriched for erroneously
inferred transcription factor binding sites, positions of nucleosomes
and regions of open chromatin. We suggest a simple masking
procedure to remove these regions and reduce false positive calls.
Availability: Files for masking out these regions are available at
Supplementary information: Supplementary data are available at
Sequencing-basedassays such as ChIP-seq,
Received on February 24, 2011; revised on June 6, 2011; accepted
on June 8, 2011
The combination of classical methods from molecular biology with
high-throughput sequencing, as used in ChIP-seq (Johnson et al.,
2007), DNaseI-seq (Boyle et al., 2008) and MNase-seq (Schones
et al., 2008), has dramatically increased the scale at which genomic
sequences can be assayed for various properties of function. In
each of these experiments, sequences of interest (for example, sites
bound by a particular transcription factor) are enriched and then
sequenced. These resulting sequences are then mapped back to a
reference genome to determine the position of their origin. It is well
appreciated that characteristics of the reference genome influence
this mapping step; for example, some sequences in the genome are
present in multiple copies, leading to ambiguity when determining
the origin of a sequencing read (Koehler et al., 2011).
∗To whom correspondence should be addressed.
†The authors wish it to be known that, in their opinion, the first two authors
should be regarded as joint First Authors.
A related issue that has received less attention in this context is
the existence of sequences that appear to be present in a single
copy in the available reference genome, but which, in reality,
are present in multiple copies in all or some individuals. Such
sequences could potentially cause artifactual peaks in sequencing-
based assays (Hesselberth et al., 2009; Zhang et al., 2008), and can
be identified as regions of high sequencing depth in genomic DNA
(Bailey et al., 2002; Vega et al., 2009). To screen for potentially
problematic regions, we used data from the 1000 Genomes
Project (1000 Genomes Project Consortium, 2010). Specifically,
we downloaded the Illumina sequencing reads derived from low-
coverage sequencing of 57 Nigerian individuals, mapped the reads
to the human genome and then calculated the coverage at each base
in the genome using only uniquely mapped reads. For full details on
the data used, see the Supplementary Material.
An example of a problematic genomic region is presented in
Figure 1A. In the genome sequencing data, there are multiple clear
peaks of reads, suggesting the presence of collapsed repeats in
the reference genome [the reference genome used throughout is
hg18; ∼10% of these regions are no longer problematic in hg19
(Supplementary Fig. S1)]. We find that 0.1% of the genome has
read depth at least twice the median, and 0.01% of the genome has
read depth at least 15 times the median (Fig. 1B). We identified
contiguous regions where the read depth exceeded thresholds
corresponding to the top 0.1, 0.01, and 0.001% of the per-base read
depths, merging regions which fall within 50 bases of each other.
At the 0.1% threshold, there are 34359 such high depth regions
(HDRs), with a mean size of 188 bases.
We then asked whether HDRs were indeed causing false positive
peaks of coverage in high-throughput molecular biology assays. To
do this, we used data from DNase-seq (Pique-Regi et al., 2011),
MNase-seq (Schones et al., 2008) and ChIP-seq from various
transcription factors (ENCODE Project Consortium, 2007) and
histone marks (Wang et al., 2008) (Supplementary Material). In
the example in Figure 1A, the regions found to be copy number
variable also show up as sensitive to DNaseI and show extremely
high read depth in the MNase assay. Overall, of the top 0.1% of
200 base pair windows in the genome with the greatest read depth
in the DNase-seq experiment, 3% overlap HDRs, and of the top
0.1% of 200 base pair windows in the MNase-seq experiment, 26%
overlap HDRs. Additionally, across many ChIP-seq experiments
on both transcription factors and histone modifications, we see
© The Author(s) 2011. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
False positives in ChIP-seq
Fig. 1. Sequences absent from the reference genome cause spurious peaks
of sequencing reads. (A)An example of such a region. In each panel, we plot
the density of uniquely mapped sequencing reads from three sources: the
Illumina data from low coverage sequencing of Yoruba individuals from the
1000 Genomes Project (summed across all individuals), a study of DNaseI
hypersensitivity (Pique-Regi et al., 2011) and a study of MNase sensitivity
(Schones et al., 2008). In the first of these, copy number is expected to
be approximately constant. In red are regions that we call as high depth
regions at a threshold of 0.1%. (B) A long tail of very high read depth for
sequences present once in the human reference. Using the coverage from the
1000 Genomes Project data, we plot the histogram of the coverage at each
base (using 500Mb of sequence). Marked are the positions corresponding to
the top 0.1 and 0.01% of the distribution. (C) Collapsed repeats cause false
peaks of sequencing reads in functional assays. For each experiment, we
plot the fraction of the genome covered occupied by the mark, as well as the
fraction of the HDRs covered by the mark. For the ChIP-seq on transcription
factors, we used the binding sites called by the ENCODE Project (ENCODE
Project Consortium, 2007) using PeakSeq (Rozowsky et al., 2009). For
the ChIP-seq on histone modifications (Wang et al., 2008), we split the
genome into windows of 200 bases and called the most extreme 0.1% of
windows as bound. Shown are selected experiments; for all experiments see
Supplementary Figures S2 and S3.
enrichment of signal in HDRs (Fig. 1C, Supplementary Figs S2
and S3). The magnitude of enrichment of ChIP-seq peaks in HDRs
depends on the choice of peak-calling algorithm; peaks called using
(Fig. 1C), while peaks called using MACS (Zhang et al., 2008)
are not (Supplementary Fig. S4). This is likely attributable to the
We next sought to confirm that HDRs are due to collapsed repeats
in the genome (as opposed to, for example, biases due to GC content
or other sequence properties during library construction or Illumina
sequencing). First, we examined the impact of GC content of a
region on sequencing coverage. As expected, there is a relationship
between GC content and coverage, but this effect is too small to
account for the dramatic peaks of coverage we see in the data
(Supplementary Fig. S5). Next, we examined copy number data
generated on separate individuals using the orthogonal technology
of array CGH (Conrad et al., 2010). The intensities of array probes
falling in HDRs is dramatically higher than that of control probes,
often approaching the limit of the dynamic range of the array
with annotated repeats. Of the most extreme outliers in the coverage
distribution (at the 0.01% point in the distribution of coverage),
92% of the regions overlap annotated repeats. Of these repeats,
81% are satellite DNA and the remainder largely consist of L1
retrotransposons and Alu elements. We conclude that the majority
of HDRs are indeed collapsed repeats, with the caveat that some
We suggest a simple masking procedure to remove false positive
have generated BED files with the coordinates of regions we suggest
masking out (available at eqtl.uchicago.edu). Files are available
at five different cutoffs. Alternatively, we have made available a
FASTA file with the sequences present in these regions. If this
FASTA file is included in the reference genome when mapping,
sequencing reads from these regions will no longer map uniquely to
the genome and can be filtered out.
In summary, we have identified a set of genomic regions in
humans which are likely to generate spurious peaks in any assay
for screening out these regions. Similar approaches will be feasible
in other organisms as resequencing data from multiple individuals
becomes available. Screening out these regions will be particularly
useful in studies, like DNase-seq and MNase-seq, where there is no
natural control experiment [apart from copy number quantification
via whole genome sequencing (Kharchenko et al., 2011), which
remains impractical for species with large genomes], and will aid
biologically relevant signal (Rozowsky et al., 2009; Vega et al.,
We thank the 1000 Genomes Project and the ENCODE Project for
making their data public and easily accessible.
Funding: Howard Hughes Medical Institute (to Jon.K.P.), National
Conflict of Interest: none declared.
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