Global variation in copy number in the human genome.
Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.
Redon
Richard
R
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Ishikawa
Shumpei
S
Fitch
Karen R
KR
Feuk
Lars
L
Perry
George H
GH
Andrews
T Daniel
TD
Fiegler
Heike
H
Shapero
Michael H
MH
Carson
Andrew R
AR
Chen
Wenwei
W
Cho
Eun Kyung
EK
Dallaire
Stephanie
S
Freeman
Jennifer L
JL
González
Juan R
JR
Gratacòs
Mònica
M
Huang
Jing
J
Kalaitzopoulos
Dimitrios
D
Komura
Daisuke
D
MacDonald
Jeffrey R
JR
Marshall
Christian R
CR
Mei
Rui
R
Montgomery
Lyndal
L
Nishimura
Kunihiro
K
Okamura
Kohji
K
Shen
Fan
F
Somerville
Martin J
MJ
Tchinda
Joelle
J
Valsesia
Armand
A
Woodwark
Cara
C
Yang
Fengtang
F
Zhang
Junjun
J
Zerjal
Tatiana
T
Zhang
Jane
J
Armengol
Lluis
L
Conrad
Donald F
DF
Estivill
Xavier
X
Tyler-Smith
Chris
C
Carter
Nigel P
NP
Aburatani
Hiroyuki
H
Lee
Charles
C
Jones
Keith W
KW
Scherer
Stephen W
SW
Hurles
Matthew E
ME
D002874:Chromosome Mapping; D018628:Gene Dosage; D014644:Genetic Variation; D005828:Genetics, Population; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D025202:Molecular Diagnostic Techniques; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D020641:Polymorphism, Single Nucleotide