Copy number variation across European populations

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Chen, Wanting ^a   Hayward, Caroline ^b   Wright, Alan F ^b   Hicks, Andrew A ^c,d   Vitart, Veronique ^b   Knott, Sara ^a   Wild, Sarah H ^e   Pramstaller, Peter P ^c,d,f   Wilson, James F ^e   Rudan, Igor ^e,g   Porteous, David J ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b WESTERN GENERAL HOSPITAL   (United Kingdom)

^c INSTITUTE FOR RENEWABLE ENERGY   (Italy)

^d UNIVERSITY OF LÜBECK   (Germany)

^e UNIVERSITY OF EDINBURGH   (United Kingdom)

^f General Central Hospital   (Italy)

^g UNIVERSITY OF SPLIT   (Croatia)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AGED; ARTICLE; COPY NUMBER VARIATION; CROATIA; EUROPEAN UNION; GENE CLUSTER; GENE DELETION; GENE DUPLICATION; GENE FREQUENCY; GENE INSERTION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; GEOGRAPHY; HAPLOTYPE; HUMAN; ITALY; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED KINGDOM; CAUCASIAN; FEMALE; GENETICS; MALE; PEDIGREE;

CROATIA; DNA COPY NUMBER VARIATIONS; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENETICS, POPULATION; HAPLOTYPES; HUMANS; ITALY; MALE; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; SCOTLAND;

EID: 79961144450     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0023087     Document Type: Article

References (50)

1. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444-454.
2. Cutler G, Kassner PD, (2008) Copy number variation in the mouse genome: implications for the mouse as a model organism for human disease. Cytogenetic and Genome Research 123: 297-306.
3. Dopman EB, Hartl DL, (2007) A portrait of copy-number polymorphism in Drosophila melanogaster. PNAS 104: 19920-19925.
4. Fadista J, Nygaard M, Holm LE, Thomsen B, Bendixen C, (2008) A Snapshot of CNVs in the Pig Genome. Plos One 3: e3916.
5. Zhang F, Gu W, Hurles ME, Lupski JR, (2009) Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 10: 451-481.
6. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, et al. (2007) Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes. Science 315: 848-853.
7. The International Schizophrenia Consortium (2008) Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature 455: 237-241.
8. Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, et al. (2010) Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466: 368-372.
9. Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, et al. (2007) Strong Association of De Novo Copy Number Mutations with Autism. Science 316: 445-449.
10. Garshasbi M, Hadavi V, Habibi H, Kahrizi K, Kariminejad R, et al. (2008) A defect in the TUSC3 gene is associated with autosomal recessive mental retardation. American Journal of Human Genetics 82 (5): 1158-64.
11. Kamatani Y, Matsuda K, Ohishi T, Ohtsubo S, Yamazaki K, et al. (2008) Identification of a significant association of a single nucleotide polymorphism in TNXB with systemic lupus erythematosus in a Japanese population. Journal of Human Genetics 53 (1): 64-73.
12. Williams NM, Zaharieva I, Martin A, Langley K, Mantripragada K, et al. (2010) Rare chromosomal deletions and duplications in attention-deficit hyperactivity disorder: a genome-wide analysis. The Lancet 376: 1401-1408.
13. Yang S, Wang K, Gregory B, Berrettini W, Wang LS, et al. (2009) Genomic landscape of a three-generation pedigree segregating affective disorder. Plos One 4: e4474.
14. Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, et al. (2007) Diet and the evolution of human amylase gene copy number variation. Nat Genet 39: 1256-1260.
15. Pielberg G, Olsson C, Syvanen AC, Andersson L, (2002) Unexpectedly High Allelic Diversity at the KIT Locus Causing Dominant White Color in the Domestic Pig. Genetics 160: 305-311.
16. Norris BJ, Whan VA, (2008) A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep. Genome Res 18: 1282-1293.
17. Bailey JA, Kidd JM, Eichler EE, (2008) Human copy number polymorphic genes. Cytogenetic and Genome Research 123: 234-243.
18. Cowell JK, Lo KC, (2009) Application of oligonucleotides arrays for coincident comparative genomic hybridization, ploidy status and loss of heterozygosity studies in human cancers. Methods Mol Biol 556: 47-65.
19. Fiegler H, Redon R, Andrews D, Scott C, Andrews R, et al. (2006) Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res 16: 1566-1574.
20. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
21. Wang J, Wang W, Li R, Li Y, Tian G, et al. (2008) Detection, breakpoint identification and detailed characterisation of a CNV at the FRA16D site using SNP assays. Cytogenetic and Genome Research 123: 322-332.
22. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, et al. (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451: 998-1003.
23. Cooper GM, Zerr T, Kidd JM, Eichler EE, Nickerson DA, (2008) Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nature Genetics 40 (10): 1199-203.
24. Colella S, Yau C, Taylor JM, Mirza G, Butler H, et al. (2007) QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucl Acids Res 35: 2013-2025.
25. Zogopoulos G, Ha KC, Naqib F, Moore S, Kim H, et al. (2007) Germ-line DNA copy number variation frequencies in a large North American population. Human Genetics 122 (3-4): 345-53.
26. Franke L, de Kovel CGE, Aulchenko YS, Trynka G, Zhernakova A, et al. (2008) Detection, imputation, and association analysis of small deletions and null alleles on oligonucleotide arrays. American Journal of Human Genetics 82: 1316-1333.
27. McQuillan R, Leutenegger AL, bdel-Rahman R, Franklin CS, Pericic M, et al. (2008) Runs of homozygosity in European populations. American Journal of Human Genetics 83: 359-372.
28. Peltonen L, (2000) Positional cloning of disease genes: advantages of genetic isolates. Hum Hered 50: 66-75.
29. Shifman S, Darvasi A, (2001) The value of isolated populations. Nat Genet 28: 309-310.
30. Wright AF, Carothers AD, Pirastu M, (1999) Population choice in mapping genes for complex diseases. Nat Genet 23: 397-404.
31. Vitart V, Biloglav Z, Hayward C, Janicijevic B, Smolej-Narancic N, et al. (2006) 3000 years of solitude: extreme differentiation in the island isolates of Dalmatia, Croatia. Eur J Hum Genet 14: 478-487.
32. Mascalzoni D, Janssens ACJ, Stewart A, Pramstaller P, Gyllensten U, et al. (2009) Comparison of participant information and informed consent forms of five European studies in genetic isolated populations. Eur J Hum Genet 18: 296-302.
33. Winchester L, Newbury DF, Monaco AP, Ragoussis J, (2008) Detection, breakpoint identification and detailed characterisation of a CNV at the FRA16D site using SNP assays. Cytogenetic and Genome Research 123: 322-332.
34. WTCCC (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464: 713-720.
35. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
36. McCarroll SA, Altshuler DM, (2007) Copy-number variation and association studies of human disease. Nature Genetics 39: S37-S42.
37. Hinds DA, Kloek AP, Jen M, Chen XY, Frazer KA, (2006) Common deletions and SNPs are in linkage disequilibrium in the human genome. Nature Genetics 38: 82-85.
38. McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, et al. (2006) Common deletion polymorphisms in the human genome. Nat Genet 38: 86-92.
39. Nguyen DQ, Webber C, Ponting CP, (2006) Bias of Selection on Human Copy-Number Variants. PLoS Genet 2: e20.
40. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nature Genetics 40: 1166-1174.
41. Kim PM, Lam HYK, Urban AE, Korbel JO, Affourtit J, et al. (2008) Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res 18: 1865-1874.
42. Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, et al. (2008) Copy number variation and evolution in humans and chimpanzees. Genome Res 18: 1698-1710.
43. Nguyen DQ, Webber C, Hehir-Kwa J, Pfundt R, Veltman J, et al. (2008) Reduced purifying selection prevails over positive selection in human copy number variant evolution. Genome Res 18: 1711-1723.
44. Vitart V, Bencic G, Hayward C, Herman JS, Huffman J, et al. (2010) Heritabilities of Ocular Biometrical Traits in Two Croatian Isolates with Extended Pedigrees. Investigative Ophthalmology & Visual Science 51: 737-743.
45. Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, et al. (2010) Diversity of Human Copy Number Variation and Multicopy Genes. Science 330: 641-646.
46. Pattaro C, Marroni F, Riegler A, Mascalzoni D, Pichler I, et al. (2007) The genetic study of three population microisolates in South Tyrol (MICROS): study design and epidemiological perspectives. BMC Medical Genetics 8: 29.
47. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. Am J Hum Genet 81: 559-575.
48. Cronin S, Blauw HM, Veldink JH, van Es MA, Ophoff RA, et al. (2008) Analysis of genome-wide copy number variation in Irish and Dutch ALS populations. Human Molecular Genetics 17 (21): 3392-8.
49. She X, Jiang Z, Clark RA, Liu G, Cheng Z, et al. (2004) Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 431: 927-930.
50. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, et al. (2002) Recent Segmental Duplications in the Human Genome. Science 297: 1003-1007.