Altshuler D, Pollara V J, Cowles C R, et al. An SNP map of the human genome generated by reduced representation shotgun sequencing.Nature, 2000, 407: 513-516
[2]
The International HapMap Consortium. A haplotype map of the human genome. Nature, 2005, 437: 1299-1320
[3]
The International HapMap 3 Consortium. Integrating common and rare genetic variation in diverse human populations. Nature, 2010, 467:52-58
[4]
Manolio T A, Brooks L D, Collins F S. A HapMap harvest of insights into the genetics of common disease. J Clin Invest, 2008, 118:1590-1605
[5]
Lupski J R. Genomic rearrangements and sporadic disease. Nat Genet, 2007, 39: S43?S47
[6]
Zhang F, Gu W, Hurles M E, et al. Copy number variation in human health, disease, and evolution. Ann Rev Genomics Hum Genet, 2009,10: 451-481
[7]
Conrad D F, Pinto D, Redon R, et al. Origins and functional impact of copy number variation in the human genome. Nature, 2010, 464:704-712
[8]
Conrad D F, Bird C, Blackburne B, et al. Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat Genet,2010, 42: 385-391
[9]
Woodward K J, Cundall M, Sperle K, et al. Heterogeneous duplications in patients with Pelizaeus-Merzbacher disease suggest a mechanismof coupled homologous and nonhomologous recombination. Am J Hum Genet, 2005, 77: 966-987
[10]
Kidd J M, Cooper G M, Donahue W F, et al. Mapping and sequencing of structural variation from eight human genomes. Nature, 2008,453: 56-64
[11]
Kidd J M, Sampas N, Antonacci F, et al. Characterization of missing human genome sequences and copy-number polymorphic insertions.Nat Methods, 2010, 7: 365-371
[12]
Carter N P. Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet, 2007, 39: S16?S21
[13]
Redon R, Ishikawa S, Fitch K R, et al. Global variation in copy number in the human genome. Nature, 2006, 444: 444-454
[14]
McCarroll S A, Kuruvilla F G, Korn J M, et al. Integrated detection and population-genetic analysis of SNPs and copy number variation.Nat Genet, 2008, 40: 1166-1174
[15]
McCarroll S A, Huett A, Kuballa P, et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn'sdisease. Nat Genet, 2008, 40: 1107-1112
[16]
Willer C J, Speliotes E K, Loos R J, et al. Six new loci associated with body mass index highlight a neuronal influence on body weightregulation. Nat Genet, 2009, 41: 25-34
[17]
Perry G H, Dominy N J, Claw K G, et al. Diet and the evolution of human amylase gene copy number variation. Nat Genet, 2007, 39:1256-1260
[18]
Gonzalez E, Kulkarni H, Bolivar H, et al. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility.Science, 2005, 307: 1434-1440
[19]
Niederer H A, Willcocks L C, Rayner T F, et al. Copy number, linkage disequilibrium and disease association in the FCGR locus. HumMol Genet, 2010, 19: 3282-3294
[20]
Stranger B E, Forrest M S, Dunning M, et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes.Science, 2007, 315: 848?853
[21]
Yang Y, Chung E K, Wu Y L, et al. Gene copy-number variation and associated polymorphisms of complement component C4 in humansystemic lupus erythematosus (SLE): Low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibilityin European Americans. Am J Hum Genet, 2007, 80: 1037?1054
[22]
Diskin S J, Hou C, Glessner J T, et al. Copy number variation at 1q21.1 associated with neuroblastoma. Nature, 2009, 459: 987?991
[23]
2 Dibbens L M, Mullen S, Helbig I, et al. Familial and sporadic 15q13.3 microdeletions in idiopathic generalized epilepsy: Precedent fordisorders with complex inheritance. Hum Mol Genet, 2009, 18: 3626-3631
[24]
3 Fernandez B A, Roberts W, Chung B, et al. Phenotypic spectrum associated with de novo and inherited deletions and duplications at16p11.2 in individuals ascertained for diagnosis of autism spectrum disorder. J Med Genet, 2010, 47: 195-203
[25]
4 de Kovel C G, Trucks H, Helbig I, et al. Recurrent microdeletions at 15q11.2 and 16p13.11 predispose to idiopathic generalized epilepsies.Brain, 2010, 133: 23?32
[26]
5 Bochukova E G, Huang N, Keogh J, et al. Large, rare chromosomal deletions associated with severe early-onset obesity. Nature, 2010,463: 666?670
[27]
Glessner J T, Wang K, Cai G, et al. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature, 2009, 459:569?573
[28]
Clayton D G, Walker N M, Smyth D J, et al. Population structure, differential bias and genomic control in a large-scale, case-control associationstudy. Nat Genet, 2005, 37: 1243?1246
[29]
Wang K, Li M, Hadley D, et al. PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detectionin whole-genome SNP genotyping data. Genome Res, 2007, 17: 1665?1674
[30]
Colella S, Yau C, Taylor J M, et al. QuantiSNP: An objective Bayes Hidden-Markov Model to detect and accurately map copy numbervariation using SNP genotyping data. Nucleic Acids Res, 2007, 35: 2013?2025
[31]
Wellcome Trust Case Control Consortium. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000shared controls[J].Nature.2010, 464:713-
[32]
Park H, Kim J I, Ju Y S, et al. Discovery of common Asian copy number variants using integrated high-resolution array CGH and mas sively parallel DNA sequencing. Nat Genet, 2010, 42: 400?405
[33]
Korn J M, Kuruvilla F G, McCarroll S A, et al. Integrated genotype calling and association analysis of SNPs, common copy numberpolymorphisms and rare CNVs. Nat Genet, 2008, 40: 1253?1260
[34]
Barnes C, Plagnol V, Fitzgerald T, et al. A robust statistical method for case-control association testing with copy number variation. NatGenet, 2008, 40: 1245?1252
[35]
Myocardial Infarction Genetics Consortium. Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphismsand copy number variants. Nat Genet, 2009, 41: 334?341
[36]
Bolstad B M, Irizarry R A, Astrand M, et al. A comparison of normalization methods for high density oligonucleotide array data based onvariance and bias. Bioinformatics, 2003, 19: 185?193
[37]
Akey J M, Biswas S, Leek J T, et al. On the design and analysis of gene expression studies in human populations. Nat Genet, 2007, 39:807?808
[38]
González J R, Subirana I, Escaramís G, et al. Accounting for uncertainty when assessing association between copy number and disease: Alatent class model. BMC Bioinformatics, 2009, 10: 172
[39]
Price A L, Patterson N J, Plenge R M, et al. Principal components analysis corrects for stratification in genome-wide association studies.Nat Genet, 2006, 38: 904?909
[40]
McCarthy S E, Makarov V, Kirov G, et al. Microduplications of 16p11.2 are associated with schizophrenia. Nat Genet, 2009, 41:1223?1227
[41]
Ji W, Foo J N, O'Roak B J, et al. Rare independent mutations in renal salt handling genes contribute to blood pressure variation. NatGenet, 2008, 40: 592?599
[42]
Rujescu D, Ingason A, Cichon S, et al. Disruption of the neurexin 1 gene is associated with schizophrenia. Hum Mol Genet, 2009, 18:988?996
[43]
Shaikh T, Gai X, Perin J, et al. High-resolution mapping and analysis of copy number variations in the human genome: A data resource forclinical and research applications. Genome Res, 2009, 19: 1682?1690
[44]
Sebat J, Lakshmi B, Malhotra D, et al. Strong association of de novo copy number mutations with autism. Science, 2007, 316: 445?449
[45]
Xu B, Roos J L, Levy S, et al. Strong association of de novo copy number mutations with sporadic schizophrenia. Nat Genet, 2008, 40:880?885
[46]
Stone J L, O'Donovan M C, Gurling H, et al. Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature, 2008,455: 237?241
[47]
Walsh T, McClellan J M, McCarthy S E, et al. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia.Science, 2008, 320: 539?543
[48]
Pinto D, Pagnamenta A T, Klei L, et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature,2010, 466: 368?372
[49]
Webber C, Hehir-Kwa J Y, Nguyen D Q, et al. Forging links between human mental retardation-associated CNVs and mouse geneknockout models. PLoS Genet, 2009, 5: e1000531
[50]
Raychaudhuri S, Plenge R M, Rossin E J, et al. Identifying relationships among genomic disease regions: Predicting genes at pathogenicSNP associations and rare deletions. PLoS Genet, 2009, 5: e1000534
[51]
Raychaudhuri S, Korn J M, McCarroll S A, et al. Accurately assessing the risk of schizophrenia conferred by rare copy-number variationaffecting genes with brain function. PLoS Genet, 2010, 6: e1001097
[52]
Sharp A J, Hansen S, Selzer R R, et al. Discovery of previously unidentified genomic disorders from the duplication architecture of thehuman genome. Nat Genet, 2006, 38: 1038?1042
[53]
Mefford H C, Cooper G M, Zerr T, et al. A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitivedisease. Genome Res, 2009, 19: 1579?1585
[54]
Stefansson H, Helgason A, Thorleifsson G, et al. A common inversion under selection in Europeans. Nat Genet, 2005, 37: 129?137
[55]
Koolen D A, Vissers L E, Pfundt R, et al. A new chromosome 17q21.31 microdeletion syndrome associated with a common inversionpolymorphism. Nat Genet, 2006, 38: 999?1001
[56]
Greenway S C, Pereira A C, Lin J C, et al. De novo copy number variants identify new genes and loci in isolated sporadic tetralogy ofFallot. Nat Genet, 2009, 41: 931?935
[57]
Mefford H C, Sharp A J, Baker C, et al. Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl JMed, 2008, 359: 1685?1699
[58]
Brunetti-Pierri N, Berg J S, Scaglia F, et al. Recurrent reciprocal 1q21.1 deletions and duplications associated with microcephaly or mac rocephaly and developmental and behavioral abnormalities. Nat Genet, 2008, 40: 1466?1471
[59]
Christiansen J, Dyck J D, Elyas B G, et al. Chromosome 1q21.1 contiguous gene deletion is associated with congenital heart disease. CircRes, 2004, 94: 1429?1435
[60]
Greenway S C, Pereira A C, Lin J C, et al. De novo copy number variants identify new genes and loci in isolated sporadic tetralogy ofFallot. Nat Genet, 2009, 41: 931?935
[61]
Weiss L A, Shen Y, Korn J M, et al. Association between microdeletion and microduplication at 16p11.2 and autism. N Engl J Med, 2008,358: 667?675
[62]
McCarthy S E, Makarov V, Kirov G, et al. Microduplications of 16p11.2 are associated with schizophrenia. Nat Genet, 2009, 41:1223?1227
[63]
0 Walters R G, Jacquemont S, Valsesia A, et al. A new highly penetrant form of obesity due to deletions on chromosome 16p11.2. Nature,2010, 463: 671?675
[64]
1 Shinawi M, Schaaf C P, Bhatt S S, et al. A small recurrent deletion within 15q13.3 is associated with a range of neurodevelopmentalphenotypes. Nat Genet, 2009, 41: 1269?1271
[65]
The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature, 2007, 449: 851-861
[66]
McCarthy M I, Abecasis G R, Cardon L R, et al. Genome-wide association studies for complex traits: Consensus, uncertainty and challenges.Nat Rev Genet, 2008, 9: 356-369
[67]
Risch N, Merikangas K. The future of genetic studies of complex human diseases. Science, 1996, 273: 1516-1517
[68]
Manolio T A, Collins F S, Cox N J, et al. Finding the missing heritability of complex diseases. Nature, 2009, 461: 747-753
[69]
Eichler E E, Flint J, Gibson G, et al. Missing heritability and strategies for finding the underlying causes of complex disease. Nat RevGenet, 2010, 11: 446-450
[70]
McClellan J, King M C. Genetic heterogeneity in human disease. Cell, 2010, 141: 210-217
[71]
Iafrate A J, Feuk L, Rivera M N, et al. Detection of large-scale variation in the human genome. Nat Genet, 2004, 36: 949-951
[72]
Sebat J, Lakshmi B, Troge J, et al. Large-scale copy number polymorphism in the human genome. Science, 2004, 305: 525-528
[73]
Tuzun E, Sharp A J, Bailey J A, et al. Fine-scale structural variation of the human genome. Nat Genet, 2005, 37: 727-732
[74]
Feuk L, Carson A R, Scherer S W. Structural variation in the human genome. Nat Rev Genet, 2006, 7: 85-97
[75]
Patel P I, Roa B B, Welcher A A, et al. The gene for the peripheral myelin protein PMP-22 is a candidate for Charcot-Marie-Tooth diseasetype 1A. Nat Genet, 1992, 1: 159-165
[76]
Merikangas A K, Corvin A P, Gallagher L. Copy-number variants in neurodevelopmental disorders: Promises and challenges. TrendsGenet, 2009, 25: 536-544
[77]
Hastings P J, Lupski J R, Rosenberg S M, et al. Mechanisms of change in gene copy number. Nat Rev Genet, 2009, 10: 551-564
[78]
Lindsay S J, Khajavi M, Lupski J R, et al. A chromosomal rearrangement hotspot can be identified from population genetic variation andis coincident with a hotspot for allelic recombination. Am J Hum Genet, 2006, 79: 890-902
[79]
Stankiewicz P, Lupski J R. Genome architecture, rearrangements and genomic disorders. Trends Genet, 2002, 18: 74-82
[80]
Turner D J, Miretti M, Rajan D, et al. Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. NatGenet, 2008, 40: S90?S95
[81]
Nachman M W, Crowell S L. Estimate of the mutation rate per nucleotide in humans. Genetics, 2000, 156: 297-304
[82]
Cooper G M, Nickerson D A, Eichler E E. Mutational and selective effects on copy-number variants in the human genome. Nat Genet,2007, 39: S22?S29
[83]
Itsara A, Cooper G M, Baker C, et al. Population analysis of large copy number variants and hotspots of human genetic disease. Am JHum Genet, 2009, 84: 148-161
[84]
Oldridge D A, Banerjee S, Setlur S R, et al. Optimizing copy number variation analysis using genome-wide short sequence oligonucleotidearrays. Nucleic Acids Res, 2010, 38: 3275-3286
[85]
de Cid R, Riveira-Munoz E, Zeeuwen P L, et al. Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factorfor psoriasis. Nat Genet, 2009, 41: 211-215
[86]
Ardlie K G, Kruglyak L, Seielstad M. Patterns of linkage disequilibrium in the human genome. Nat Rev Genet, 2002, 3: 299-309
[87]
Schrider D R, Hahn M W. Lower linkage disequilibrium at CNVs is due to both recurrent mutation and transposing duplications. Mol BiolEvol, 2010, 27: 103-111
[88]
Kato M, Kawaguchi T, Ishikawa S, et al. Population-genetic nature of copy number variations in the human genome. Hum Mol Genet,2010, 19: 761-773
[89]
Jakobsson M, Scholz S W, Scheet P, et al. Genotype, haplotype and copy-number variation in worldwide human populations. Nature,2008, 451: 998-1003
[90]
Xue Y, Sun D, Daly A, et al. Adaptive evolution of UGT2B17 copy-number variation. Am J Hum Genet, 2008, 83: 337-346
[91]
McCarroll S A, Bradner J E, Turpeinen H, et al. Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-hostdisease. Nat Genet, 2009, 41: 1341-1344
[92]
Marchini J, Cardon L R, Phillips M S, et al. The effects of human population structure on large genetic association studies. Nat Genet,2004, 36: 512-517
[93]
Yim S H, Kim T M, Hu H J, et al. Copy number variations in East-Asian population and their evolutionary and functional implications.Hum Mol Genet, 2010, 19: 1001-1008
[94]
Lee C, Iafrate A J, Brothman A R. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet, 2007,39: S48?S54
[95]
Koolen D A, Pfundt R, de Leeuw N, et al. Genomic microarrays in mental retardation: A practical workflow for diagnostic applications.Hum Mutat, 2009, 30: 283-292
[96]
Bailey J A, Kidd J M, Eichler E E. Human copy number polymorphic genes. Cytogenet Genome Res, 2008, 123: 234-243
[97]
Fanciulli M, Norsworthy P J, Petretto E, et al. FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat Genet, 2007, 39: 721-723
[98]
Zhernakova A, van Diemen C C, Wijmenga C. Detecting shared pathogenesis from the shared genetics of immune-related diseases. NatRev Genet, 2009, 10: 43-55
[99]
Aitman T J, Dong R, Vyse T J, et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature,2006, 439: 851-855
[100]
Mamtani M, Rovin B, Brey R, et al. CCL3L1 gene-containing segmental duplications and polymorphisms in CCR5 affect risk of systemiclupus erythaematosus. Ann Rheum Dis, 2008, 67: 1076-1083
[101]
Fellermann K, Stange D E, Schaeffeler E, et al. A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copynumber predisposes to Crohn disease of the colon. Am J Hum Genet, 2006, 79: 439-448
[102]
Hollox E J, Huffmeier U, Zeeuwen P L, et al. Psoriasis is associated with increased beta-defensin genomic copy number. Nat Genet, 2008,40: 23-25
[103]
Mamtani M, Anaya J M, He W, et al. Association of copy number variation in the FCGR3B gene with risk of autoimmune diseases. GenesImmun, 2010, 11: 155-160
[104]
McKinney C, Merriman M E, Chapman P T, et al. Evidence for an influence of chemokine ligand 3-like 1 (CCL3L1) gene copy number onsusceptibility to rheumatoid arthritis. Ann Rheum Dis, 2008, 67: 409-413
[105]
Lv J, Yang Y, Zhou X, et al. FCGR3B copy number variation is not associated with lupus nephritis in a Chinese population. Lupus, 2010,19: 158-161