Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions

Genome Research

Volumn 21, Issue 12, 2011, Pages 2004-2013

  Schlattl, Andreas ^a   Anders, Simon ^a   Waszak, Sebastian M ^a   Huber, Wolfgang ^a,b   Korbel, Jan O ^a,b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; COPY NUMBER VARIATION; FEMALE; GENE DELETION; GENE DUPLICATION; GENE EXPRESSION; GENE FUNCTION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC VARIABILITY; HUMAN; MAJOR CLINICAL STUDY; MALE; PRIORITY JOURNAL; QUANTITATIVE GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA COPY NUMBER VARIATIONS; FEMALE; GENE DOSAGE; GENE EXPRESSION REGULATION; GENOTYPE; HUMANS; MALE; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; TRANSCRIPTOME;

EID: 83055168377     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.122614.111     Document Type: Article

References (48)

1. The 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
2. Ait Yahya-Graison E, Aubert J, Dauphinot L, Rivals I, Prieur M, Golfier G, Rossier J, Personnaz L, Creau N, Blehaut H, et al. 2007. Classification of human chromosome 21 gene-expression variations in Down syndrome: Impact on disease phenotypes. Am J Hum Genet 81: 475-491.
3. An P, Johnson R, Phair J, Kirk GD, Yu XF, Donfield S, Buchbinder S, Goedert JJ,Winkler CA. 2009. APOBEC3B deletion and risk of HIV-1 acquisition. J Infect Dis 200: 1054-1058.
4. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106. doi: 10.1186/gb-2010-11-10-r106.
5. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57: 289-300.
6. Chaignat E, Yahya-Graison EA, Henrichsen CN, Chrast J, Schutz F, Pradervand S, Reymond A. 2011. Copy number variation modifies expression time courses. Genome Res 21: 106-113.
7. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, et al. 2010. Origins and functional impact of copy number variation in the human genome. Nature 464: 704-712.
8. Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, et al. 2010. Genomewide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464: 713-720.
9. Deng X, Disteche CM. 2010. Genomic responses to abnormal gene dosage: The X chromosome improved on a common strategy. PLoS Biol 8: e1000318. doi: 10.1371/journal.pbio.1000318.
10. Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, Attar-Cohen H, Ingle C, Beazley C, Arcelus MG, Sekowska M, et al. 2009. Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325: 1246-1250.
11. Fanciulli M, Norsworthy PJ, Petretto E, Dong R, Harper L, Kamesh L, Heward JM, Gough SC, de Smith A, Blakemore AI, et al. 2007. FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat Genet 39: 721-723. (Pubitemid 46848593)
12. Gilad Y, Rifkin SA, Pritchard JK. 2008. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet 24: 408-415.
13. Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, Nibbs RJ, Freedman BI, Quinones MP, Bamshad MJ, et al. 2005. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307: 1434-1440. (Pubitemid 40321934)
14. Henrichsen CN, Chaignat E, Reymond A. 2009. Copy number variants, diseases and gene expression. Hum Mol Genet 18: R1-R8.
15. Hollox EJ, Huffmeier U, Zeeuwen PL, Palla R, Lascorz J, Rodijk-Olthuis D, van de Kerkhof PC, Traupe H, de Jongh G, den Heijer M, et al. 2008. Psoriasis is associated with increased b-defensin genomic copy number. Nat Genet 40: 23-25.
16. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. 2004. Detection of large-scale variation in the human genome. Nat Genet 36: 949-951. (Pubitemid 39167488)
17. The International HapMap Consortium. 2005. A haplotype map of the human genome. Nature 437: 1299-1320.
18. KasowskiM, Grubert F, Heffelfinger C, Hariharan M, Asabere A,Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, et al. 2010. Variation in transcription factor binding among humans. Science 328: 232-235.
19. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, et al. 2008. Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64. (Pubitemid 351630326)
20. Kidd JM, Graves T, Newman TL, Fulton R, Hayden HS, Malig M, Kallicki J, Kaul R, Wilson RK, Eichler EE. 2010a. A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell 143: 837-847.
21. Kidd JM, Sampas N, Antonacci F, Graves T, Fulton R, Hayden HS, Alkan C, Malig M, Ventura M, Giannuzzi G, et al. 2010b. Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Methods 7: 365-371.
22. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, et al. 2007. Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420-426. (Pubitemid 47614521)
23. Korbel JO, Kim PM, Chen X, Urban AE,Weissman S, Snyder M, Gerstein MB. 2008. The current excitement about copy-number variation: how it relates to gene duplications and protein families. Curr Opin Struct Biol 18: 366-374.
24. Kurth I, Klopocki E, Stricker S, van Oosterwijk J, Vanek S, Altmann J, Santos HG, van Harssel JJ, de Ravel T, Wilkie AO, et al. 2009. Duplications of noncoding elements 59 of SOX9 are associated with brachydactylyanonychia. Nat Genet 41: 862-863.
25. Li Y,Wu G, Zuo J, Gao J, Chang Y, Fang FD. 2007. Genetic variations of the CDC2L2 gene are associated with type 2 diabetes in a Han Chinese cohort. Diabetes Metab Res Rev 23: 455-461. (Pubitemid 47520902)
26. Lupski JR, Stankiewicz P. 2005. Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet 1: e49. doi: 10.1371/journal.pgen.0010049.
27. McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ, et al. 2006. Common deletion polymorphisms in the human genome. Nat Genet 38: 86-92. (Pubitemid 43011887)
28. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A, et al. 2008. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40: 1166-1174.
29. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, et al. 2011. Mapping copy number variation by population-scale genome sequencing. Nature 470: 59-65.
30. Montgomery SB, Sammeth M, Gutierrez-ArcelusM, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET. 2010. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
31. Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, et al. 2007. A survey of genetic human cortical gene expression. Nat Genet 39: 1494-1499. (Pubitemid 350191339)
32. Pang AW, MacDonald JR, Pinto D, Wei J, Rafiq MA, Conrad DF, Park H, Hurles ME, Lee C, Venter JC, et al. 2010. Towards a comprehensive structural variation map of an individual human genome. Genome Biol 11: R52. doi: 10.1186/gb-2010-11-5-r52.
33. Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP, et al. 2010. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet 42: 400-405.
34. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. 2010. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.
35. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, et al. 2006. Global variation in copy number in the human genome. Nature 444: 444-454. (Pubitemid 44809057)
36. Ricard G, Molina J,Chrast J, GuW, Gheldof N, Pradervand S, Schütz F, Young JI, Lupski JR, Reymond A, et al. 2010. Phenotypic consequences of copy number variation: Insights from Smith-Magenis and Potocki-Lupski syndrome mouse models. PLoS Biol 8: e1000543. doi: 10.1371/ journal.pbio.1000543.
37. Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B,Wang S, Suver C, et al. 2008. Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6: e107. doi: 10.1371/ journal.pbio. 0060107.
38. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, et al. 2004. Large-scale copy number polymorphism in the human genome. Science 305: 525-528. (Pubitemid 38971344)
39. Stegle O, Parts L, Durbin R,Winn J. 2010. A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies. PLoS Comput Biol 6: e1000770. doi: 10.1371/journal.pcbi. 1000770.
40. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, et al. 2007. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315: 848-853.
41. Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Eichler EE. 2010. Diversity of human copy number variation and multicopy genes. Science 330: 641-646.
42. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, et al. 2005. Fine-scale structural variation of the human genome. Nat Genet 37: 727-732. (Pubitemid 41754889)
43. Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, Pritchard JK. 2008. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet 4: e1000214. doi: 10.1371/journal.pgen. 1000214.
44. Waszak SM, Hasin Y, Zichner T, Olender T, Keydar I, Khen M, Stutz AM, Schlattl A, Lancet D, Korbel JO. 2010. Systematic inference of copynumber genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity. PLoS Comput Biol 6: e1000988. doi: 10.1371/journal.pcbi.1000988.
45. Wu TD, Nacu S. 2010. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.
46. Yamanaka M, Kato Y, Angata T, Narimatsu H. 2009. Deletion polymorphism of SIGLEC14 and its functional implications. Glycobiology 19: 841-846.
47. Zeller T, Wild P, Szymczak S, Rotival M, Schillert A, Castagne R, Maouche S, Germain M, Lackner K, Rossmann H, et al. 2010. Genetics and beyond-The transcriptome of human monocytes and disease susceptibility. PLoS ONE 5: e10693. doi: 10.1371/journal.pone.0010693.
48. Zhang Y, Malone JH, Powell SK, Periwal V, Spana E, Macalpine DM, Oliver B. 2010. Expression in aneuploid Drosophila S2 cells. PLoS Biol 8: e1000320. doi: 10.1371/journal.pbio.1000320.