doi:10.

1038/nature08516

ARTICLES
Origins and functional impact of copy
number variation in the human genome
Donald F. Conrad1*, Dalila Pinto2*, Richard Redon1,3, Lars Feuk2,4, Omer Gokcumen5, Yujun Zhang1, Jan Aerts1,
T. Daniel Andrews1, Chris Barnes1, Peter Campbell1, Tomas Fitzgerald1, Min Hu1, Chun Hwa Ihm5,
Kati Kristiansson1, Daniel G. MacArthur1, Jeffrey R. MacDonald2, Ifejinelo Onyiah1, Andy Wing Chun Pang2,
Sam Robson1, Kathy Stirrups1, Armand Valsesia1, Klaudia Walter1, John Wei2, Wellcome Trust Case Control
Consortium{, Chris Tyler-Smith1, Nigel P. Carter1, Charles Lee5, Stephen W. Scherer2,6 & Matthew E. Hurles1
Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are
still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a
comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been
validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European,
African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition
has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by
correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are
candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the
patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by
genome-wide association studies will not be accounted for by common CNVs.
Genomes vary from one another in multifarious ways, and the totality
of this genetic variation underpins the heritability of human traits.
Over the past two years, the human reference sequence1 has been
followed by other genome sequences from individual humans
(reviewed in ref. 2) with fruitful comparisons. These studies show
the landscape of genetic variation, and allow estimation of the relative
contributions of sequence (base substitutions) and structural variation (indels (that is, insertions or deletions), CNVs and inversions).
For simplicity, in this study we use the term CNV to describe collectively all quantitative variation in the genome, including tandem
arrays of repeats as well as deletions and duplications.
Despite this growing genomic clarity, these classes of variation are
not equivalently recognized in human genetic studies. To appreciate
the functional impact and selective history of a variant, its correlation
with nearby variants must be characterized3 allowing imputation into
previously assayed genomes4, and experimental reagents and protocols are needed for the variant to be assayed in a cost-effective manner
in different samples.
Genome re-sequencing studies have shown that most bases that vary
among genomes reside in CNVs of at least 1 kilobase (kb)5,6.
Population-based surveys have identified thousands of CNVs, most
of which, due to limited resolution, are larger than 5 kb79. Their functional impact has been demonstrated across the full range of biology10,
from cellular phenotypes, such as gene expression11, to all classes of
human disease with an underlying genetic basis: sporadic, Mendelian,
complex and infectious (reviewed in ref. 12). This class of variation is,
nonetheless, poorly integrated into human genetic studies at all levels.
Not only are CNVsespecially smaller onesunderrepresented in

existing databases, but with at least one notable exception8, previous

studies have tended to focus on CNV discovery and not genotyping,
owing in part to the technical challenges of their assays. Nevertheless,
the potential utility of a reference set of CNV genotypes is exemplified
by the observation that of 67 CNVs genotyped in a previous genomewide survey of CNV9, four have subsequently become associated with
complex traits: a 20-kb deletion upstream of the IRGM gene with
Crohns disease13, a 45-kb deletion upstream of NEGR1 with body
mass index14, a 32-kb deletion that removes two late-cornified envelope genes with psoriasis15, and a 117-kb deletion of UGT2B17 with
osteoporosis16.
Clinical geneticists need to discriminate pathogenic from benign
CNVs in their patients, and have made extensive use of data from CNV
surveys of apparently healthy individuals17. The mere presence or
absence of a variant in such control data sets is only partially informative, as the determination of the pathogenicity of inherited CNVs is at
present limited by the lack of information on their frequency and
combination in apparently healthy individuals of a given age.
As successive surveys for CNVs have yielded higher resolution data,
smaller variants have been discovered, along with increased precision of
the breakpoints for each CNV8,18,19. Precise breakpoint sequences are
required, not only to assess the functional content of a variant, but also
to design robust genotyping assays and to identify signatures of the
underlying mutational mechanisms. CNVs are generated by diverse
mutational mechanisms (recently reviewed in ref. 20)including
meiotic recombination, homology-directed and non-homologous
repair of double-strand breaks, and errors in replicationbut the relative contribution of these different mechanisms is not well appreciated.

1
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK. 2The Centre for Applied Genomics and Program in Genetics and Genomic
Biology, The Hospital for Sick Children, MaRS CentreEast Tower, 101 College Street, Room 14-701, Toronto, Ontario M5G 1L7, Canada. 3Inserm UMR915, Linstitut du thorax, Nantes
44035, France. 4Uppsala: Department of Genetics and Pathology, Rudbeck Laboratory Uppsala University, Uppsala 751 85, Sweden. 5Department of Pathology, Brigham and Womens
Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA. 6Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada.
*These authors contributed equally to this work.
{Lists of participants and affiliations appear in Supplementary Information.

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2009 Macmillan Publishers Limited. All rights reserved

ARTICLES

NATURE

Here we describe a comprehensive survey to detect common CNVs

larger than 1 kb in size in the human genome, and the development and
application of experimental protocols to allow these CNVs to be
assayed. The HapMap sample set has previously been well-characterized
for other forms of variation, and we now add CNV genotypes for these
samples. These unprecedented resources have allowed us to discern key
features of the mutational mechanisms underlying CNVs, to investigate
the effect of selection on CNVs, and to identify candidate CNVs that
may be the causal variant on haplotypes associated with complex traits.
CNV discovery and genotyping
We designed an experimental strategy to discover CNVs greater than
,500 base pairs (bp) in individuals with European or West African
ancestry (Fig. 1). Using a set of 20 NimbleGen arrays, each comprising ,2.1-million long oligonucleotide probes covering the assayable
portion of the genome (median spacing of 56 bp), we performed
800 comparative genome hybridization (CGH) experiments with
female lymphoblastoid cell-line DNA competed against a common
male European reference sample (NA10851). The female test DNAs
comprised 19 CEU (Utah residents with ancestry from northern and
western Europe)-European HapMap individuals, 20 YRI (Yoruba
from Ibadan, Nigeria)-West Africans, and a Polymorphism
Discovery Resource individual (NA15510). It was estimated that
40 samples would provide 95% power to sample variants with minor
allele frequencies of 5% in either population.
We used stringent calling criteria (minimum 10 consecutive
probes) to identify 51,997 putative CNV segments in the 41 samples
(40 test samples and 1 reference sample). The median numbers of
segments in CEU and YRI individuals were 1,117 and 1,488, respectively, reflecting both the higher genetic diversity in Africa and the use
of a CEU reference sample. CNV sizes ranged from 443 bp to
1.28 megabases (Mb), with a median size of 2.9 kb. We merged these
calls across samples to identify 11,700 putative CNV loci (median size
of 2.7 kb), of which 49% were called in a single individual (Supplementary Methods and Supplementary Table 1). Using quantitative PCR (qPCR) for initial validation, we confirmed 79 of 99
randomly selected loci as varying in copy number, suggesting a preliminary false-discovery rate of ,20% (Supplementary Methods).
Within the context of a CNV association study conducted by the
Wellcome Trust Case Control Consortium (WTCCC), a CNV-typing
array was designed by the WTCCC in collaboration with the other coauthors of this paper in which a preliminary version of our discovery
CNV discovery
40 test samples: 20 YRI, 1 PDR, 19 CEU

data was shared at an early stage with the WTCCC. The array used the
Agilent CGH platform and comprised 105,000 long oligonucleotide
probes. Its targets include 10,819 out of 11,700 (92%) of the candidate
CNV loci, and 375 other loci from published CNV surveys, including
292 new sequence insertions (Supplementary Methods)5,18. To perform
large-scale validation of candidate CNVs, we ran each of the 41 DNA
samples used in the discovery phase of this study on the CNV-typing
array against a pooled reference sample to minimize reference-specific
artefacts. By comparing the correlation between the discovery data and
the CNV-typing data across the same samples at each locus, we could
distinguish probable false-positives and true CNVs (Supplementary
Methods). Using this approach we estimated the false discovery rate
to be 15%, in good agreement with the estimate obtained from the
much smaller set of independent validation experiments using qPCR.
We then assayed 450 HapMap samples (180 CEU, 180 YRI, 45 JPT
(individuals in Tokyo, Japan) and 45 CHB (individuals in Beijing,
China)) across our CNV-typing array. We used a Bayesian algorithm
to genotype CNVs (more precisely: to assign individuals to diploid
copy number classes), and then manually curated the selection of the
optimal normalization and cluster locations for every locus (Supplementary Methods). We applied quality-control filters to identify
5,238 non-redundant CNVs (4,978 from the CNVs discovered here)
that could be genotyped with high confidence in at least one HapMap
population (3,320 were polymorphic in CEU, 3,985 in YRI and 1,957
in JPT1CHB), and these genotypes exhibited high concordance
across replicate experiments (Supplementary Table 2 and Supplementary Methods).
We also analysed data on 242 HapMap samples on an Illumina
Infinium genotyping platform (Human660W), developed in conjunction with the WTCCC 2 experiments, which incorporates probes
in 8,914 of our CNVs (biased towards those with high frequency in
CEU), using recently published CNV genotyping software21. We
observed that 2,513 CNVs could be genotyped, 2,175 (87%) of which
were also genotyped on the Agilent CGH microarrays. This high
concordance suggests that the genomic properties of the CNV rather
than the performance characteristics of the technology platform
determine whether a CNV can be reliably typed. Given the extensive
overlap, and the smaller number of HapMap samples run on the
Illumina array, subsequent analyses of genotyped CNVs focus solely
on data from the array-CGH CNV-typing.
We developed a new statistical method (Supplementary Methods) to
estimate the absolute copy number of each genotyped CNV, allowing us

Reference sample
(NA10851)

375 loci from other

CNV maps
Genome-tiling set of 20 arrays
(42 million long oligo probes)

CNV genotyping
CNV genotyping array
(2 105K arrays)

Copy number signal

(log2 ratio)

180 YRI

90 JPT+CHB

51,997 CNV calls

11,700 CNV loci
8,599 validated CNVs

Chromosomal
coordinates
10,819
CNV loci

30
20
10
0

CNV map

Figure 1 | Overview of experimental strategy for CNV discovery and

genotyping. Overview of the discovery and genotyping phases of this
project, with the former generating a new map of CNV locations and the

180 CEU

40

1.5

1.0

0.5
0.0
log2ratio

0.5

CNV genotypes
for 5,238 loci

latter allowing a reference set of CNV genotypes to be constructed. Data are

available at the Database of Genomic Variants50 and http://
www.sanger.ac.uk/humgen/cnv/42mio.

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NATURE

to distinguish deletions (0, 1 or 2 diploid copy number), duplications

(2, 3 or 4 diploid copy number) and multiallelic CNVs (greater than 3
possible diploid copy numbers). Of the 5,238 genotyped CNVs, 77%
were deletions, 16% were duplications and 7% were multi-allelic
(Supplementary Fig. 1.1 and Supplementary Table 1.1). The 5:1 ratio
of deletions to duplications probably partly reflects the greater technical
challenge of robustly genotyping duplications.
For all subsequent analyses (except where noted) we examine a set
of 8,599 validated CNVs, 70% (6,024 out of 8,599) of which have not
been previously characterized (Supplementary Methods).
The improved resolution of CNV breakpoints provided an opportunity to assess the extent to which distinct CNVs overlap in our data
set. This is a complex problem in the absence of sequenced breakpoints for all variants, but we can use all validated CNVs, which may
have some residual redundancy (that is, a single CNV could be split
into two overlapping loci), to estimate an upper bound on this, and
our non-redundant genotyped loci, which are probably biased
against genotyping overlapping loci, to estimate a lower bound
(Supplementary Methods). In this manner, we estimate the proportion of CNVs overlapping other CNVs to be in the range of 6% to
29%, which is far higher than the proportion of SNPs that are triallelic (that is, three different bases observed at the same site).
Genomic effect of CNVs
We identified an average of 1,098 validated CNVs, and a cumulative
CNV locus length of 24 Mb (0.78% of the genome) when comparing
two genomes by CGH. The 8,599 validated CNVs discovered in these
41 individuals cover a total of 112.7 Mb (3.7%) of the genome.
On average per comparison of two diploid genomes by CGH, we
found that 445 out of 1,098 (40.5%) of the validated CNVs overlapped with 622 out of 20,174 (3.1%) RefSeq genes (including intronic CNVs), altering the structure of 835 out of 30,917 (2.7%) gene
transcripts, and directly altering the coding sequence of 323 out of
27,761 (1.2%) messenger RNAs (Table 1). When all samples were
considered together, we found that 3,340 (38.8%) of the validated
CNVs overlapped 2,698 (13.4%) RefSeq genes (including intronic
CNVs), altering the structure of 3,863 (12.5%) gene transcripts,
and directly altering the coding sequence of 1,519 (5.5%) mRNAs
(Table 1). Over half of the partial gene deletions that encompass
exons are predicted to induce frameshifts, and combining these
alleles with whole gene deletions identifies unambiguous loss of function alleles for 267 genes (Supplementary Table 1.2).
We observed a paucity of autosomal CNVs overlapping RefSeq
genes, compared to random permutations (Supplementary Fig. 1.2).
This impoverishment is more strongly associated with deletions than
duplications or multiallelic loci (Fig. 2a), and in common CNVs
(minor allele frequency (MAF) . 10%) compared to rare CNVs
(MAF , 1%) (Fig. 2b). The bias of common deletions away from
genes is stronger in YRI than in CEU (Fig. 2b), which is also consistent
with weaker selection against deleterious base substitutions in CEU
than YRI22. There was also a bias of CNVs away from enhancers and
ultra-conserved elements, but not from promoters or DNaseI hypersensitive sites (Supplementary Fig. 1.2). Indeed duplications seem to

Candidate loci
Validated loci
Validated genotyped

Validated genotyped deletions

Validated genotyped duplications
Validated genotyped multi-allelic
0%

20%

40%

60%

Full gene
Exon or promoter
Stop codon

80% 100%

Within intron
Intergenic

Common
Intermediate
Rare
Common deletions
Intermediate deletions
Rare deletions
Common duplications
Intermediate duplications
Rare duplications

YRI common
CEU common
ASN common
0%

20%

40%

60%

80%

100%

Figure 2 | Functional impact of CNVs by type, frequency and population.

a, Impact on genes of sets of CNV at different stages of characterization
(candidate, validated, validated/genotyped loci). Genotyped CNVs are split
into different classes (deletion, duplication and multiallelic). b, Impact on
genes of CNV classes based on population frequency. Frequency classes:
common (MAF $ 0.1 in any population), intermediate (0.1 . MAF . 0.01),
rare (MAF # 0.01 in all populations). ASN denotes JPT1CHB.

be significantly enriched among promoters and stop codons, perhaps

corroborating a previous observation of indel enrichment at either
end of genes23.
Gene ontology analysis showed an enrichment of genes involved in
extracellular biological processes such as cell adhesion, recognition
and communication in CNVs. However, genes involved in intracellular processes such as biosynthetic and metabolic pathways were
underrepresented in CNV regions (Supplementary Methods and
Supplementary Fig. 1.3). These findings confirm and extend previous
observations that CNVs are preferentially found in genes at the periphery of cellular networks24.
We also identified 56 potential fusion genes (Supplementary
Table 1.3) and experimentally validated four (AKR7LAKR7A3,
BTNL3BTNL8, LCE1DLCE1E and SIGLEC5SIGLEC14) of five

Table 1 | Number of RefSeq genes affected by CNVs

CNV loci
total (avg sample)

Intron
total (avg/sample)

Whole-gene
total (avg/sample)

Promoter (TSS 2 500 bp)

total (avg/sample)

Exon
total (avg/sample)

Stop codon
total (avg/sample

8,599 validated (1,098)*

4,977 genotyped (670)
3,811 deletions (549)
874 duplications (97)
292 multi-allelic (24)

1,236 (269)
1,036 (198)
909 (177)
203 (20)
47 (5)

893 (204)
494 (67)
222 (26)
244 (36)
62 (5)

238 (42)
278 (20)
147 (9)
93 (9)
49 (2)

183 (38)
134 (18)
80 (11)
45 (7)
21 (1)

270 (70)
163 (28)
74 (10)
90 (16)
15 (2)

Overlap analysis was performed to identify CNV loci that were completely confined to introns and intergenic regions, as well as those that overlapped gene regions. The latter group was further
subdivided in succession into complete CNV-gene overlaps, partial CNV-gene overlaps that included stop codons, and partial CNV-gene overlaps that included the promoter region. The remainder
of CNV loci overlapping other (internal) exons was considered as a separate group. Counts are given for the total number of CNV loci (that is, among all samples) as well as for the number of CNVs
detected per sample on average (avg/sample). For the validated CNVs the avg/sample is actually an average per CGH comparison of two diploid genomes.
TSS, transcription start site.
* In total, 247 (12%) genes in the Online Mendelian Inheritance in Man (OMIM) database overlapped with validated CNV loci, averaging 45 (2.2%) OMIM genes per sample affected by 48 (4.4%)
CNVs.

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ARTICLES

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tested. Interestingly, 55% of the gene fusions arise between paralogous

gene family members, which may be less likely to generate truly novel
gene functions.
Mechanisms of CNV formation
The precision of CNV breakpoint mapping determines how reliably
mutation mechanisms might be inferred. We determined the precision of our breakpoint estimates by identifying 350 CNVs in two
samples (194 breakpoints in NA15510 and 156 in NA12878) for which
breakpoint sequences have been published18,19,25. Comparing our
breakpoint estimates to these sequences revealed excellent precision
(median estimation error ,60 bp), representing an improvement of
more than an order of magnitude over previous population-based
CNV surveys8, with similarly accurate estimation for both samples
(NA15510: 1 bp17.1 kb, median 54 bp; NA12878: 0 bp5.5 kb,
median 62 bp). These findings were supported by high-concordance
of breakpoint estimation between replicate experiments (Supplementary Methods).
CNV formation mediated by recombination between interspersed
duplicated sequences by non-allelic homologous recombination
(NAHR), or corresponding to tandem arrays of variable numbers
of tandem repeats (VNTR), can readily be identified at the resolution
afforded in our experiments by analyses of local sequence homology
(Supplementary Methods). Although germline mutation processes at
VNTR, like NAHR, are primarily driven by meiotic recombination,
detailed mutation analyses have shown a major role for complex
intra- and inter-allelic exchanges at VNTR that are not a major source
of CNV at interspersed duplicated sequences26. Sequence analysis of
CNV breakpoints is required to estimate the contribution to CNV
formation of other mechanisms including non-homologous end
joining and microhomology-mediated break-induced repair.
We found the relative contribution of NAHR and VNTRmediated CNV formation to be largely dependent on CNV size.
NAHR was estimated to be 7 times more likely than VNTR to be
the underlying mechanism for CNVs in the largest size decile,
whereas VNTR were 3.5 times more frequent in the bottom decile.
Overall, NAHR and VNTR contribute similarly (13.5% and 11.2% of
validated CNVs, respectively; Supplementary Fig. 1.4). Owing to the
challenges of designing validation and genotyping assays for VNTR,
these loci are probably underrepresented in our genotyping data

b
Motif density

+ * dbSNP_129_indels_reduced
+ motif15
+ motif11
+ motif18
+ * simple_repeats_under_100bp
motif0
motif6
+ degen_myers
+ motif19
+ * lifted_over_quadruplexes
+ motif2
motif5
motif14
motif8
+ * cpg
motif7
motif9
+ motif12
+ motif10
+ slipped_dna
+ * simple_repeats_over_100bp
Z_dna
motif13
motif16
cruciforms_2
+ * segdup_pairs
motif1
motif17
motif3
+ * uniq_segdups
motif4
triplexes_2
human_pseudogenes

Duplications
Deletions
0.00

0.05
0.10
0.15
Proportion of events

Left flank

CNV

Right flank

Left flank

CNV

Right flank

0.004

0.002
0.000

c
Density of
hotspot motif

(5.6% of genotyped CNVs), although we have PCR-validated 11

out of 12 randomly selected VNTR to demonstrate that this class
of loci is genuinely polymorphic (Supplementary Table 1.4 and Supplementary Fig. 1.5).
Short sequence motifs thought to form non-B-DNA structures
may predispose to chromosomal rearrangements27. We tested the
hypothesis that primary DNA sequence can predict CNV formation
by screening CNV breakpoints for enrichment of 13 published motifs
and genomic annotations (Fig. 3a and Supplementary Methods).
Two motifs forming non-B-DNA structures were strongly overrepresented at CNV breakpoints (G-quadruplexes P , 1023, slipped DNA
P , 1023), as were CpGs and a 13-bp motif predictive of recombination hotspots and genome instability in humans28. In the latter case
the association seems to be due solely to VNTR containing the hotspot motif (Fig. 3c). Our results indicate that the previous observations of recombination hotspots flanking a few well-characterized
highly polymorphic VNTR29, probably reflects a genome-wide association between hotspots and a large subset of VNTR. The known
enrichment of G-quadruplexes and CpGs in gene promoters30 may
partly explain the enrichment of CNVs we observed in promoters
(Supplementary Figs 1.6 and 1.7).
As a complementary approach to testing previously described
sequence motifs, we collated a large set of sequences likely to contain
CNV breakpoints and used machine learning31 to discover new
mutagenic motifs (Supplementary Methods and Supplementary
Fig. 1.8). The motifs that we obtained, although significant, showed
a modest enrichment for CNVs ranging from 1.2- to 1.5-fold. The
most readily interpretable finding among these is a 14 bp CNV motif
that is present in most Alu and SVA elements and has previously been
shown to be associated with CNV breakpoints in Alu-Alu recombination events32 (Fig. 3b). This motif represents a binding site in the Alu
secondary structure for the signal recognition particle ribonucleoprotein and is highly conserved across Alu elements.
The central role of sequence homology in the fidelity of DNA repair
and replication indicates that regions of the genome with higher
diversity may be more prone to replication and repair errors.
Notably, we found evidence of an enrichment of small indels from
the SNP database (dbSNP) (1.7-fold, P , 1023) and microsatellites
(1.24-fold, P , 1023) near CNV breakpoints (Fig. 3a). This observation suggests that simple variation may precipitate more mutations,

0.008
VNTR

0.000

Non-VNTR

0.20

Figure 3 | DNA sequence context enrichments around CNV breakpoints.

Thirty DNA sequence motifs thought to be associated with genome
instability were compared to estimated CNV breakpoints. a, The proportion
of CNV breakpoint regions containing each motif was plotted separately for
deletions (green circles) and duplications (red circles). Motifs generated
through machine-learning in the current study are indicated with green
labels, and the remainder are from the literature. Asterisks denote motifs
that show significant enrichment in duplication breakpoints compared to
deletion breakpoints; 1 denotes motifs that are significantly

overrepresented in the total set of CNV breakpoint sequences compared to

matched control sequence. b, Density of Alu signal recognition particle
(SRP) binding motif in 50-bp bins within (red) and flanking (white) CNV
breakpoints, showing significant enrichment of the motif at CNV
breakpoints; bootstrap 95% confidence intervals are indicated by blue bars.
c, The density of the 13-bp motif predictive of recombination hotspots seems
to be increased directly adjacent to VNTR CNVs but not around non-VNTR
CNVs.

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both substitutional and structural, as suggested by recent comparative

genomic analyses33.
We assessed the statistical significance of differences in the breakpoint signatures of deletions and duplications (Supplementary
Methods). We found that duplications are more likely to be formed
by NAHR, VNTR and retrotransposition, and are more enriched for
breakpoint-associated sequence motifs than deletions (Fig. 3a).
These findings indicate that the formation of duplications is more
likely to be sequence-dependent than deletions.
Next, we extended our investigation of mutation mechanisms to
identify probable dispersed duplications among the CNVs. The array
data themselves do not identify chromosomal location, but polymorphic dispersed duplications can be identified by considering
other sources of information. We took five complementary
approaches to identify dispersed duplications among our CNVs:
(1) precise mapping to inter-chromosomal segmental duplications;
(2) evidence for inter-chromosomal mappings from sequence data34;
(3) inter-chromosomal linkage disequilibrium; (4) poly-A and target
site duplication signatures of retrotransposition; and (5) in silico
splicing of CNV discovery data in known transcripts to identify retroposed genes (Supplementary Methods and Supplementary Fig. 1.9).
By integrating these different sources of data we identified 75
probable dispersed duplications (Fig. 4 and Supplementary Tables
1.5 and 1.6). We developed PCR assays for four of these and genotyped
them across 270 HapMap samples, with complete concordance with
the array-based genotypes (Supplementary Notes, Supplementary
Table 1.7 and Supplementary Fig. 1.10). These dispersed duplications
appear randomly distributed among chromosomes. Some of the dispersed duplications can be confidently ascribed to retrotransposition

Figure 4 | Circular map showing the genomic distribution of different

classes of CNVs and their population differentiation. Chromosomes are
shown colour-coded in the penultimate circle. The innermost circle shows
lines connecting the origin and the new location of 58 putative interchromosomal duplications, coloured according to their chromosome of
origin. The next circle out shows a stacked histogram representing the
number of deletions (red), duplications (green) and multiallelic (blue) loci
in 5-Mb bins. The next circle out shows a stacked histogram representing the
number of CNVs generated by NAHR (blue), VNTR (red) and other (grey)
mechanisms in each 5-Mb bin. The outermost circle shows the VST measure
of population differentiation between CEU and YRI discovery samples for
each CNV.

using the signatures described earlier, but other mechanisms may also
generate dispersed duplications. Interestingly, a subset of these retrotransposition events does not comprise retroposed repeat elements or
known RNA transcripts, some but not all of which seem likely to result
from L1 transduction35.
Population genetics of CNV
Although rates of CNV mutation have been well characterized at
a small number of loci using experimental techniques, a reliable
estimate of the genome-wide mutation rate has yet to be obtained.
With a set of CNVs ascertained in a consistent manner we used the
Watterson estimator of the population-scaled mutation rate, hW, to
estimate the average per-generation rate of CNV formation, m. The
ascertainment-corrected number of segregating sites (.500 bp) leads
to an estimate of m 5 3 3 1022 mutations per haploid genome, per
generation; however at the base-pair level, heterogeneity in this rate is
expected to vary by several orders of magnitude among sites
(Supplementary Methods). This estimate does not account for
purifying selection, and so it probably represents a lower bound on
the true rate.
A key parameter for linkage-disequilibrium-based studies of
human variation is the proportion of CNVs that can be tagged well
by nearby SNPs. Such taggability depends on CNV allele frequency
and local SNP density, but not on CNV size (Supplementary
Methods). Overall, the taggability of biallelic CNVs genotyped with
high confidence seems to be largely similar to that of frequencymatched SNPs, except that rare CNVs are more poorly tagged; in
CEU, 77% of CNVs .5% MAF are captured with r2 5 0.8, whereas
only 23% of CNVs ,5% MAF are similarly tagged. These results are
similar to others in a smaller data set8. Interestingly, deletions are
much better tagged by nearby SNPs than by duplications (average
difference in maximum r2 is 0.25; P , 10216), while controlling for
allele frequency and local SNP density; this may be a result of the
chromosomal dispersion of some duplications and an increased frequency of reversions and repeat mutations at some duplications36.
To estimate the strength of purifying selection acting on CNVs in
different functional categories, we fitted a population genetic model
of demography and selection37 to the site frequency spectrum of
deletions and duplications in the CEU population, corrected for
incomplete ascertainment (Supplementary Methods). We observed
the strongest purifying selection acting on exonic CNVs, then intronic CNVs then intergenic CNVs (Fig. 5a). Stronger purifying selection at intronic CNVs than intergenic CNVs has also been observed
in Drosophila38 and intronic deletions can be pathogenic if they interfere with proper splicing39. Differences in the ascertainment and in
the precision of estimates of key population genetic parameters
between CNV and published base substitution data sets render direct
comparison of average fitness coefficients between CNVs and substitutions potentially misleading.
One signal of recent positive selection is an unusually long haplotype around the selected marker, but it is difficult to fine-map the
selected variant within such long haplotypes on the basis of population genetic data alone. Large CNVs, by virtue of their potential
functional impact, may make a useful first screen for deconstructing
such signals. Accordingly, we have surveyed our CNVs for signs of
recent positive selection using population differentiation9 and two
previously described approaches40,41 relying on haplotype structure
(integrated haplotype score: iHS, and cross-population extended
haplotype homozygosity: XP-EHH). Several of the CNVs exhibited
iHS in the top 1% of the genomic distribution: 7 in CEU, 1 in
CHB1JPT, 18 in YRI, all of which seem to represent populationspecific signals. The most impressive signal is around CNVR8151.1
in YRI: a standardized iHS of 3.39, in the top 700 out of 2.26 million
markers (top 0.03% of the genome). This deletion lies between the
APOL2 and APOL4 genes involved in pathogen immunity and previously reported to have been under positive selection in primates42. The
top XP-EHH signal is CNVR3685.1, a deletion at .80% frequency in
5

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Proportion of
segregating sites

a
0.3
0.2
0.1
0.0

Derived allele count

4
3

XP-EHH

0.4

IKBKB

POLB VDAC SLC20A2

10

1.0
0.8
0.6

r2

CNV exonic = 17
CNV intron = 8
CNV inter
= 5

0.4

0.2

0.0
42.25
42.35
Chr8 position (Mb) NCBI36

155.35
155.45
Chr5 position (Mb) NCBI36

Figure 5 | Population properties of CNV show functional impact. a, Expected

derived allele frequency spectrum among 40 CEU chromosomes for different
classes of genetic variation, on the basis of the estimated strength of purifying
selection acting on each class (see text for details). The estimated value of c, the
average scaled population selection coefficient, is indicated in the legend for
each class of variant: exonic (c 5 217, P , 10230), intronic (c 5 28,
P , 10210), and intergenic (c 5 25, P , 10230) CNVs. The P values are
estimated using a Likelihood Ratio Test of neutrality (c 5 0). If we do not
correct for incomplete ascertainment for these three classes of CNV we
estimate c to be 213, 27 and 24, respectively. Similarly, if we consider only
sites .1 kb, which have more complete ascertainment we estimate c to be
215, 210 and 25, thus showing this ordering of classes of CNV to be robust.
b, A CNV showing increased XP-EHH in analysis of merged SNP-CNV
HapMap haplotypes; blue line and symbols, CEU-YRI; grey, CEU-CHB1JPT;
green, CHB1JPT-YRI. The locations of potential functional variants are
indicated by symbols: filled diamond, CNV; cross, non-synonymous SNP; x,
synonymous SNP; triangle, UTR SNP. c, Linkage disequilibrium between
CNV2659.1 (pink bar) and multiple sclerosis GWAS hit SNPs (pink
diamonds). Near perfect linkage disequilibrium (r2 5 0.95) was observed with
the top hit SNP (rs47049). Patterns of linkage disequilibrium between the
CNV and other HapMap SNPs are shown with black points.

CEU and CHB1JPT but almost absent from YRI, 500 bp 39 to another
immune-related gene, IKBKB (Fig. 5b).
Recent positive selection can also drive increased population differentiation. The VST statistic9 for population differentiation (Fig. 4) is
distinct from haplotype-based measures of recent positive selection as
it allows assessment of all loci, not just those with biallelic genotype
calls (for example, unclusterable events and multiallelic CNVs). The
CNV with the highest value of VST between CEU and YRI is an intronic
deletion of the PDLIM3 gene, which encodes an abundant protein in
skeletal and cardiac muscle. We noted that also among the top five
most highly differentiated loci was an intronic VNTR of the gene
encoding ACTN2, the sarcomeric protein binding-partner of
PDLIM3. Four other pathways with two genes under recent selection
have been identified in SNP-based selection scans40,43 (EDAR and
EDA2R, SLC24A5 and SLC45A2, NRG and ERBB4, and LARGE and
DMD). The possibility that these two highly differentiated CNVs in
genes encoding interacting proteins contribute to population44 or
individual differences in cardiac or skeletal muscle phenotypes
warrants further investigation. Mutations in ACTN3, the close paralogue of ACTN2, alter muscle function in humans and mice45, and a
recent study has highlighted an enrichment of genes involved in
muscle development among signals of recent positive selection46.
We tested for biases of certain mutation processes or functional
locations for CNVs with high VST values. We noted that VNTR are
significantly enriched in both tails of the VST distribution (Supplementary Fig. 1.11), whereas CNVs formed by NAHR seem to be

uniformly distributed across the spectrum of VST. The enrichment of

VNTR in the low end of the VST distribution is expected given the
recurrent mutation at these loci, but the enrichment at the highest
decile of population differentiation suggests that among all CNVs,
VNTR may be enriched for functional impact. The most differentiated CNV between CEU and YRI previously identified9 encompasses the CCL3L1 gene, and remains the most differentiated
exonic CNV here. However, we identified 21 more highly differentiated loci, all of which are intronic or intergenic, suggesting a role in
gene regulation might underpin any recent positive selection.
Complex trait genetics of CNV
We explored whether the CNVs from this study might be plausible
candidates for causal variants for known complex trait associations
from genome-wide association studies (GWAS). We examined 1,554
trait-associated SNPs from 279 publications (NHGRI GWAS website47, downloaded on 15 June 2009), In the CEU, 474 out of 1,521
polymorphic trait-associated SNPs fell within a recombination hotspot interval that also contained a CNV. We then examined whether
the CNVs in these intervals were in strong linkage disequilibrium
with the trait-associated SNP in the different HapMap populations.
For genotyped biallelic CNVs we assessed linkage disequilibrium
using correlation (r2) within phased haplotypes, but to include multiallelic and ungenotyped CNVs in this analysis we also considered the
squared Pearson correlation coefficient between the SNP genotypes
and the copy number intensity data. We identified 34 trait-associated
SNP to CNV correlations with an r2 of greater than 0.5, at 30 loci
across 22 traits (Fig. 5c, Table 2 and Supplementary Fig. 1.12), five of
which were found in the HLA. These CNVs include three previously
identified CNV-trait associations1315, which represent all the positive
controls for this analysis, thus the remainder represent plausible
candidates for the causal variants. Further fine-mapping experiments
in large sample sets are required to assess which variants on these
associated haplotypes are indeed causal.
What, if anything, does the low (,5%) proportion of trait-associated
SNPs that might plausibly be tagging a causal CNV tell us about the
contribution of common (MAF .5%) CNVs to complex disease susceptibility? The fact that most (77%) of our common genotyped CNVs
are well-tagged by SNPs suggests that existing GWAS studies have
already indirectly screened for the potential effect of these variants
relatively effectively. By modelling the ascertainment of genotyped
CNVs in this study (Supplementary Methods), we estimate that we
have genotyped ,2535% of all common CNVs greater than 1 kb in
size. Thus, unless ungenotyped and poorly tagged common CNVs have
a much higher effect on disease risk than the well-tagged common
CNVs we were able to genotype, extrapolating from our incomplete
ascertainment of CNV could only explain a small minority of the
disease risk already accounted for existing GWAS studies, let alone
the larger (for most diseases) bulk of missing heritability that remains
unaccounted for by GWASs. Further large-scale association studies that
directly assay all classes of CNV are required to precisely estimate the
contribution of common CNVs to the heritability of complex traits.
Conclusions and discussion
We have discovered an unprecedented number of CNVs and
assembled a reference set of genotypes from new genotyping platforms developed from this information. These new resources will
facilitate association studies of CNVs in human disease, including
using imputation of CNV genotypes into the hundreds of thousands
of genomes that have already been densely genotyped.
Despite being the most comprehensive population-based CNV
map so far, still to be well-characterized are CNVs ,500 bp, insertions of new sequences relative to the reference sequence, subtle
changes in the total number of copies of high-copy number dispersed
repeats such as Alu elements and LINEs, and CNVs on the Y chromosome and heterochromatic regions. Notwithstanding, we estimate
that in this study we have discovered about 8090% of common

6
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ARTICLES

NATURE

Table 2 | Trait-associated SNPs with possible causal CNVs

SNP

CNV

Location*

r2 {

Population{

Data1

Reported gene

Trait

PMID

rs10492972
rs11809207
rs2815752
rs7553864
rs4085613
rs11265260
rs12029454
rs6725887
rs9311171
rs3772255
rs9291683
rs9291683
rs401681
rs11747270
rs11747270
rs4704970
rs12191877
rs10484554
rs3129934
rs9277535
rs9277535
rs210138
rs2301436
rs2705293
rs1602565
rs1602565
rs7395662
rs9300212
rs1495377
rs3118914
rs763014
rs8049607
rs7188697
rs1805007

CNVR65.1
CNVR118.1
CNVR217.1
CNVR240.1
CNVR358.1
CNVR381.1
CNVR384.1
CNVR1111.1
CNVR1355.1
CNVR1591.1
CNVR1819.6
CNVR1819.1
CNVR2293.1
CNVR2646.1
CNVR2647_full
CNVR2659.1
CNVR2841.6
CNVR2841.6
CNVR2845.21
CNVR2846.3
CNVR2846.5
CNVR2850.1
CNVR3164.1
CNVR4074.1
CNVR5123.2
CNVR5123.1
CNVR5165.1
CNVR5492.1
CNVR5583.1
CNVR5871.1
CNVR6576.1
CNVR6636.1
CNVR6746.1
CNVR6887.1

chr1: 1040513710406094
chr1: 2633215726337219
chr1: 7253887072584557
chr1: 8738582787386846
chr1: 150822234150856715
chr1: 157915386157916253
chr1: 160497369160497846
chr2: 203607766203612122
chr3: 3795347437961880
chr3: 157574746157576258
chr4: 97832529843664
chr4: 98204199843664
chr5: 13860431386897
chr5: 150157836150161778
chr5: 150183562150203623
chr5: 155409234155427600
chr6: 3138450531397416
chr6: 3138450531397416
chr6: 3251988532887814
chr6: 3315633833162718
chr6: 3315968233163323
chr6: 3369191733693857
chr6: 167408121167409138
chr8: 138980822138981379
chr11: 2909595329096982
chr11: 2909611429096643
chr11: 4855743248560877
chr12: 3360639633608182
chr12:69818942-69819932
chr13: 4996734749973131
chr16: 601068603588
chr16: 1159153811592052
chr16: 5723110757233858
chr16: 8842359988425903

0.92
0.61
0.96
0.76
0.97
0.62
0.57
1.00
1.00
0.90
0.51
0.51
0.68
1.00
1.00
0.95
0.79
0.79
0.87
0.62
0.67
0.55
0.71
0.51
0.64
0.61
1.00
0.84
0.72
0.69
0.68
0.88
0.61
0.87

CEU
CEU
CEU
CEU
CEU
CHB1JPT
CHB1JPT
CEU
CHB1JPT
CEU
YRI
YRI
YRI
CEU
CEU
CEU
CEU
CEU
CEU
CEU
CEU
CEU
CEU
YRI
CEU
CEU
CEU
CEU
CEU
CEU
CEU
CHB1JPT
YRI
CEU

Phased
Phased
Phased
Intensities
Phased
Phased
Phased
Phased
Phased
Phased
Intensities
Intensities
Intensities
Phased
Phased
Phased
Phased
Phased
Phased
Intensities
Intensities
Phased
Intensities
Intensities
Intensities
Intensities
Phased
Phased
phased
Phased
Intensities
Phased
Phased
Phased

KIF1B
CATSPER4
NEGR1
AK002179
LCE3D, LCE3A
CRP
NOS1AP
WDR12
CTDSPL
KCNAB1
NR
NR
CLPTM1L
IRGM
IRGM
SGCD
HLA-C
HLA-C
HLA-DRB1
HLA-DPB1
HLA-DPB1
BAK1
CCR6
AK127771
Intergenic
Intergenic
MADD, FOLH1
Intergenic
NR
DLEU7
RAB40C
LITAF
NDRG4
MC1R

Multiple sclerosis
Height
Body mass index
Smoking behaviour
Psoriasis
C-reactive protein
QT interval
Myocardial infarction (early onset)
Prostate cancer
Ageing traits
Bone mineral density
Bone mineral density
Lung cancer
Crohns disease
Crohns disease
Multiple sclerosis (age of onset)
Psoriasis
AIDS progression
Multiple sclerosis
Hepatitis B
Hepatitis B
Testicular germ cell tumour
Crohns disease
Neuroticism
Schizophrenia
Schizophrenia
HDL cholesterol
Cognitive test performance
Type 2 diabetes
Height
Height
QT interval
QT interval
Skin sensitivity to sun

18997785
19343178
19079261
19247474
19169255
18439552
19305408
19198609
17903305
17903295
17903296
17903296
18978787
18587394
18587394
19010793
19169254
19115949
18941528
19349983
19349983
19483681
18587394
18762592
18677311
18677311
19060911
17903297
17554300
19343178
18391950
19305409
19305409
18488028

List of CNV correlations with trait-associated SNPs with r2 . 0.5 (see main text for details). When a locus-trait association has been reported several times, only the results for the most recently
published trait-associated SNPs are shown in this table. Some trait-associated SNPs are strongly correlated with more than one CNV in the same recombination hotspot interval. NR, no gene
reported in original study; PMID, PubMed accession of the paper reporting the trait-associated SNP.
* Location of the CNV.
{ Squared correlation coefficient.
{ Population in which correlation observed; some SNP-CNV correlations are observed in several populations.
1 CNV data that correlates with the hit-SNP. Phased, phased SNP1CNV haplotypes; intensities, CNV intensity data and SNP genotypes. If present in phased and intensity data only phased data
reported.

CNVs (MAF . 5%) greater than 1 kb in length, and have been able to
genotype approximately 40% of these (Supplementary Methods). The
remaining CNVs will probably be best captured by genome sequencing experiments.
The CNVs most difficult to genotype directly were duplications
and multiallelic loci (including VNTR). They are also the categories
of CNVs least likely to be tagged well by SNPs, and therefore most
likely to be overlooked by linkage-disequilibrium-based association
testing. The observation that VNTR are enriched among loci exhibiting high population differentiation provides evidence for the functional importance of this CNV class, which highlights the need for
development of genome-wide assays for incorporating this often
recalcitrant class of variants into human genetic studies.
We found that the mutational mechanisms generating CNVs vary
depending on the different size of the genomic alteration. NAHR has
more of a role in larger CNV formation, whereas VNTR and dispersed
duplications (whose role in CNV formation was previously underappreciated) are more commonly observed with smaller CNVs.
Although some sequence motifs (for example, some non-B-DNA
structures) were more mutagenic than others, the sequence context
was not strongly predictive of the location of CNVs, unlike the link
between segmental duplications and larger CNVs mediated by NAHR.
We observed that non-B-DNA forming sequences that are
enriched in promoter regions are also enriched in CNV breakpoints,
suggesting that the same properties that enable regulation of transcription may also be mildly mutagenic for the formation of CNVs,
and as a consequence, CNVs may influence the evolution of gene
regulation. We also discovered that there are substantive differences
in both the mutation mechanisms and the selection pressures of
deletions and duplications.

Despite the fact that we identified several new CNVs that are potential causal variants on trait-associated haplotypes, collectively these
CNVs could explain less than 5% of previously reported GWAS hits.
Nonetheless, these observations emphasize the need to consider all
classes of variation (SNPs and all structural variants, common and rare)
when fine-mapping causal variants within association intervals.
Sequence insertions relative to the reference sequence represent a particular challenge for both fine-mapping and association studies, because
their presence on an associated haplotype might be easily overlooked.
Our results provide some guidance as to how resources might best
be targeted to identify genetic variation underlying the missing
heritability for complex traits that remains unexplained by recent
GWAS. Although common CNVs seem highly unlikely to account
for much of this missing heritability, the striking strength of purifying
selection acting on exonic and intronic deletions suggests that CNVs
might contribute appreciably to rare variants involved in common and
rare diseases, and that study designs that focus on ascertaining rare
sequence and structural variants will maximise power to detect new
causal variation.
METHODS SUMMARY
Samples. HapMap and Polymorphism Discovery Resource DNA samples were
obtained from the Coriell Cell Repository. The reference DNA in genotyping
experiments on the Agilent 105K array was a pool of 10 genomic cell-line DNAs
from the European Collection of Cell Cultures.
CNV discovery experiments. Probes on the 20 array set were designed with a
relaxed threshold for multiple matches to the reference genome to maximise
coverage and allow screening of moderately repetitive sequences. The array data
were generated at NimbleGens Icelandic service facility. Experiments were
repeated and quality-control filters were applied to improve the data consistency.
Data were normalized to minimize variation between experiments; putative
7

2009 Macmillan Publishers Limited. All rights reserved

ARTICLES

NATURE

CNVs were detected as chromosomal segments with unusually high or low log2
ratios of fluorescent intensity between the test and reference genomes using the
genome alteration detection analysis (GADA) algorithm48. Further filtering
reduced false positives.
Validation experiments. qPCR experiments were performed by Applied
Biosystems. Further validation was conducted by Sequenom and the co-authors
of this paper.
CNV genotyping experiments. The Agilent 105K CNV genotyping array was
designed by the WTCCC in collaboration with the other co-authors of this paper.
After pilot experiments, each locus was targeted with at least 10 probes. Agilent
array data were generated by Oxford Gene Technologies at their UK service facility
as part of the pipeline developed for the large WTCCC association experiment
(pipeline to be described elsewhere). We assessed the quality of the experiments
on the 450 HapMap samples and repeated 90 poorer quality experiments to
improve data consistency. The Illumina 660W array data were generated by
Illumina Inc.
Statistical and population analysis. We devised statistical methods for CNV
genotyping, absolute copy number estimation, breakpoint enrichment testing,
and estimation of discovery power. We phased CNVs and SNPs into haplotypes
using BEAGLE 3.0.3 (ref. 49), and used NestedMICA31 for breakpoint motif
discovery.
Received 14 August; accepted 21 September 2009.
Published online 7 October 2009.
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Supplementary Information is linked to the online version of the paper at

www.nature.com/nature.
Acknowledgements We would like to thank A. Boyko, J. J. Emerson, J. Pickrell,
S. Kudaravalli, J. Pritchard, T. Down, S. McCarroll, J. Collins, C. Beazley,
M. Dermitzakis, P. Eis, T. Richmond, M. Hogan, D. Bailey, S. Giles, G. Speight,
N. Sparkes, D. Peiffer, C. Chen, K. Li, P. Oeth, D. Stetson and D. Church for advice,
sharing data, sharing software and technical assistance. We are grateful for the
efforts and support of our colleagues at NimbleGen, Agilent, Illumina, Applied
Biosystems and Sequenom. We thank J. Barrett for comments on an earlier version
of the manuscript. The Centre for Applied Genomics at the Hospital for Sick
Children and Wellcome Trust Sanger Institute are acknowledged for database,
technical assistance and bioinformatics support. This research was supported by
the Wellcome Trust (grant no. 077006/Z/05/Z; to M.E.H., N.P.C., C.T.-S.),
Canada Foundation of Innovation and Ontario Innovation Trust (to S.W.S.),
Canadian Institutes of Health Research (CIHR) (to S.W.S.), Genome Canada/
Ontario Genomics Institute (to S.W.S.), the McLaughlin Centre for Molecular
Medicine (to S.W.S.), Ontario Ministry of Research and Innovation (to S.W.S.), the
Hospital for Sick Children Foundation (to S.W.S.), the Department of Pathology at
Brigham and Womens Hospital (to C.L.) and the National Institutes of Health
(NIH) (grants HG004221 and GM081533; to C.L.). K.K. is supported by the
Academy of Finland. D.P. is supported by fellowships from the Royal Netherlands
Academy of Arts and Sciences (TMF/DA/5801) and the Netherlands
Organization for Scientific Research (Rubicon 825.06.031). S.W.S. holds the

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2009 Macmillan Publishers Limited. All rights reserved

ARTICLES

NATURE

GlaxoSmithKline Pathfinder Chair in Genetics and Genomics at the University of

Toronto and the Hospital for Sick Children.
Author Contributions C.T.-S., N.P.C., C.L., S.W.S. and M.E.H. are all joint senior
authors, and planned and managed the project. D.F.C. and D.P. lead the data analysis.
Data analyses were performed by D.F.C., D.P., R.R., L.F., O.G., Y.Z., J.A., T.D.A., C.B.,
P.C., T.F., M.H., C.H.I., K.K., D.G.M., J.R.M., I.O., A.W.C.P., S.R., K.S., A.V., K.W., J.W.
and M.E.H. The WTCCC collaborated on array design. Validation experiments were
performed by Y.Z. and M.H. D.F.C., D.P., S.W.S. and M.E.H. wrote the paper.

Author Information The CNV discovery and CNV genotyping data are available at
ArrayExpress (http://www.ebi.ac.uk/microarray-as/ae/) under accession
numbers E-MTAB-40 and E-MTAB-142, respectively. Normalized CNV discovery
data are available at http://www.sanger.ac.uk/humgen/cnv/42mio. CNVs are
displayed at the Database of Genomic Variants (http://projects.tcag.ca/
variation). CNV locations and genotypes are reported in Supplementary Tables 1
and 2. Reprints and permissions information is available at www.nature.com/
reprints. Correspondence and requests for materials should be addressed to
M.E.H. ([email protected]) or S.W.S. ([email protected]).

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2009 Macmillan Publishers Limited. All rights reserved