Extent of differential allelic expression of candidate breast cancer genes is similar in blood and breast

Breast Cancer Research

Volumn 11, Issue 6, 2009, Pages

  Maia, Ana Teresa ^a   Spiteri, Inmaculada ^a   Lee, Alvin J X ^a,d   O'Reilly, Martin ^a   Jones, Linda ^b   Caldas, Carlos ^a,b   Ponder, Bruce A J ^a,c  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b Li Ka Shing Centre   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

5,10 METHYLENETETRAHYDROFOLATE REDUCTASE (FADH2); BRCA1 PROTEIN; BRCA2 PROTEIN; COMPLEMENT COMPONENT C1Q; COMPLEMENT COMPONENT C1QA; CYCLIN D3; GLUTATHIONE PEROXIDASE 1; NIBRIN; PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE; PROTEIN; PROTEIN EMSY; PROTEIN MLH3; PROTEIN P53; THIOREDOXIN REDUCTASE 2; UNCLASSIFIED DRUG;

ALLELE; ALLELIC IMBALANCE; ARTICLE; BLOOD; BREAST; BREAST CANCER; CANCER SUSCEPTIBILITY; CELL TRANSFORMATION; CONTROLLED STUDY; DIFFERENTIAL ALLELIC EXPRESSION; EPSTEIN BARR VIRUS; GENE EXPRESSION; GENE MAPPING; GENETIC LINKAGE; GENOTYPE; HETEROZYGOTE; HUMAN; HUMAN CELL; HUMAN TISSUE; LYMPHOBLAST; LYMPHOBLASTOID CELL; PHENOTYPE; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR GENE; B LYMPHOCYTE; BREAST TUMOR; CASE CONTROL STUDY; FEMALE; GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION; GENETICS; METABOLISM; MONONUCLEAR CELL; PHYSIOLOGY;

ALLELES; B-LYMPHOCYTES; BREAST NEOPLASMS; CASE-CONTROL STUDIES; FEMALE; GENE EXPRESSION REGULATION; GENE EXPRESSION REGULATION, NEOPLASTIC; GENETIC PREDISPOSITION TO DISEASE; HUMANS; LEUKOCYTES, MONONUCLEAR; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77950867186     PISSN: 14655411     EISSN: 1465542X     Source Type: Journal    
DOI: 10.1186/bcr2458     Document Type: Article

References (42)

1. Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, Ballinger DG, Struewing JP, Morrison J, Field H, Luben R, Wareham N, Ahmed S, Healey CS, Bowman R, collaborators S, Meyer KB, Haiman CA, Kolonel LK, Henderson BE, Le Marchand L, Brennan P, Sangrajrang S, Gaborieau V, Odefrey F, Shen CY, Wu PE, Wang HC, Eccles D, Evans DG, Peto J, et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 2007, 447:1087-1093. 10.1038/nature05887, 2714974, 17529967.
2. Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE, Wacholder S, Wang Z, Welch R, Hutchinson A, Wang J, Yu K, Chatterjee N, Orr N, Willett WC, Colditz GA, Ziegler RG, Berg CD, Buys SS, McCarty CA, Feigelson HS, Calle EE, Thun MJ, Hayes RB, Tucker M, Gerhard DS, Fraumeni JF, Hoover RN, Thomas G, Chanock SJ. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 2007, 39:870-874. 10.1038/ng2075, 17529973.
3. Stacey SN, Manolescu A, Sulem P, Rafnar T, Gudmundsson J, Gudjonsson SA, Masson G, Jakobsdottir M, Thorlacius S, Helgason A, Aben KK, Strobbe LJ, Albers-Akkers MT, Swinkels DW, Henderson BE, Kolonel LN, Le Marchand L, Millastre E, Andres R, Godino J, Garcia-Prats MD, Polo E, Tres A, Mouy M, Saemundsdottir J, Backman VM, Gudmundsson L, Kristjansson K, Bergthorsson JT, Kostic J, et al. Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 2007, 39:865-869. 10.1038/ng2064, 17529974.
4. Stacey SN, Manolescu A, Sulem P, Thorlacius S, Gudjonsson SA, Jonsson GF, Jakobsdottir M, Bergthorsson JT, Gudmundsson J, Aben KK, Strobbe LJ, Swinkels DW, van Engelenburg KCA, Henderson BE, Kolonel LN, Le Marchand L, Millastre E, Andres R, Saez B, Lambea J, Godino J, Polo E, Tres A, Picelli S, Rantala J, Margolin S, Jonsson T, Sigurdsson H, Jonsdottir T, Hrafnkelsson J, et al. Common variants on chromosome 5p12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 2008, 40:703-706. 10.1038/ng.131, 18438407.
5. Ahmed S, Thomas G, Ghoussaini M, Healey CS, Humphreys MK, Platte R, Morrison J, Maranian M, Pooley KA, Luben R, Eccles D, Evans DG, Fletcher O, Johnson N, dos Santos Silva I, Peto J, Stratton MR, Rahman N, Jacobs K, Prentice R, Anderson GL, Rajkovic A, Curb JD, Ziegler RG, Berg CD, Buys SS, McCarty CA, Feigelson HS, Calle EE, Thun MJ, et al. Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2. Nat Genet 2009, 41:585-590. 10.1038/ng.354, 2748125, 19330027.
6. Meyer KB, Maia AT, O'Reilly M, Teschendorff AE, Chin SF, Caldas C, Ponder BA. Allele-Specific Up-Regulation of FGFR2 Increases Susceptibility to Breast Cancer. PLoS Biol 2008, 6:e108. 10.1371/journal.pbio.0060108, 2365982, 18462018.
7. Dermitzakis E, Stranger B. Genetic variation in human gene expression. Mamm Genome 2006, 17:503-508. 10.1007/s00335-006-0005-y, 16783632.
8. Yan H, Zhou W. Allelic variations in gene expression. Current opinion in oncology 2004, 16:39-43. 10.1097/00001622-200401000-00008, 14685091.
9. Chen X, Weaver J, Bove BA, Vanderveer LA, Weil SC, Miron A, Daly MB, Godwin AK. Allelic Imbalance in BRCA1 and BRCA2 Gene Expression Is Associated with an Increased Breast Cancer Risk. Hum Mol Genet 2008, 17:1336-1348. 10.1093/hmg/ddn022, 18204050.
10. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH. Genetics of gene expression surveyed in maize, mouse and man. Nature 2003, 422:297-302. 10.1038/nature01434, 12646919.
11. Cheung V, Conlin L, Weber T, Arcaro M, Jen K, Morley M, Spielman R. Natural variation in human gene expression assessed in lymphoblastoid cells. Nat Genet 2003, 33:422-425. 10.1038/ng1094, 12567189.
12. Bray N, Buckland P, Owen M, O'Donovan M. Cis-acting variation in the expression of a high proportion of genes in human brain. Hum Genet 2003, 113:149-153.
13. Cheung V, Spielman R, Ewens K, Weber T, Morley M, Burdick J. Mapping determinants of human gene expression by regional and genome-wide association. Nature 2005, 437:1365-1369. 10.1038/nature04244, 16251966.
14. Lo H, Wang Z, Hu Y, Yang H, Gere S, Buetow K, Lee M. Allelic variation in gene expression is common in the human genome. Genome Res 2003, 13:1855-1862. 10.1101/gr.885403, 403776, 12902379.
15. Morley M, Molony C, Weber T, Devlin J, Ewens K, Spielman R, Cheung V. Genetic analysis of genome-wide variation in human gene expression. Nature 2004, 430:743-747. 10.1038/nature02797, 15269782.
16. Pant P, Tao H, Beilharz E, Ballinger D, Cox D, Frazer K. Analysis of allelic differential expression in human white blood cells. Genome Res 2006, 16:331-339. 10.1101/gr.4559106, 1415206, 16467561.
17. Stranger B, Forrest M, Clark A, Minichiello M, Deutsch S, Lyle R, Hunt S, Kahl B, Antonarakis S, Tavaré S, Deloukas P, Dermitzakis E. Genome-wide associations of gene expression variation in humans. PLoS Genet 2005, 1:e78. 10.1371/journal.pgen.0010078, 1315281, 16362079.
18. Yan H, Yuan W, Velculescu V, Vogelstein B, Kinzler K. Allelic variation in human gene expression. Science 2002, 297:1143. 10.1126/science.1072545, 12183620.
19. Lee PD, Ge B, Greenwood CM, Sinnett D, Fortin Y, Brunet S, Fortin A, Takane M, Skamene E, Pastinen T, Hallett M, Hudson TJ, Sladek R. Mapping cis-acting regulatory variation in recombinant congenic strains. Physiol Genomics 2006, 25:294-302. 10.1152/physiolgenomics.00168.2005, 16449383.
20. Tao H, Cox DR, Frazer KA. Allele-specific KRT1 expression is a complex trait. PLoS Genet 2006, 2:e93. 10.1371/journal.pgen.0020093, 1475705, 16789827.
21. GuhaThakurta D, Xie T, Anand M, Edwards SW, Li G, Wang SS, Schadt EE. Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations. BMC Genomics 2006, 7:235. 10.1186/1471-2164-7-235, 1618400, 16978413.
22. Pastinen T, Ge B, Gurd S, Gaudin T, Dore C, Lemire M, Lepage P, Harmsen E, Hudson TJ. Mapping common regulatory variants to human haplotypes. Hum Mol Genet 2005, 14:3963-3971. 10.1093/hmg/ddi420, 16301213.
23. Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, Cheung VG. Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet 2007, 39:226-231. 10.1038/ng1955, 17206142.
24. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, Montgomery S, Tavare S, Deloukas P, Dermitzakis ET. Population genomics of human gene expression. Nat Genet 2007, 39:1217-1224. 10.1038/ng2142, 2683249, 17873874.
25. Wilkins JM, Southam L, Price AJ, Mustafa Z, Carr A, Loughlin J. Extreme context specificity in differential allelic expression. Hum Mol Genet 2007, 16:537-546. 10.1093/hmg/ddl488, 17220169.
26. Campbell CD, Kirby A, Nemesh J, Daly MB, Hirschhorn JN. A survey of allelic imbalance in F1 mice. Genome Res 2008, 18:555-563. 10.1101/gr.068692.107, 2279243, 18256236.
27. Team RDC: R: A Language and Environment for Statistical Computing. , http://www.r-project.org/
28. Pharoah PD, Tyrer J, Dunning AM, Easton DF, Ponder BA, . SEARCH Investigators Association between common variation in 120 candidate genes and breast cancer risk. PLoS Genet 2007, 3:e42. 10.1371/journal.pgen.0030042, 1828694, 17367212, SEARCH Investigators.
29. Racila E, Racila DM, Ritchie JM, Taylor C, Dahle C, Weiner GJ. The pattern of clinical breast cancer metastasis correlates with a single nucleotide polymorphism in the C1qA component of complement. Immunogenetics 2006, 58:1-8. 10.1007/s00251-005-0077-y, 16465510.
30. Song H, Ramus SJ, Quaye L, DiCioccio RA, Tyrer J, Lomas E, Shadforth D, Hogdall E, Hogdall C, McGuire V, Whittemore AS, Easton DF, Ponder BA, Kjaer SK, Pharoah PD, Gayther SA. Common variants in mismatch repair genes and risk of invasive ovarian cancer. Carcinogenesis 2006, 27:2235-2242. 10.1093/carcin/bgl089, 16774946.
31. Udler M, Maia AT, Cebrian A, Brown C, Greenberg D, Shah M, Caldas C, Dunning A, Easton D, Ponder B, Pharoah P. Common germline genetic variation in antioxidant defense genes and survival after diagnosis of breast cancer. J Clin Oncol 2007, 25:3015-3023. 10.1200/JCO.2006.10.0099, 17634480.
32. Ryan JL, Kaufmann WK, Raab-Traub N, Oglesbee SE, Carey LA, Gulley ML. Clonal evolution of lymphoblastoid cell lines. Lab Invest 2006, 86:1193-1200. 10.1038/labinvest.3700472, 17053803.
33. Attanasio C, Reymond A, Humbert R, Lyle R, Kuehn MS, Neph S, Sabo PJ, Goldy J, Weaver M, Lee K, Haydock A, Dermitzakis ET, Dorschner MO, Antonarakis SE, Stamatoyannopoulos JA. Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells. Genome Biol 2008, 9:R168. 10.1186/gb-2008-9-12-r168, 2646272, 19055709.
34. Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, Shaw SY, Wolfish CS, Slavik JM, Cotsapas C, Rivas M, Dermitzakis ET, Cahir-McFarland E, Kieff E, Hafler D, Daly MJ, Altshuler D. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet 2008, 4:e1000287. 10.1371/journal.pgen.1000287, 2583954, 19043577.
35. Williams RB, Chan EK, Cowley MJ, Little PF. The influence of genetic variation on gene expression. Genome Res 2007, 17:1707-1716. 10.1101/gr.6981507, 18063559.
36. Bjornsson HT, Albert TJ, Ladd-Acosta CM, Green RD, Rongione MA, Middle CM, Irizarry RA, Broman KW, Feinberg AP. SNP-specific array-based allele-specific expression analysis. Genome Res 2008, 18:771-779. 10.1101/gr.073254.107, 2336807, 18369178.
37. Cheung VG, Bruzel A, Burdick JT, Morley M, Devlin JL, Spielman RS. Monozygotic Twins Reveal Germline Contribution to Allelic Expression Differences. Am J Hum Genet 2008, 82:1357-1360. 10.1016/j.ajhg.2008.05.003, 2427304, 18513681.
38. Verlaan DJ, Ge B, Grundberg E, Hoberman R, Lam K, Koka V, Dias J, Gurd S, Martin N, Mallmin H, Nilsson O, Harmsen E, Kwan T, Pastinen TM. Targeted screening of cis-regulatory variation in human haplotypes. Genome Res 2008, 19:118-127. 10.1101/gr.084798.108, 2612965, 18971308.
39. Serre D, Gurd S, Ge B, Sladek R, Sinnett D, Harmsen E, Bibikova M, Chudin E, Barker DL, Dickinson T, Fan JB, Hudson TJ. Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet 2008, 4:e1000006. 10.1371/journal.pgen.1000006, 2265535, 18454203.
40. Pastinen T, Ge B, Hudson TJ. Influence of human genome polymorphism on gene expression. Hum Mol Genet 2006, 15(Spec No 1):R9-16. 10.1093/hmg/ddl044, 16651375.
41. Pastinen T, Hudson T. Cis-acting regulatory variation in the human genome. Science 2004, 306:647-650. 10.1126/science.1101659, 15499010.
42. Valle L, Serena-Acedo T, Liyanarachchi S, Hampel H, Comeras I, Li Z, Zeng Q, Zhang HT, Pennison MJ, Sadim M, Pasche B, Tanner SM, de la Chapelle A. Germline allele-specific expression of TGFBR1 confers an increased risk of colorectal cancer. Science 2008, 321:1361-1365. 10.1126/science.1159397, 2672914, 18703712.