Breast Cancer Research and Treatment

, Volume 114, Issue 3, pp 463–477 | Cite as

A pilot genome-wide association study of early-onset breast cancer

  • Muhammad G. KibriyaEmail author
  • Farzana Jasmine
  • Maria Argos
  • Irene L. Andrulis
  • Esther M. John
  • Jenny Chang-Claude
  • Habibul AhsanEmail author
Preclinical Study


High-density oligonucleotide microarrays containing a large number of single nucleotide polymorphisms (SNPs) have enabled genome-wide association (GWA) analysis to become a reality. We used the early access Affymetrix Mendel Nsp 250K chips in a GWA case–control pilot study to identify genomic regions associated with breast cancer. We included 30 randomly sampled incident invasive breast cancer cases aged <45 years without deleterious mutations in the BRCA1 or BRCA2 genes, and 30 population controls individually matched on age, ethnicity and geographical area. The overall genotype call rate was 97.13 ± 1.33% for controls and 97.48 ± 1.42% for cases. Comparison was made between cases and controls for 203,477 genotyped SNPs using (a) unconditional logistic regression (ULR), (b) conditional logistic regression (CLR) models with adjustment for the matched pairs, (c) allelic tests for single marker tests and (d) haplotype trend regression (HTR). Genomic control and EIGENSTRAT methods were used for correction of population stratification in appropriate models. We demonstrate the similarity and dissimilarity of results from different statistical analyses. We found several possible significant regions harboring biologically meaningful known candidate genes, such as genes encoding fibroblast growth factor, transforming growth factor, epidermal growth factor, and estrogen synthesis enzymes to be associated with early-onset breast cancer. In single marker analysis, none of the SNPs were statistically significant after correction for multiple testing. However, haplotype association tests, using 90730 tag-SNPs, suggested two regions in GLG1 and UGT1 genes retaining significance even after Bonferroni correction. Nevertheless, without systematic replication, findings from this pilot study, especially the associations of breast cancer in relation to specific SNPs, should be interpreted with great caution.


Genome-wide association Breast cancer Microarray Affymetrix GeneChip Genome scan 



Single nucleotide polymorphism


Genome-wide association


Linkage disequilibrium



Support This work was supported in part by grants from the National Cancer Institute Grant # UO1 CA 122171. The authors wish to thank all the members of the Breast Cancer Family Registry (BCFR) and the German Breast Cancer Study (GBCS).


  1. 1.
    Hall JM, Friedman L, Guenther C et al (1992) Closing in on a breast cancer gene on chromosome 17q. Am J Hum Genet 50(6):1235–1242PubMedGoogle Scholar
  2. 2.
    Wooster R, Neuhausen SL, Mangion J et al (1994) Localization of a breast cancer susceptibility gene, brca2, to chromosome 13q12-13. Science 265(5181):2088–2090PubMedCrossRefGoogle Scholar
  3. 3.
    Loman N, Bladstrom A, Johannsson O, Borg A, Olsson H (2003) Cancer incidence in relatives of a population-based set of cases of early-onset breast cancer with a known brca1 and brca2 mutation status. Breast Cancer Res 5(6):R175–R186PubMedCrossRefGoogle Scholar
  4. 4.
    Dite GS, Jenkins MA, Southey MC et al (2003) Familial risks, early-onset breast cancer, and brca1 and brca2 germline mutations. J Natl Cancer Inst 95(6):448–457PubMedCrossRefGoogle Scholar
  5. 5.
    Pharoah PD, Day NE, Duffy S, Easton DF, Ponder BA (1997) Family history and the risk of breast cancer: a systematic review and meta-analysis. Int J Cancer 71(5):800–809PubMedCrossRefGoogle Scholar
  6. 6.
    Collaborative Group on Hormonal Factorin Breast Cancer (2001) Familial breast cancer: collaborative reanalysis of individual data from 52 epidemiological studies including 58,209 women with breast cancer and 101,986 women without the disease. Lancet 358(9291):1389–1399CrossRefGoogle Scholar
  7. 7.
    Easton D, Ford D, Peto J (1993) Inherited susceptibility to breast cancer. Cancer Surv 18:95–113PubMedGoogle Scholar
  8. 8.
    Hopper JL (2001) Genetic epidemiology of female breast cancer. Semin Cancer Biol 11(5):367–374PubMedCrossRefGoogle Scholar
  9. 9.
    Oesterreich S, Fuqua SA (1999) Tumor suppressor genes in breast cancer. Endocr Relat Cancer 6(3):405–419PubMedCrossRefGoogle Scholar
  10. 10.
    Rahman N, Seal S, Thompson D et al (2007) Palb2, which encodes a brca2-interacting protein, is a breast cancer susceptibility gene. Nat Genet 39(2):165–167PubMedCrossRefGoogle Scholar
  11. 11.
    Seal S, Thompson D, Renwick A et al (2006) Truncating mutations in the fanconi anemia j gene brip1 are low-penetrance breast cancer susceptibility alleles. Nat Genet 38(11):1239–1241PubMedCrossRefGoogle Scholar
  12. 12.
    Claus EB, Schildkraut J, Iversen ES Jr, Berry D, Parmigiani G (1998) Effect of brca1 and brca2 on the association between breast cancer risk and family history. J Natl Cancer Inst 90(23):1824–1829PubMedCrossRefGoogle Scholar
  13. 13.
    Cui J, Antoniou AC, Dite GS et al (2001) After brca1 and brca2-what next? Multifactorial segregation analyses of three-generation, population-based Australian families affected by female breast cancer. Am J Hum Genet 68(2):420–431PubMedCrossRefGoogle Scholar
  14. 14.
    Malone KE, Daling JR, Thompson JD et al (1998) Brca1 mutations and breast cancer in the general population: analyses in women before age 35 years and in women before age 45 years with first-degree family history. J Am Med Assoc 279(12):922–929CrossRefGoogle Scholar
  15. 15.
    Antoniou AC, Pharoah PD, McMullan G et al (2002) A comprehensive model for familial breast cancer incorporating brca1, brca2 and other genes. Br J Cancer 86(1):76–83PubMedCrossRefGoogle Scholar
  16. 16.
    Rahman N, Teare MD, Seal S et al (2000) Absence of evidence for a familial breast cancer susceptibility gene at chromosome 8p12-p22. Oncogene 19(36):4170–4173PubMedCrossRefGoogle Scholar
  17. 17.
    Thomas DC, Witte JS (2002) Point: population stratification: a problem for case–control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev 11(6):505–512PubMedGoogle Scholar
  18. 18.
    Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273(5281):1516–1517PubMedCrossRefGoogle Scholar
  19. 19.
    Wang WY, Barratt BJ, Clayton DG, Todd JA (2005) Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet 6(2):109–118PubMedCrossRefGoogle Scholar
  20. 20.
    Hirschhorn JN, Daly MJ (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6(2):95–108PubMedCrossRefGoogle Scholar
  21. 21.
    John EM, Hopper JL, Beck JC et al (2004) The breast cancer family registry: an infrastructure for cooperative multinational, interdisciplinary and translational studies of the genetic epidemiology of breast cancer. Breast Cancer Res 6(4):R375–R389PubMedCrossRefGoogle Scholar
  22. 22.
    Chang-Claude J, Eby N, Kiechle M, Bastert G, Becher H (2000) Breastfeeding and breast cancer risk by age 50 among women in Germany. Cancer Causes Control 11(8):687–695PubMedCrossRefGoogle Scholar
  23. 23.
    Reich DE, Goldstein DB (2001) Detecting association in a case–control study while correcting for population stratification. Genet Epidemiol 20(1):4–16PubMedCrossRefGoogle Scholar
  24. 24.
    Price AL, Patterson NJ, Plenge RM et al (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38(8):904–909PubMedCrossRefGoogle Scholar
  25. 25.
    Zaykin DV (2004) Bounds and normalization of the composite linkage disequilibrium coefficient. Genet Epidemiol 27(3):252–257PubMedCrossRefGoogle Scholar
  26. 26.
    Zaykin DV, Westfall PH, Young SS et al (2002) Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum Hered 53(2):79–91PubMedCrossRefGoogle Scholar
  27. 27.
    Dempster AP, Laird NM, Rubin D (1977) Maximum likelihood from incomplete data via the em algorithm. J Roy Stat Soc B 39:1–38Google Scholar
  28. 28.
    Zaykin DV, Zhivotovsky LA (2005) Ranks of genuine associations in whole-genome scans. Genetics 171(2):813–823PubMedCrossRefGoogle Scholar
  29. 29.
    Lambert GC (2007) Helixtree software version 6.0.2. Golden helix, Inc.
  30. 30.
    Carlson CS, Eberle MA, Rieder MJ et al (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74(1):106–120PubMedCrossRefGoogle Scholar
  31. 31.
    Easton DF, Pooley KA, Dunning AM et al (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447(7148):1087–1093PubMedCrossRefGoogle Scholar
  32. 32.
    Hunter DJ, Kraft P, Jacobs KB et al (2007) A genome-wide association study identifies alleles in fgfr2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 39(7):870–874PubMedCrossRefGoogle Scholar
  33. 33.
    Stacey SN, Manolescu A, Sulem P et al (2007) Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 39(7):865–869PubMedCrossRefGoogle Scholar
  34. 34.
    Fackenthal JD, Olopade OI (2007) Breast cancer risk associated with brca1 and brca2 in diverse populations. Nat Rev Cancer 7(12):937–948PubMedCrossRefGoogle Scholar
  35. 35.
    John EM, Miron A, Gong G et al (2007) Prevalence of pathogenic brca1 mutation carriers in 5 us racial/ethnic groups. J Am Med Assoc 298(24):2869–2876CrossRefGoogle Scholar
  36. 36.
    Yamaguchi F, Morrison RS, Gonatas NK et al (2003) Identification of mg-160, a fgf binding medial golgi sialoglycoprotein, in brain tumors: an index of malignancy in astrocytomas. Int J Oncol 22(5):1045–1049PubMedGoogle Scholar
  37. 37.
    Cui Y, Liao YC, Lo SH (2004) Epidermal growth factor modulates tyrosine phosphorylation of a novel tensin family member, tensin3. Mol Cancer Res 2(4):225–232PubMedGoogle Scholar
  38. 38.
    Rakha E, Ellis I, Reis-Filho J (2008) Are triple-negative and basal-like breast cancer synonymous? Clin Cancer Res 14(2):618PubMedCrossRefGoogle Scholar
  39. 39.
    Rakha EA, El-Sayed ME, Green AR et al (2007) Prognostic markers in triple-negative breast cancer. Cancer 109(1):25–32PubMedCrossRefGoogle Scholar
  40. 40.
    Yeager M, Orr N, Hayes RB et al (2007) Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 39(5):645–649PubMedCrossRefGoogle Scholar
  41. 41.
    Tommerup N, Vissing H (1995) Isolation and fine mapping of 16 novel human zinc finger-encoding cdnas identify putative candidate genes for developmental and malignant disorders. Genomics 27(2):259–264PubMedCrossRefGoogle Scholar
  42. 42.
    Basu NK, Kubota S, Meselhy MR et al (2004) Gastrointestinally distributed udp-glucuronosyltransferase 1a10, which metabolizes estrogens and nonsteroidal anti-inflammatory drugs, depends upon phosphorylation. J Biol Chem 279(27):28320–28329PubMedCrossRefGoogle Scholar
  43. 43.
    Elahi A, Bendaly J, Zheng Z et al (2003) Detection of ugt1a10 polymorphisms and their association with orolaryngeal carcinoma risk. Cancer 98(4):872–880PubMedCrossRefGoogle Scholar
  44. 44.
    Huo D, Kim HJ, Adebamowo CA et al (2007) Genetic polymorphisms in uridine diphospho-glucuronosyltransferase 1a1 and breast cancer risk in africans. Breast Cancer Res Treat. doi: 10.1007/s10549-007-9720-7

Copyright information

© Springer Science+Business Media, LLC. 2008

Authors and Affiliations

  • Muhammad G. Kibriya
    • 1
    Email author
  • Farzana Jasmine
    • 1
  • Maria Argos
    • 1
  • Irene L. Andrulis
    • 2
    • 3
  • Esther M. John
    • 4
    • 5
  • Jenny Chang-Claude
    • 6
  • Habibul Ahsan
    • 1
    • 7
    • 8
    • 9
    Email author
  1. 1.Department of Health StudiesThe University of ChicagoChicagoUSA
  2. 2.Samuel Lunenfeld Research Institute, Mount Sinai HospitalTorontoCanada
  3. 3.Department of Molecular GeneticsUniversity of TorontoTorontoCanada
  4. 4.Northern California Cancer CenterFremontUSA
  5. 5.Department of Health Research and PolicyStanford School of MedicineStanfordUSA
  6. 6.German Cancer Research CenterHeidelbergGermany
  7. 7.Department of Human GeneticsThe University of ChicagoChicagoUSA
  8. 8.Department of MedicineThe University of ChicagoChicagoUSA
  9. 9.Cancer Research CenterThe University of ChicagoChicagoUSA

Personalised recommendations