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Milne RL, Antoniou AC. Genetic modifiers of cancer risk for BRCA1 and BRCA2 mutation carriers. Ann Oncol 2011; 22 Suppl 1:i11-7. [PMID: 21285145 DOI: 10.1093/annonc/mdq660] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Germline mutations in BRCA1 and BRCA2 confer high risks of female breast and ovarian cancer. However, there is strong evidence that these risks are modified by other factors, including familial or genetic factors. Genome-wide association studies have identified several breast cancer genetic susceptibility variants in the general population that are also associated with breast cancer risk for mutation carriers. The patterns of association for these variants vary between BRCA1 and BRCA2 mutation carriers and this variation appears to be driven by their differential associations with breast cancer subtypes defined by estrogen receptor status. We review the latest evidence regarding genetic modifiers of cancer risk for female BRCA1 and BRCA2 mutation carriers emerging from candidate gene studies, variants found in genome-wide association studies (GWAS) to be associated with cancer risk in the general population and GWAS specifically in mutation carriers. We also discuss the implications of these findings for cancer risk prediction in these women. BRCA1 and BRCA2 mutation carriers could potentially be among the first groups of individuals for whom clinically applicable risk profiling could be developed using the common breast cancer susceptibility variants identified through GWAS.
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Affiliation(s)
- R L Milne
- Genetic and Molecular Epidemiology Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Spain
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352
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Potential novel candidate polymorphisms identified in genome-wide association study for breast cancer susceptibility. Hum Genet 2011; 130:529-37. [PMID: 21424380 PMCID: PMC3178778 DOI: 10.1007/s00439-011-0973-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 03/02/2011] [Indexed: 01/16/2023]
Abstract
Previous genome-wide association studies (GWAS) have shown several risk alleles to be associated with breast cancer. However, the variants identified so far contribute to only a small proportion of disease risk. The objective of our GWAS was to identify additional novel breast cancer susceptibility variants and to replicate these findings in an independent cohort. We performed a two-stage association study in a cohort of 3,064 women from Alberta, Canada. In Stage I, we interrogated 906,600 single nucleotide polymorphisms (SNPs) on Affymetrix SNP 6.0 arrays using 348 breast cancer cases and 348 controls. We used single-locus association tests to determine statistical significance for the observed differences in allele frequencies between cases and controls. In Stage II, we attempted to replicate 35 significant markers identified in Stage I in an independent study of 1,153 cases and 1,215 controls. Genotyping of Stage II samples was done using Sequenom Mass-ARRAY iPlex platform. Six loci from four different gene regions (chromosomes 4, 5, 16 and 19) showed statistically significant differences between cases and controls in both Stage I and Stage II testing, and also in joint analysis. The identified variants were from EDNRA, ROPN1L, C16orf61 and ZNF577 gene regions. The presented joint analyses from the two-stage study design were not significant after genome-wide correction. The SNPs identified in this study may serve as potential candidate loci for breast cancer risk in a further replication study in Stage III from Alberta population or independent validation in Caucasian cohorts elsewhere.
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353
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Han W, Woo JH, Yu JH, Lee MJ, Moon HG, Kang D, Noh DY. Common genetic variants associated with breast cancer in Korean women and differential susceptibility according to intrinsic subtype. Cancer Epidemiol Biomarkers Prev 2011; 20:793-8. [PMID: 21415360 DOI: 10.1158/1055-9965.epi-10-1282] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Recently identified genetic variants from genome-wide association studies (GWAS) on breast cancer have not been validated in Asian populations, except in China. In this study, we sought to confirm the association between known variants and breast cancer in Korean women and further evaluate the associations of individual single nucleotide polymorphisms (SNP) with different intrinsic subtypes of breast cancer. METHODS In total, 3,321 invasive breast cancer patients and 3,500 healthy controls were genotyped for five SNPs by using the TaqMan assay. The SNPs genotyped included rs2046210 (6q25.1), rs2981582 (FGFR2), rs889312 (MAP3K1), rs3803662 (TOX3/TNRC9), and rs4973768 (SLC4A7). Tumors were classified into four intrinsic subtypes based on estrogen receptor (ER), progesterone receptor, HER2, and Ki67 expression. RESULTS All five SNPs were significantly associated with risk of breast cancer in dominant, recessive, and additive models. ORs per risk allele (95% CI) were 1.29 (1.16-1.43), 1.40 (1.18-1.68), 1.22 (1.06-1.41), 1.52 (1.30-1.77), and 1.20 (1.08-1.33) for rs2046210, rs2981582, rs889312, rs3803662, and rs4973768, respectively. A multigene logistic regression risk model was generated with the SNPs. In subtype analysis, all 5 SNPs were associated with the Luminal A subtype. Two SNPs (rs2046210 and rs3803662) were linked to the ER(-)HER2(+) subtype, and only rs2046210 SNP was associated with the triple-negative subtype. CONCLUSIONS The five SNPs from GWAS were significantly associated with breast cancer risk in Korean women. Associations were heterogeneous according to the intrinsic subtype of breast cancer. IMPACT Our result is an important contribution to the literature about genetic susceptibility for breast cancer in nonwhite populations.
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Affiliation(s)
- Wonshik Han
- Cancer Research Institute, Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
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354
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Harlid S, Ivarsson MIL, Butt S, Hussain S, Grzybowska E, Eyfjörd JE, Lenner P, Försti A, Hemminki K, Manjer J, Dillner J, Carlson J. A candidate CpG SNP approach identifies a breast cancer associated ESR1-SNP. Int J Cancer 2011; 129:1689-98. [PMID: 21105050 DOI: 10.1002/ijc.25786] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 10/25/2010] [Indexed: 11/10/2022]
Abstract
Altered DNA methylation is often seen in malignant cells, potentially contributing to carcinogenesis by suppressing gene expression. We hypothesized that heritable methylation potential might be a risk factor for breast cancer and evaluated possible association with breast cancer for single nucleotide polymorphisms (SNPs) either involving CpG sequences in extended 5'-regulatory regions of candidate genes (ESR1, ESR2, PGR, and SHBG) or CpG and missense coding SNPs in genes involved in methylation (MBD1, MECP2, DNMT1, MGMT, MTHFR, MTR, MTRR, MTHFD1, MTHFD2, BHMT, DCTD, and SLC19A1). Genome-wide searches for genetic risk factors for breast cancers have in general not investigated these SNPs, because of low minor allele frequency or weak haplotype associations. Genotyping was performed using Mass spectrometry-Maldi-Tof in a screening panel of 538 cases and 1,067 controls. Potential association to breast cancer was identified for 15 SNPs and one of these SNPs (rs7766585 in ESR1) was found to associate strongly with breast cancer, OR 1.30 (95% CI 1.17-1.45; p-value 2.1 × 10(-6)), when tested in a verification panel consisting of 3,211 unique breast cancer cases and 4,223 unique controls from five European biobank cohorts. In conclusion, a candidate gene search strategy focusing on methylation-related SNPs did identify a SNP that associated with breast cancer at high significance.
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Affiliation(s)
- Sophia Harlid
- Department of Medical Microbiology, Lund University, Malmö, Sweden
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355
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Politopoulos I, Gibson J, Tapper W, Ennis S, Eccles D, Collins A. Composite likelihood-based meta-analysis of breast cancer association studies. J Hum Genet 2011; 56:377-82. [DOI: 10.1038/jhg.2011.23] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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356
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Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One 2011; 6:e17490. [PMID: 21364760 PMCID: PMC3045451 DOI: 10.1371/journal.pone.0017490] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 02/03/2011] [Indexed: 12/21/2022] Open
Abstract
We used deep sequencing technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+) and negative breast cancer. Total mRNA sequence, gene copy number, and genomic CpG island methylation were carried out using the Illumina Genome Analyzer. Sequences were mapped to the human genome to obtain digitized gene expression data, DNA copy number in reference to the non-tumor cell line (MCF10A), and methylation status of 21,570 CpG islands to identify differentially expressed genes that were correlated with methylation or copy number changes. These were evaluated in a dataset from 129 primary breast tumors. Gene expression in cell lines was dominated by ER-associated genes. ER+ and ER− cell lines formed two distinct, stable clusters, and 1,873 genes were differentially expressed in the two groups. Part of chromosome 8 was deleted in all ER− cells and part of chromosome 17 amplified in all ER+ cells. These loci encoded 30 genes that were overexpressed in ER+ cells; 9 of these genes were overexpressed in ER+ tumors. We identified 149 differentially expressed genes that exhibited differential methylation of one or more CpG islands within 5 kb of the 5′ end of the gene and for which mRNA abundance was inversely correlated with CpG island methylation status. In primary tumors we identified 84 genes that appear to be robust components of the methylation signature that we identified in ER+ cell lines. Our analyses reveal a global pattern of differential CpG island methylation that contributes to the transcriptome landscape of ER+ and ER− breast cancer cells and tumors. The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations.
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357
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Cai Q, Wen W, Qu S, Li G, Egan KM, Chen K, Deming SL, Shen H, Shen CY, Gammon MD, Blot WJ, Matsuo K, Haiman CA, Khoo US, Iwasaki M, Santella RM, Zhang L, Fair AM, Hu Z, Wu PE, Signorello LB, Titus-Ernstoff L, Tajima K, Henderson BE, Chan KYK, Kasuga Y, Newcomb PA, Zheng H, Cui Y, Wang F, Shieh YL, Iwata H, Le Marchand L, Chan SY, Shrubsole MJ, Trentham-Dietz A, Tsugane S, Garcia-Closas M, Long J, Li C, Shi J, Huang B, Xiang YB, Gao YT, Lu W, Shu XO, Zheng W. Replication and functional genomic analyses of the breast cancer susceptibility locus at 6q25.1 generalize its importance in women of chinese, Japanese, and European ancestry. Cancer Res 2011; 71:1344-55. [PMID: 21303983 DOI: 10.1158/0008-5472.can-10-2733] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We evaluated the generalizability of a single nucleotide polymorphism (SNP), rs2046210 (A/G allele), associated with breast cancer risk that was initially identified at 6q25.1 in a genome-wide association study conducted among Chinese women. In a pooled analysis of more than 31,000 women of East-Asian, European, and African ancestry, we found a positive association for rs2046210 and breast cancer risk in Chinese women [ORs (95% CI) = 1.30 (1.22-1.38) and 1.64 (1.50-1.80) for the AG and AA genotypes, respectively, P for trend = 1.54 × 10⁻³⁰], Japanese women [ORs (95% CI) = 1.31 (1.13-1.52) and 1.37 (1.06-1.76), P for trend = 2.51 × 10⁻⁴], and European-ancestry American women [ORs (95% CI) = 1.07 (0.99-1.16) and 1.18 (1.04-1.34), P for trend = 0.0069]. No association with this SNP, however, was observed in African American women [ORs (95% CI) = 0.81 (0.63-1.06) and 0.85 (0.65-1.11) for the AG and AA genotypes, respectively, P for trend = 0.4027]. In vitro functional genomic studies identified a putative functional variant, rs6913578. This SNP is 1,440 bp downstream of rs2046210 and is in high linkage disequilibrium with rs2046210 in Chinese (r(2) = 0.91) and European-ancestry (r² = 0.83) populations, but not in Africans (r² = 0.57). SNP rs6913578 was found to be associated with breast cancer risk in Chinese and European-ancestry American women. After adjusting for rs2046210, the association of rs6913578 with breast cancer risk in African Americans approached borderline significance. Results from this large consortium study confirmed the association of rs2046210 with breast cancer risk among women of Chinese, Japanese, and European ancestry. This association may be explained in part by a putatively functional variant (rs6913578) identified in the region.
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Affiliation(s)
- Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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358
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Fletcher O, Johnson N, dos Santos Silva I, Orr N, Ashworth A, Nevanlinna H, Heikkinen T, Aittomäki K, Blomqvist C, Burwinkel B, Bartram CR, Meindl A, Schmutzler RK, Cox A, Brock I, Elliott G, Reed MWR, Southey MC, Smith L, Spurdle AB, Hopper JL, Couch FJ, Olson JE, Wang X, Fredericksen Z, Schürmann P, Waltes R, Bremer M, Dörk T, Devilee P, van Asperen CJ, Tollenaar RAEM, Seynaeve C, Hall P, Czene K, Humphreys K, Liu J, Ahmed S, Dunning AM, Maranian M, Pharoah PDP, Chenevix-Trench G, Beesley J, Bogdanova NV, Antonenkova NN, Zalutsky IV, Anton-Culver H, Ziogas A, Brauch H, Ko YD, Hamann U, Fasching PA, Strick R, Ekici AB, Beckmann MW, Giles GG, Severi G, Baglietto L, English DR, Milne RL, Benítez J, Arias JI, Pita G, Nordestgaard BG, Bojesen SE, Flyger H, Kang D, Yoo KY, Noh DY, Mannermaa A, Kataja V, Kosma VM, García-Closas M, Chanock S, Lissowska J, Brinton LA, Chang-Claude J, Wang-Gohrke S, Broeks A, Schmidt MK, van Leeuwen FE, Van't Veer LJ, Margolin S, Lindblom A, Humphreys MK, Morrison J, Platte R, Easton DF, Peto J. Missense variants in ATM in 26,101 breast cancer cases and 29,842 controls. Cancer Epidemiol Biomarkers Prev 2011; 19:2143-51. [PMID: 20826828 DOI: 10.1158/1055-9965.epi-10-0374] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Truncating mutations in ATM have been shown to increase the risk of breast cancer but the effect of missense variants remains contentious. METHODS We have genotyped five polymorphic (minor allele frequency, 0.9-2.6%) missense single nucleotide polymorphisms (SNP) in ATM (S49C, S707P, F858L, P1054R, and L1420F) in 26,101 breast cancer cases and 29,842 controls from 23 studies in the Breast Cancer Association Consortium. RESULTS Combining the data from all five SNPs, the odds ratio (OR) was 1.05 for being a heterozygote for any of the SNPs and 1.51 for being a rare homozygote for any of the SNPs with an overall trend OR of 1.06 (P(trend) = 0.04). The trend OR among bilateral and familial cases was 1.12 (95% confidence interval, 1.02-1.23; P(trend) = 0.02). CONCLUSIONS In this large combined analysis, these five missense ATM SNPs were associated with a small increased risk of breast cancer, explaining an estimated 0.03% of the excess familial risk of breast cancer. IMPACT Testing the combined effects of rare missense variants in known breast cancer genes in large collaborative studies should clarify their overall contribution to breast cancer susceptibility.
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Affiliation(s)
- Olivia Fletcher
- British Breast Cancer Study, The Breakthrough Breast Cancer Research Centre, London, United Kingdom.
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359
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Li Y, Li Y, Wedrén S, Li G, Charn TH, Desai KV, Bonnard C, Czene K, Humphreys K, Darabi H, Einarsdóttir K, Heikkinen T, Aittomäki K, Blomqvist C, Chia KS, Nevanlinna H, Hall P, Liu ET, Liu J. Genetic variation of ESR1 and its co-activator PPARGC1B is synergistic in augmenting the risk of estrogen receptor-positive breast cancer. Breast Cancer Res 2011; 13:R10. [PMID: 21269472 PMCID: PMC3109578 DOI: 10.1186/bcr2817] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 12/03/2010] [Accepted: 01/26/2011] [Indexed: 12/27/2022] Open
Abstract
Introduction Given the role of estrogen in breast carcinogenesis and the modification of estrogen receptor (ER) activity by its biochemical cofactors, we hypothesize that genetic variation within ER cofactor genes alters cellular response to estrogen exposure and consequently modifies the risk for ER-positive breast cancer. Methods We genotyped 790 tagging SNPs within 60 ER cofactor genes in 1,257 cases and 1,464 controls from Sweden and in 2,215 cases and 1,265 controls from Finland, and tested their associations with either ER-positive or ER-negative breast cancer. Results Seven SNPs showed consistent association with ER-positive breast cancer in the two independent samples, and six of them were located within PPARGC1B, encoding an ER co-activator, with the strongest association at rs741581 (odds ratio = 1.41, P = 4.84 × 10-5) that survived Bonferroni correction for multiple testing in the combined ER-positive breast cancer sample (Pcorrected = 0.03). Moreover, we also observed significant synergistic interaction (Pinteraction = 0.008) between the genetic polymorphisms within PPARGC1B and ESR1 in ER-positive breast cancer. By contrast, no consistent association was observed in ER-negative breast cancer. Furthermore, we found that administration of estrogen in the MCF-7 cell line induced PPARGC1B expression and enhanced occupancies of ER and RNA polymerase II within the region of SNP association, suggesting the upregulation of PPARGC1B expression by ESR1 activation. Conclusions Our study revealed that DNA polymorphisms of PPARGC1B, coding a bona fide ER co-activator, are associated with ER-positive breast cancer risk. The feed-forward transcriptional regulatory loop between PPARGC1B and ESR1 further augments their protein interaction, which provides a plausible mechanistic explanation for the synergistic genetic interaction between PPARGC1B and ESR1 in ER-positive breast cancer. Our study also highlights that biochemically and genomically informed candidate gene studies can enhance the discovery of interactive disease susceptibility genes.
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Affiliation(s)
- Yuqing Li
- Human Genetics, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
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360
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Fletcher O, Johnson N, Orr N, Hosking FJ, Gibson LJ, Walker K, Zelenika D, Gut I, Heath S, Palles C, Coupland B, Broderick P, Schoemaker M, Jones M, Williamson J, Chilcott-Burns S, Tomczyk K, Simpson G, Jacobs KB, Chanock SJ, Hunter DJ, Tomlinson IP, Swerdlow A, Ashworth A, Ross G, dos Santos Silva I, Lathrop M, Houlston RS, Peto J. Novel breast cancer susceptibility locus at 9q31.2: results of a genome-wide association study. J Natl Cancer Inst 2011; 103:425-35. [PMID: 21263130 DOI: 10.1093/jnci/djq563] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified several common genetic variants associated with breast cancer risk. It is likely, however, that a substantial proportion of such loci have not yet been discovered. METHODS We compared 296,114 tagging single-nucleotide polymorphisms in 1694 breast cancer case subjects (92% with two primary cancers or at least two affected first-degree relatives) and 2365 control subjects, with validation in three independent series totaling 11,880 case subjects and 12,487 control subjects. Odds ratios (ORs) and associated 95% confidence intervals (CIs) in each stage and all stages combined were calculated using unconditional logistic regression. Heterogeneity was evaluated with Cochran Q and I(2) statistics. All statistical tests were two-sided. RESULTS We identified a novel risk locus for breast cancer at 9q31.2 (rs865686: OR = 0.89, 95% CI = 0.85 to 0.92, P = 1.75 × 10(-10)). This single-nucleotide polymorphism maps to a gene desert, the nearest genes being Kruppel-like factor 4 (KLF4, 636 kb centromeric), RAD23 homolog B (RAD23B, 794 kb centromeric), and actin-like 7A (ACTL7A, 736 kb telomeric). We also identified two variants (rs3734805 and rs9383938) mapping to 6q25.1 estrogen receptor 1 (ESR1), which were associated with breast cancer in subjects of northern European ancestry (rs3734805: OR = 1.19, 95% CI = 1.11 to 1.27, P = 1.35 × 10(-7); rs9383938: OR = 1.18, 95% CI = 1.11 to 1.26, P = 1.41 × 10(-7)). A variant mapping to 10q26.13, approximately 300 kb telomeric to the established risk locus within the second intron of FGFR2, was also associated with breast cancer risk, although not at genome-wide statistical significance (rs10510102: OR = 1.12, 95% CI = 1.07 to 1.17, P = 1.58 × 10(-6)). CONCLUSIONS These findings provide further evidence on the role of genetic variation in the etiology of breast cancer. Fine mapping will be needed to identify causal variants and to determine their functional effects.
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Affiliation(s)
- Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
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361
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Pérez-Losada J, Castellanos-Martín A, Mao JH. Cancer evolution and individual susceptibility. Integr Biol (Camb) 2011; 3:316-28. [PMID: 21264404 DOI: 10.1039/c0ib00094a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cancer susceptibility is due to interactions between inherited genetic factors and exposure to environmental carcinogens. The genetic component is constituted mainly by weakly acting low-penetrance genetic variants that interact among themselves, as well as with the environment. These low susceptibility genes can be categorized into two main groups: one includes those that control intrinsic tumor cell activities (i.e. apoptosis, proliferation or DNA repair), and the other contains those that modulate the function of extrinsic tumor cell compartments (i.e. stroma, angiogenesis, or endocrine and immune systems). Genome-Wide Association Studies (GWAS) of human populations have identified numerous genetic loci linked with cancer risk and behavior, but nevertheless the major component of cancer heritability remains to be explained. One reason may be that GWAS cannot readily capture gene-gene or gene-environment interactions. Mouse model approaches offer an alternative or complementary strategy, because of our ability to control both the genetic and environmental components of risk. Recently developed genetic tools, including high-throughput technologies such as SNP, CGH and gene expression microarrays, have led to more powerful strategies for refining quantitative trait loci (QTL) and identifying the critical genes. In particular, the cross-species approaches will help to refine locations of QTLs, and reveal their genetic and environmental interactions. The identification of human tumor susceptibility genes and discovery of their roles in carcinogenesis will ultimately be important for the development of methods for prediction of risk, diagnosis, prevention and therapy for human cancers.
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Affiliation(s)
- Jesús Pérez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Instituto Mixto Universidad de Salamanca/CSIC, Campus Miguel de Unamuno s/n, Salamanca, 37007, Spain.
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CHO WCS, 南 娟. [Recent progress in genetic variants associated with cancer and their implications in diagnostics development]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2011; 14:C1-5. [PMID: 21219822 PMCID: PMC6134425 DOI: 10.3779/j.issn.1009-3419.2011.01.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- William CS CHO
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong,William CS Cho, PhD, FIBMS, Chartered Scientist. Department of Clinical Oncology, Queen Elizabeth Hospital, 30 Gascoigne Road, Kowloon, Hong Kong Tel: +852 2958 5441; Fax: +852 2958 5455; E-mail:
| | - 娟 南
- 天津医科大学总医院,天津市肺癌研究所,天津市肺癌转移与肿瘤微环境重点实验室
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363
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Loizidou MA, Hadjisavvas A, Ioannidis JPA, Kyriacou K. Replication of genome-wide discovered breast cancer risk loci in the Cypriot population. Breast Cancer Res Treat 2011; 128:267-72. [PMID: 21210208 DOI: 10.1007/s10549-010-1319-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 12/18/2010] [Indexed: 01/08/2023]
Abstract
Genome-wide association studies (GWAS) have identified associations with robust statistical support for influencing breast cancer susceptibility. Most GWAS and replications have been conducted in Northern European populations and to a lesser extent in Asians, and Ashkenazi Jews. It is important to evaluate whether these variants confer risk across different populations and also to assess the magnitude of risk conferred. The aim of this study was to evaluate previously GWAS-identified breast cancer risk variants in the Cypriot population. Eleven GWAS-discovered single nucleotide polymorphisms (SNPs) were analyzed for association with breast cancer in 1,109 Cypriot female breast cancer patients and 1,177 healthy female controls. Four of the 11 SNPs evaluated were found to be nominally significantly associated (P < 0.05) with breast cancer risk in the Cypriot population. Based on estimated power, five associations would be expected to be nominally significant. The correlation coefficient of effect sizes (per-allele odds ratio) between the Cypriot population and the original GWAS populations where these SNPs had been discovered was 0.58 (P = 0.064), while allele frequencies were very similar (r = 0.88, P < 0.001). Overall, we show modest concordance for breast cancer GWAS-discovered alleles and their effect sizes in the Cypriot population. The effects sizes of GWAS-discovered SNPs need to be verified separately in different populations.
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Affiliation(s)
- Maria A Loizidou
- Department of Electron Microscope / Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Ayios Dometios, 23462, 1683, Nicosia, Cyprus
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Hosking FJ, Dobbins SE, Houlston RS. Genome-wide association studies for detecting cancer susceptibility. Br Med Bull 2011; 97:27-46. [PMID: 21247937 DOI: 10.1093/bmb/ldq038] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome-wide association (GWA) studies search for genetic variants, across the entire genome, which display differences in frequencies between cases and controls. Studies in PubMed using the keywords 'genomewide association' and 'cancer' are reported together with selected literature. Since 2007, GWA studies have successfully yielded risk loci for most common cancers. Findings have provided insights into the biological basis of cancer susceptibility implicating previously unsuspected genes in tumourogenesis. The variants identified typically account for only a small proportion of the familial risk of cancer and thus their application for individual risk prediction is poor. Furthermore, the genotyped variants are unlikely to be directly causal and identifying the causal basis is a major challenge. Methodological developments are desirable to fully utilize existing data sets and to enable more complex models of inherited predisposition to be investigated. Annotation of low frequency variation coupled with next-generation sequencing is making the search for rare disease-causing variants a realistic prospect.
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Affiliation(s)
- Fay J Hosking
- Section of Cancer Genetics, Institute of Cancer Research, Surrey, UK
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365
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Abstract
Epigenetic mechanisms alter the structure of local chromosome domains to dynamically regulate gene expression by signalling and propagating transcriptional states. Nuclear receptors, a stimulus-inducible class of transcription factors, interact with chromatin to regulate transcription. To promote transcription, nuclear receptors interact with genomic regulatory elements that are epigenetically marked by modified histone tails, DNA methylation status, histone variants, chromatin accessibility and long-range interactions. Advances in throughput have allowed the profiling of regulatory factor activity on a genome-wide scale, with recent evidence from genomic analyses highlighting novel aspects of DNA-binding factor actions on chromatin. In the present review, the current knowledge of the mechanisms regulating nuclear receptor occupancy at cis-regulatory elements is discussed, with particular emphasis on the glucocorticoid, oestrogen and androgen receptors. Epigenetic regulation of genomic elements direct cell-specific regulatory factor binding and contribute to human variation in factor occupancy. Through regulating nuclear receptor activity, the epigenome is a critical checkpoint in nuclear receptor induced gene expression in health and disease.
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Affiliation(s)
- S C Biddie
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Faculty of Medicine and Dentistry, University of Bristol, Bristol, UK.
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366
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Jiang Y, Han J, Liu J, Zhang G, Wang L, Liu F, Zhang X, Zhao Y, Pang D. Risk of genome-wide association study newly identified genetic variants for breast cancer in Chinese women of Heilongjiang Province. Breast Cancer Res Treat 2011; 128:251-7. [PMID: 21197568 DOI: 10.1007/s10549-010-1327-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Accepted: 12/20/2010] [Indexed: 12/30/2022]
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367
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Cho WCS. Recent progress in genetic variants associated with cancer and their implications in diagnostics development. Expert Rev Mol Diagn 2010; 10:699-703. [PMID: 20843192 DOI: 10.1586/erm.10.64] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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368
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Hartman M, Suo C, Lim WY, Miao H, Teo YY, Chia KS. Ability to predict breast cancer in Asian women using a polygenic susceptibility model. Breast Cancer Res Treat 2010; 127:805-12. [DOI: 10.1007/s10549-010-1279-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 11/18/2010] [Indexed: 01/14/2023]
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369
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Yamashita H, Iwase H, Toyama T, Takahashi S, Sugiura H, Yoshimoto N, Endo Y, Fujii Y, Kobayashi S. Estrogen receptor-positive breast cancer in Japanese women: trends in incidence, characteristics, and prognosis. Ann Oncol 2010; 22:1318-1325. [PMID: 21119029 DOI: 10.1093/annonc/mdq596] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The incidence of breast cancer in Japanese women has doubled in all age groups over the past two decades. PATIENTS AND METHODS We examined the characteristics of the tumors treated in three time periods between 1982 and 2010. Estrogen receptor (ER), progesterone receptor (PgR) and HER2 status were assessed by immunohistochemistry. Correlation of hormone receptor levels with clinicopathological factors and prognosis was analyzed in ER-positive, HER2-negative breast cancer in two age groups (≤50 years versus >50 years). RESULTS The frequency of ER-positive breast cancer in women aged 50 years or younger increased greatly over the interval studied (1982-1991: 52.5%, 1992-2001: 72.6%, 2002-2010: 87.1%, P < 0.0001). The frequency of ER-positive tumors also significantly increased in women over 50 years of age (1982-1991: 69.4%, 1992-2001: 73.3%, 2002-2010: 78.6%, P = 0.029). In ER-positive, HER2-negative breast cancer, tumor grade was negatively correlated with expression levels of ER and PgR. Prognosis for patients with ER-positive, HER2-negative disease significantly improved over time, due to advances in adjuvant therapies. CONCLUSION It is necessary to establish risk factors, both genetic and environmental, capable of predicting the risk of ER-positive breast cancer and thus enable the efficient selection of candidates for hormone receptor-targeted chemoprevention.
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Affiliation(s)
- H Yamashita
- Oncology, Immunology, and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya.
| | - H Iwase
- Department of Breast and Endocrine Surgery, Kumamoto University, Kumamoto
| | - T Toyama
- Oncology, Immunology, and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya
| | - S Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - H Sugiura
- Oncology, Immunology, and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya
| | - N Yoshimoto
- Oncology, Immunology, and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya
| | - Y Endo
- Oncology, Immunology, and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya
| | - Y Fujii
- Oncology, Immunology, and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya
| | - S Kobayashi
- Oncology, Immunology, and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya
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370
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Beeghly-Fadiel A, Shu XO, Lu W, Long J, Cai Q, Xiang YB, Zheng Y, Zhao Z, Gu K, Gao YT, Zheng W. Genetic variation in VEGF family genes and breast cancer risk: a report from the Shanghai Breast Cancer Genetics Study. Cancer Epidemiol Biomarkers Prev 2010; 20:33-41. [PMID: 21119072 DOI: 10.1158/1055-9965.epi-10-0793] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In addition to mediating aspects of physiologic and pathologic angiogenesis, the VEGF family also contributes to carcinogenesis. METHODS We comprehensively characterized genetic variation across four VEGF family genes and evaluated associations with breast cancer risk with odds ratios (OR) and 95% CIs for participants of the two-stage case-control Shanghai Breast Cancer Genetics Study (SBCGS). Stage 1 evaluated 200 single nucleotide polymorphisms (SNP) across two VEGF ligands (VEGFA and VEGFC) and two VEGF receptors (FLT1/VEGFR1 and KDR/VEGFR2) among 2,079 cases and 2,148 controls. Five SNPs with promising associations were assessed in stage 2 among 4,419 cases and 1,851 controls. RESULTS Two SNPs were consistently associated with breast cancer risk across our two study stages and were significant in combined analyses. Compared with FLT1 rs9551471 major allele homozygotes (AA), reduced risks were associated with AG (OR = 0.92, 95% CI: 0.84-1.00) and GG (OR = 0.78, 95% CI: 0.64-0.95) genotypes (P(trend) = 0.005). Compared with VEGFA rs833070 major allele carriers (CC or CT), increased risk was associated with TT genotypes (OR = 1.26, 95% CI: 1.05-1.52, P = 0.016). CONCLUSION Results from our study indicate that common genetic variation in VEGFA and FLT1 (VEGFR1) may contribute to breast cancer susceptibility. IMPACT Our findings provide clues for future studies on VEGF family genes in relation to cancer susceptibility and survival.
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Affiliation(s)
- Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
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Antoniou AC, Beesley J, McGuffog L, Sinilnikova OM, Healey S, Neuhausen SL, Ding YC, Rebbeck TR, Weitzel JN, Lynch HT, Isaacs C, Ganz PA, Tomlinson G, Olopade OI, Couch FJ, Wang X, Lindor NM, Pankratz VS, Radice P, Manoukian S, Peissel B, Zaffaroni D, Barile M, Viel A, Allavena A, Dall'Olio V, Peterlongo P, Szabo CI, Zikan M, Claes K, Poppe B, Foretova L, Mai PL, Greene MH, Rennert G, Lejbkowicz F, Glendon G, Ozcelik H, Andrulis IL, Thomassen M, Gerdes AM, Sunde L, Cruger D, Birk Jensen U, Caligo M, Friedman E, Kaufman B, Laitman Y, Milgrom R, Dubrovsky M, Cohen S, Borg A, Jernström H, Lindblom A, Rantala J, Stenmark-Askmalm M, Melin B, Nathanson K, Domchek S, Jakubowska A, Lubinski J, Huzarski T, Osorio A, Lasa A, Durán M, Tejada MI, Godino J, Benitez J, Hamann U, Kriege M, Hoogerbrugge N, van der Luijt RB, van Asperen CJ, Devilee P, Meijers-Heijboer EJ, Blok MJ, Aalfs CM, Hogervorst F, Rookus M, Cook M, Oliver C, Frost D, Conroy D, Evans DG, Lalloo F, Pichert G, Davidson R, Cole T, Cook J, Paterson J, Hodgson S, Morrison PJ, Porteous ME, Walker L, Kennedy MJ, Dorkins H, Peock S, Godwin AK, Stoppa-Lyonnet D, de Pauw A, Mazoyer S, Bonadona V, Lasset C, Dreyfus H, Leroux D, Hardouin A, Berthet P, Faivre L, Loustalot C, Noguchi T, Sobol H, Rouleau E, Nogues C, Frénay M, Vénat-Bouvet L, Hopper JL, Daly MB, Terry MB, John EM, Buys SS, Yassin Y, Miron A, Goldgar D, Singer CF, Dressler AC, Gschwantler-Kaulich D, Pfeiler G, Hansen TVO, Jønson L, Agnarsson BA, Kirchhoff T, Offit K, Devlin V, Dutra-Clarke A, Piedmonte M, Rodriguez GC, Wakeley K, Boggess JF, Basil J, Schwartz PE, Blank SV, Toland AE, Montagna M, Casella C, Imyanitov E, Tihomirova L, Blanco I, Lazaro C, Ramus SJ, Sucheston L, Karlan BY, Gross J, Schmutzler R, Wappenschmidt B, Engel C, Meindl A, Lochmann M, Arnold N, Heidemann S, Varon-Mateeva R, Niederacher D, Sutter C, Deissler H, Gadzicki D, Preisler-Adams S, Kast K, Schönbuchner I, Caldes T, de la Hoya M, Aittomäki K, Nevanlinna H, Simard J, Spurdle AB, Holland H, Chen X, Platte R, Chenevix-Trench G, Easton DF. Common breast cancer susceptibility alleles and the risk of breast cancer for BRCA1 and BRCA2 mutation carriers: implications for risk prediction. Cancer Res 2010; 70:9742-54. [PMID: 21118973 DOI: 10.1158/0008-5472.can-10-1907] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The known breast cancer susceptibility polymorphisms in FGFR2, TNRC9/TOX3, MAP3K1, LSP1, and 2q35 confer increased risks of breast cancer for BRCA1 or BRCA2 mutation carriers. We evaluated the associations of 3 additional single nucleotide polymorphisms (SNPs), rs4973768 in SLC4A7/NEK10, rs6504950 in STXBP4/COX11, and rs10941679 at 5p12, and reanalyzed the previous associations using additional carriers in a sample of 12,525 BRCA1 and 7,409 BRCA2 carriers. Additionally, we investigated potential interactions between SNPs and assessed the implications for risk prediction. The minor alleles of rs4973768 and rs10941679 were associated with increased breast cancer risk for BRCA2 carriers (per-allele HR = 1.10, 95% CI: 1.03-1.18, P = 0.006 and HR = 1.09, 95% CI: 1.01-1.19, P = 0.03, respectively). Neither SNP was associated with breast cancer risk for BRCA1 carriers, and rs6504950 was not associated with breast cancer for either BRCA1 or BRCA2 carriers. Of the 9 polymorphisms investigated, 7 were associated with breast cancer for BRCA2 carriers (FGFR2, TOX3, MAP3K1, LSP1, 2q35, SLC4A7, 5p12, P = 7 × 10(-11) - 0.03), but only TOX3 and 2q35 were associated with the risk for BRCA1 carriers (P = 0.0049, 0.03, respectively). All risk-associated polymorphisms appear to interact multiplicatively on breast cancer risk for mutation carriers. Based on the joint genotype distribution of the 7 risk-associated SNPs in BRCA2 mutation carriers, the 5% of BRCA2 carriers at highest risk (i.e., between 95th and 100th percentiles) were predicted to have a probability between 80% and 96% of developing breast cancer by age 80, compared with 42% to 50% for the 5% of carriers at lowest risk. Our findings indicated that these risk differences might be sufficient to influence the clinical management of mutation carriers.
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Affiliation(s)
- Antonis C Antoniou
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
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Caution in generalizing known genetic risk markers for breast cancer across all ethnic/racial populations. Eur J Hum Genet 2010; 19:243-5. [PMID: 21102626 DOI: 10.1038/ejhg.2010.185] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified common variants associated with breast cancer risk among women of European and Asian ancestries. To assess the generalizability across ethnic/racial populations of a risk score derived from genotyping 12 highly replicated breast cancer GWAS hits, we performed a case-control study (2224 cases and 2827 controls) nested in the Multiethnic Cohort (MEC) study, which was initiated in 1993-1996 and consists of subjects mainly from European-American, African-American, Native Hawaiian, Japanese and Latino populations. When viewed as a summary risk score, the total number of risk alleles carried by women was significantly associated with breast cancer risk overall (OR per allele, 1.09; 95% CI, 1.06-1.12; P=2.0 × 10(-10)) and in all populations except African-Americans, in which no significant association was observed (OR, 1.03; 95% CI, 0.98-1.08). In aggregate, the number of risk alleles is strongly associated with breast cancer risk in all populations studied except African-Americans. These results emphasize the need for large-scale association studies of multiple racial/ethnic groups for discovery and characterization of risk alleles relevant to all populations in the United States.
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373
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Bonifaci N, Górski B, Masojć B, Wokołorczyk D, Jakubowska A, Dębniak T, Berenguer A, Serra Musach J, Brunet J, Dopazo J, Narod SA, Lubiński J, Lázaro C, Cybulski C, Pujana MA. Exploring the link between germline and somatic genetic alterations in breast carcinogenesis. PLoS One 2010; 5:e14078. [PMID: 21124932 PMCID: PMC2989917 DOI: 10.1371/journal.pone.0014078] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 11/02/2010] [Indexed: 12/19/2022] Open
Abstract
Recent genome-wide association studies (GWASs) have identified candidate genes contributing to cancer risk through low-penetrance mutations. Many of these genes were unexpected and, intriguingly, included well-known players in carcinogenesis at the somatic level. To assess the hypothesis of a germline-somatic link in carcinogenesis, we evaluated the distribution of somatic gene labels within the ordered results of a breast cancer risk GWAS. This analysis suggested frequent influence on risk of genetic variation in loci encoding for "driver kinases" (i.e., kinases encoded by genes that showed higher somatic mutation rates than expected by chance and, therefore, whose deregulation may contribute to cancer development and/or progression). Assessment of these predictions using a population-based case-control study in Poland replicated the association for rs3732568 in EPHB1 (odds ratio (OR) = 0.79; 95% confidence interval (CI): 0.63-0.98; P(trend) = 0.031). Analyses by early age at diagnosis and by estrogen receptor α (ERα) tumor status indicated potential associations for rs6852678 in CDKL2 (OR = 0.32, 95% CI: 0.10-1.00; P(recessive) = 0.044) and rs10878640 in DYRK2 (OR = 2.39, 95% CI: 1.32-4.30; P(dominant) = 0.003), and for rs12765929, rs9836340, rs4707795 in BMPR1A, EPHA3 and EPHA7, respectively (ERα tumor status P(interaction)<0.05). The identification of three novel candidates as EPH receptor genes might indicate a link between perturbed compartmentalization of early neoplastic lesions and breast cancer risk and progression. Together, these data may lay the foundations for replication in additional populations and could potentially increase our knowledge of the underlying molecular mechanisms of breast carcinogenesis.
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Affiliation(s)
- Núria Bonifaci
- Biomarkers and Susceptibility Unit, Spanish Biomedical Research Centre Network for Epidemiology and Public Health, Catalan Institute of Oncology, L'Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet, Barcelona, Spain
| | - Bohdan Górski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Bartlomiej Masojć
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Dominika Wokołorczyk
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Tadeusz Dębniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Antoni Berenguer
- Biomarkers and Susceptibility Unit, Spanish Biomedical Research Centre Network for Epidemiology and Public Health, Catalan Institute of Oncology, L'Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet, Barcelona, Spain
| | - Jordi Serra Musach
- Biomarkers and Susceptibility Unit, Spanish Biomedical Research Centre Network for Epidemiology and Public Health, Catalan Institute of Oncology, L'Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet, Barcelona, Spain
| | - Joan Brunet
- Hereditary Cancer Programme, Catalan Institute of Oncology, IdIBGi, Girona, Spain
| | - Joaquín Dopazo
- Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe, Functional Genomics Node and Spanish Biomedical Research Centre Network for Rare Diseases, Valencia, Spain
| | - Steven A. Narod
- Womens College Research Institute, University of Toronto and Women's College Hospital, Toronto, Ontario, Canada
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Conxi Lázaro
- Hereditary Cancer Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Barcelona, Spain
| | - Cezary Cybulski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Miguel Angel Pujana
- Biomarkers and Susceptibility Unit, Spanish Biomedical Research Centre Network for Epidemiology and Public Health, Catalan Institute of Oncology, L'Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet, Barcelona, Spain
- Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Barcelona, Spain
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Li J, Humphreys K, Darabi H, Rosin G, Hannelius U, Heikkinen T, Aittomäki K, Blomqvist C, Pharoah PD, Dunning AM, Ahmed S, Hooning MJ, Hollestelle A, Oldenburg RA, Alfredsson L, Palotie A, Peltonen-Palotie L, Irwanto A, Low HQ, Teoh GH, Thalamuthu A, Kere J, D'Amato M, Easton DF, Nevanlinna H, Liu J, Czene K, Hall P. A genome-wide association scan on estrogen receptor-negative breast cancer. Breast Cancer Res 2010; 12:R93. [PMID: 21062454 PMCID: PMC3046434 DOI: 10.1186/bcr2772] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 10/06/2010] [Accepted: 11/09/2010] [Indexed: 12/20/2022] Open
Abstract
Introduction Breast cancer is a heterogeneous disease and may be characterized on the basis of whether estrogen receptors (ER) are expressed in the tumour cells. ER status of breast cancer is important clinically, and is used both as a prognostic indicator and treatment predictor. In this study, we focused on identifying genetic markers associated with ER-negative breast cancer risk. Methods We conducted a genome-wide association analysis of 285,984 single nucleotide polymorphisms (SNPs) genotyped in 617 ER-negative breast cancer cases and 4,583 controls. We also conducted a genome-wide pathway analysis on the discovery dataset using permutation-based tests on pre-defined pathways. The extent of shared polygenic variation between ER-negative and ER-positive breast cancers was assessed by relating risk scores, derived using ER-positive breast cancer samples, to disease state in independent, ER-negative breast cancer cases. Results Association with ER-negative breast cancer was not validated for any of the five most strongly associated SNPs followed up in independent studies (1,011 ER-negative breast cancer cases, 7,604 controls). However, an excess of small P-values for SNPs with known regulatory functions in cancer-related pathways was found (global P = 0.052). We found no evidence to suggest that ER-negative breast cancer shares a polygenic basis to disease with ER-positive breast cancer. Conclusions ER-negative breast cancer is a distinct breast cancer subtype that merits independent analyses. Given the clinical importance of this phenotype and the likelihood that genetic effect sizes are small, greater sample sizes and further studies are required to understand the etiology of ER-negative breast cancers.
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Affiliation(s)
- Jingmei Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden.
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375
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[Search for new genes involved in breast tumorigenesis by "Omics" analysis]. Bull Cancer 2010; 97:1365-80. [PMID: 21051317 DOI: 10.1684/bdc.2010.1212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The high heterogeneity of clinical, histological, biological and genetic features in breast cancer is due in part to the extreme molecular complexity of these tumors. This review article presents the major technological advances of the past ten years, in particular the development of microarray approaches, which have enabled genome-wide ("Omics") analysis of these tumors. Numerous genetic and epigenetic alterations involving a small number of altered signalling pathways (PI3K, NK-κB, FGF, etc.) have been described. The next decade will be even more prolific in terms of discovery with the advent of next-generation sequencing (NGS) technologies that will provide fast and low cost constitutional and somatic genome sequences. The full catalogue of somatic genetic alterations will result in a completely new individual management for breast cancer patients.
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376
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Turnbull C, Hines S, Renwick A, Hughes D, Pernet D, Elliott A, Seal S, Warren-Perry M, Gareth Evans D, Eccles D, Stratton MR, Rahman N. Mutation and association analysis of GEN1 in breast cancer susceptibility. Breast Cancer Res Treat 2010; 124:283-8. [PMID: 20512659 PMCID: PMC3632835 DOI: 10.1007/s10549-010-0949-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 05/11/2010] [Indexed: 10/19/2022]
Abstract
GEN1 was recently identified as a key Holliday junction resolvase involved in homologous recombination. Somatic truncating GEN1 mutations have been reported in two breast cancers. Together these data led to the proposition that GEN1 is a breast cancer predisposition gene. In this article we have formally investigated this hypothesis. We performed full-gene mutational analysis of GEN1 in 176 BRCA1/2-negative familial breast cancer samples and 159 controls. We genotyped six SNPs tagging the 30 common variants in the transcribed region of GEN1 in 3,750 breast cancer cases and 4,907 controls. Mutation analysis revealed one truncating variant, c.2515_2519delAAGTT, which was present in 4% of cases and 4% of controls. We identified control individuals homozygous for the deletion, demonstrating that the last 69 amino acids of GEN1 are dispensable for its function. We identified 17 other variants, but their frequency did not significantly differ between cases and controls. Analysis of 3,750 breast cancer cases and 4,907 controls demonstrated no evidence of significant association with breast cancer for six SNPs tagging the 30 common GEN1 variants. These data indicate that although it also plays a key role in double-strand DNA break repair, GEN1 does not make an appreciable contribution to breast cancer susceptibility by acting as a high- or intermediate-penetrance breast cancer predisposition gene like BRCA1, BRCA2, CHEK2, ATM, BRIP1 and PALB2 and that common GEN1 variants do not act as low-penetrance susceptibility alleles analogous to SNPs in FGFR2. Furthermore, our analyses demonstrate the importance of undertaking appropriate genetic investigations, typically full gene screening in cases and controls together with large-scale case-control association analyses, to evaluate the contribution of genes to cancer susceptibility.
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Affiliation(s)
- Clare Turnbull
- Section of Cancer Genetics, the Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
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Stadler ZK, Vijai J, Thom P, Kirchhoff T, Hansen NA, Kauff ND, Robson M, Offit K. Genome-wide Association Studies of Cancer Predisposition. Hematol Oncol Clin North Am 2010; 24:973-96. [DOI: 10.1016/j.hoc.2010.06.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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378
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A combined analysis of genome-wide association studies in breast cancer. Breast Cancer Res Treat 2010; 126:717-27. [PMID: 20872241 DOI: 10.1007/s10549-010-1172-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 09/09/2010] [Indexed: 01/03/2023]
Abstract
In an attempt to identify common disease susceptibility alleles for breast cancer, we performed a combined analysis of three genome-wide association studies (GWAS), involving 2,702 women of European ancestry with invasive breast cancer and 5,726 controls. Tests for association were performed for 285,984 SNPs. Evidence for association with SNPs in genes in specific pathways was assessed using a permutation-based approach. We confirmed associations with loci reported by previous GWAS on 1p11.2, 2q35, 3p, 5p12, 8q24, 10q23.13, 14q24.1 and 16q. Six SNPs with the strongest signals of association with breast cancer, and which have not been reported previously, were typed in two further studies; however, none of the associations could be confirmed. Suggestive evidence for an excess of associations was found for genes involved in the regulation of actin cytoskeleton, glycan degradation, alpha-linolenic acid metabolism, circadian rhythm, hematopoietic cell lineage and drug metabolism. Androgen and oestrogen metabolism, a pathway previously found to be associated with the development of postmenopausal breast cancer, was marginally significant (P = 0.051 [unadjusted]). These results suggest that further analysis of SNPs in these pathways may identify associations that would be difficult to detect through agnostic single SNP analyses. More effort focused in these aspects of oncology can potentially open up promising avenues for the understanding of breast cancer and its prevention.
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379
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Stadler ZK, Thom P, Robson ME, Weitzel JN, Kauff ND, Hurley KE, Devlin V, Gold B, Klein RJ, Offit K. Genome-wide association studies of cancer. J Clin Oncol 2010; 28:4255-67. [PMID: 20585100 PMCID: PMC2953976 DOI: 10.1200/jco.2009.25.7816] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 04/19/2010] [Indexed: 12/20/2022] Open
Abstract
Knowledge of the inherited risk for cancer is an important component of preventive oncology. In addition to well-established syndromes of cancer predisposition, much remains to be discovered about the genetic variation underlying susceptibility to common malignancies. Increased knowledge about the human genome and advances in genotyping technology have made possible genome-wide association studies (GWAS) of human diseases. These studies have identified many important regions of genetic variation associated with an increased risk for human traits and diseases including cancer. Understanding the principles, major findings, and limitations of GWAS is becoming increasingly important for oncologists as dissemination of genomic risk tests directly to consumers is already occurring through commercial companies. GWAS have contributed to our understanding of the genetic basis of cancer and will shed light on biologic pathways and possible new strategies for targeted prevention. To date, however, the clinical utility of GWAS-derived risk markers remains limited.
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Affiliation(s)
- Zsofia K. Stadler
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Peter Thom
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Mark E. Robson
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Jeffrey N. Weitzel
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Noah D. Kauff
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Karen E. Hurley
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Vincent Devlin
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Bert Gold
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Robert J. Klein
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
| | - Kenneth Offit
- From the Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, NY, NY; Division of Clinical Cancer Genetics, City of Hope, Duarte, CA; and the Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute–Frederick, Frederick, MD
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380
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Sakoda LC, Blackston CR, Doherty JA, Ray RM, Lin MG, Gao DL, Stalsberg H, Feng Z, Thomas DB, Chen C. Selected estrogen receptor 1 and androgen receptor gene polymorphisms in relation to risk of breast cancer and fibrocystic breast conditions among Chinese women. Cancer Epidemiol 2010; 35:48-55. [PMID: 20846920 DOI: 10.1016/j.canep.2010.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 08/12/2010] [Accepted: 08/14/2010] [Indexed: 11/16/2022]
Abstract
BACKGROUND Polymorphisms in sex hormone receptor-encoding genes may alter the activity of sex hormone receptors and thereby affect susceptibility to breast cancer and related outcomes. METHODS In a case-control study of women from Shanghai, China, we examined the risk of breast cancer and fibrocystic breast conditions associated with the ESR1 PvuII (rs2234693) and XbaI (rs9340799) and AR CAG repeat ((CAG)(n)) and GGC repeat ((GGC)(n)) polymorphisms among 614 women with breast cancer, 467 women with fibrocystic conditions, and 879 women without breast disease. We also evaluated whether risk differed by the presence/absence of proliferative changes (in the extratumoral epithelium or fibrocystic lesion), menopausal status, or body mass index (BMI). Age-adjusted odds ratios (ORs) and 95% confidence intervals (95% CI) were calculated using logistic regression. RESULTS Only associations with AR (CAG)(n) and (GGC)(n) genotypes were detected. Allocating AR (CAG)(n) genotypes into six categories, with the (CAG)(22-24)/(CAG)(22-24) genotype category designated as the reference group, the (CAG)(>24)/(CAG)(>24) genotype category was associated with an increased risk of fibrocystic breast conditions (OR, 1.8; 95% CI, 1.1-3.0). Relative to the AR (GGC)(17)/(GGC)(17) genotype, the (GGC)(17)/(GGC)(14) genotype was associated with elevated risks of incident breast cancer (OR, 2.6; 95% CI, 1.3-5.4) and fibrocystic conditions (OR, 2.3; 95% CI, 1.1-4.5). Results did not differ according to proliferation status, menopausal status, or BMI. CONCLUSION Although these data lend support for a link between AR variation and breast disease development, given the low frequency of the putative risk-conferring genotypes and other constraints, further confirmation of our results is needed.
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Affiliation(s)
- Lori C Sakoda
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
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381
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Shu XO, Long J, Cai Q, Qi L, Xiang YB, Cho YS, Tai ES, Li X, Lin X, Chow WH, Go MJ, Seielstad M, Bao W, Li H, Cornelis MC, Yu K, Wen W, Shi J, Han BG, Sim XL, Liu L, Qi Q, Kim HL, Ng DPK, Lee JY, Kim YJ, Li C, Gao YT, Zheng W, Hu FB. Identification of new genetic risk variants for type 2 diabetes. PLoS Genet 2010; 6:e1001127. [PMID: 20862305 PMCID: PMC2940731 DOI: 10.1371/journal.pgen.1001127] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 08/17/2010] [Indexed: 12/19/2022] Open
Abstract
Although more than 20 genetic susceptibility loci have been reported for type 2 diabetes (T2D), most reported variants have small to moderate effects and account for only a small proportion of the heritability of T2D, suggesting that the majority of inter-person genetic variation in this disease remains to be determined. We conducted a multistage, genome-wide association study (GWAS) within the Asian Consortium of Diabetes to search for T2D susceptibility markers. From 590,887 SNPs genotyped in 1,019 T2D cases and 1,710 controls selected from Chinese women in Shanghai, we selected the top 2,100 SNPs that were not in linkage disequilibrium (r2<0.2) with known T2D loci for in silico replication in three T2D GWAS conducted among European Americans, Koreans, and Singapore Chinese. The 5 most promising SNPs were genotyped in an independent set of 1,645 cases and 1,649 controls from Shanghai, and 4 of them were further genotyped in 1,487 cases and 3,316 controls from 2 additional Chinese studies. Consistent associations across all studies were found for rs1359790 (13q31.1), rs10906115 (10p13), and rs1436955 (15q22.2) with P-values (per allele OR, 95%CI) of 6.49×10−9 (1.15, 1.10–1.20), 1.45×10−8 (1.13, 1.08–1.18), and 7.14×10−7 (1.13, 1.08–1.19), respectively, in combined analyses of 9,794 cases and 14,615 controls. Our study provides strong evidence for a novel T2D susceptibility locus at 13q31.1 and the presence of new independent risk variants near regions (10p13 and 15q22.2) reported by previous GWAS. Type 2 diabetes, a complex disease affecting more than a billion people worldwide, is believed to be caused by both environmental and genetic factors. Although some studies have shown that certain genes may make some people more susceptible to type 2 diabetes than others, the genes reported to date have only a small effect and account for a small proportion of type 2 diabetes cases. Furthermore, few of these studies have been conducted in Asian populations, although Asians are known to be more susceptible to insulin resistance than people living in Western countries, and incidence of type 2 diabetes has been increasing alarmingly in Asian countries. We conducted a multi-stage study involving 9,794 type 2 diabetes cases and 14,615 controls, predominantly Asians, to discover genes related to susceptibility to type 2 diabetes. We identified 3 genetic regions that are related to increased risk of type 2 diabetes.
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Affiliation(s)
- Xiao Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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382
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Long J, Shu XO, Cai Q, Gao YT, Zheng Y, Li G, Li C, Gu K, Wen W, Xiang YB, Lu W, Zheng W. Evaluation of breast cancer susceptibility loci in Chinese women. Cancer Epidemiol Biomarkers Prev 2010; 19:2357-65. [PMID: 20699374 PMCID: PMC2936687 DOI: 10.1158/1055-9965.epi-10-0054] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Recent genome-wide association studies (GWAS), mostly conducted among women of European ancestry, have identified 16 single-nucleotide polymorphisms (SNP) associated with breast cancer. METHODS We evaluated these SNPs with the risk of breast cancer and further by estrogen receptor status in a population-based study of 6,498 cases and 3,999 controls in Chinese women. We also searched for novel genetic risk variants in four loci, 2q35, 5p12/MRPS30, 8q24.21, and 17q23.2/COX11, in a two-stage study. In stage I, 868 SNPs were analyzed in 2,073 cases and 2,084 controls. In stage II, 58 SNPs selected from stage I were evaluated, including 4,425 cases and 1,915 controls. RESULTS Statistically significant associations (P < 0.05) were observed for eight GWAS-identified SNPs, including rs4973768 (3p24/SLC4A7), rs889312 (5q11.2MAP3K1), rs2046210 (6q25.1), rs1219648 (10q26.13/FGFR2), rs2981582 (10q26.13/FGFR2), rs3817198 (11p15.5/LSP1), rs8051542 (16q12.1/TOX3), and rs3803662 (16q12.1/TOX3). Two additional SNPs, rs10941679 (5p12/MRPS30) and rs13281615 (8q24.21), showed a marginally significant association. Some of these associations varied by estrogen receptor status. In the fine-mapping analysis, five SNPs showed a consistent association with breast cancer risk in both stages: rs10169372 (2q35), rs283720 (8q24.21), rs10515083 (17q23.2/COX11), rs16955329 (17q23.2/COX11), and rs2787487 (17q23.2/COX11). CONCLUSIONS This study shows that approximately half of the SNPs initially reported from GWAS of breast cancer in European descendants can be directly replicated in Chinese. Our fine-mapping analyses revealed several candidates of risk variants that can be further evaluated in studies with a larger sample size. IMPACT Findings from this study may help guide future fine-mapping studies to identify causal variants for breast cancer.
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Affiliation(s)
- Jirong Long
- Division of Epidemiology, Department ofMedicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203-1738, USA.
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383
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MMP9 polymorphisms and breast cancer risk: a report from the Shanghai Breast Cancer Genetics Study. Breast Cancer Res Treat 2010; 126:507-13. [PMID: 20725776 DOI: 10.1007/s10549-010-1119-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 08/06/2010] [Indexed: 10/19/2022]
Abstract
In addition to tumor invasion and angiogenesis, matrix metalloproteinase (MMP)9 also contributes to carcinogenesis and tumor growth. Genetic variation that may influence MMP9 expression was evaluated among participants of the Shanghai Breast Cancer Genetics Study (SBCGS) for associations with breast cancer susceptibility. In stage 1, 11 MMP9 single nucleotide polymorphisms (SNPs) were genotyped by the Affymetrix Targeted Genotyping System and/or the Affymetrix Genome-Wide Human SNP Array 6.0 among 4,227 SBCGS participants. One SNP was further genotyped using the Sequenom iPLEX MassARRAY platform among an additional 6,270 SBCGS participants. Associations with breast cancer risk were evaluated by odds ratios (OR) and 95% confidence intervals (CI) from logistic regression models that included adjustment for age, education, and genotyping stage when appropriate. In Stage 1, rare allele homozygotes for a promoter SNP (rs3918241) or a non-synonymous SNP (rs2274756, R668Q) tended to occur more frequently among breast cancer cases (P value = 0.116 and 0.056, respectively). Given their high linkage disequilibrium (D' = 1.0, r (2) = 0.97), one (rs3918241) was selected for additional analysis. An association with breast cancer risk was not supported by additional Stage 2 genotyping. In combined analysis, no elevated risk of breast cancer among homozygotes was found (OR: 1.2, 95% CI: 0.8-1.8). Common genetic variation in MMP9 was not found to be significantly associated with breast cancer susceptibility among participants of the Shanghai Breast Cancer Genetics Study.
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384
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Diamandis M, White NMA, Yousef GM. Personalized medicine: marking a new epoch in cancer patient management. Mol Cancer Res 2010; 8:1175-87. [PMID: 20693306 DOI: 10.1158/1541-7786.mcr-10-0264] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Personalized medicine (PM) is defined as "a form of medicine that uses information about a person's genes, proteins, and environment to prevent, diagnose, and treat disease." The promise of PM has been on us for years. The suite of clinical applications of PM in cancer is broad, encompassing screening, diagnosis, prognosis, prediction of treatment efficacy, patient follow-up after surgery for early detection of recurrence, and the stratification of patients into cancer subgroup categories, allowing for individualized therapy. PM aims to eliminate the "one size fits all" model of medicine, which has centered on reaction to disease based on average responses to care. By dividing patients into unique cancer subgroups, treatment and follow-up can be tailored for each individual according to disease aggressiveness and the ability to respond to a certain treatment. PM is also shifting the emphasis of patient management from primary patient care to prevention and early intervention for high-risk individuals. In addition to classic single molecular markers, high-throughput approaches can be used for PM including whole genome sequencing, single-nucleotide polymorphism analysis, microarray analysis, and mass spectrometry. A common trend among these tools is their ability to analyze many targets simultaneously, thus increasing the sensitivity, specificity, and accuracy of biomarker discovery. Certain challenges need to be addressed in our transition to PM including assessment of cost, test standardization, and ethical issues. It is clear that PM will gradually continue to be incorporated into cancer patient management and will have a significant impact on our health care in the future.
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Affiliation(s)
- Maria Diamandis
- Department of Laboratory Medicine, University of Toronto, Toronto, Canada
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385
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Barnholtz-Sloan JS, Shetty PB, Guan X, Nyante SJ, Luo J, Brennan DJ, Millikan RC. FGFR2 and other loci identified in genome-wide association studies are associated with breast cancer in African-American and younger women. Carcinogenesis 2010; 31:1417-23. [PMID: 20554749 PMCID: PMC2950798 DOI: 10.1093/carcin/bgq128] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 05/28/2010] [Accepted: 06/11/2010] [Indexed: 01/21/2023] Open
Abstract
Twenty-nine single-nucleotide polymorphisms (SNPs) from previously published genome-wide association studies (GWAS) and multiple ancestry informative markers were genotyped in the Carolina Breast Cancer Study (CBCS) (742 African-American (AA) cases, 1230 White cases; 658 AA controls, 1118 White controls). In the entire study population, 9/10 SNPs in fibroblast growth factor receptor 2 (FGFR2) were significantly associated with breast cancer after adjusting for age, race and European ancestry [odds ratios (OR) range 1.17-1.81]. Associations were observed for SNPs in FGFR2, LSP1, H19, TLR1/TLR6 and RELN for AA; FGFR2, TNRC9, H19 and MAP3K1 for Whites; FGFR2, TNRC9, Msc5A1 and chromosome 8q for women > or =50 years old and FGFR2 and TNRC9 for women <50 years old. FGFR2 haplotypes based upon rs11200014, rs2981579, rs1219648 and rs2420946 were associated with increased risk of breast cancer, including the GTGT haplotype in AAs [OR = 1.27, 95% confidence interval (CI) 1.04-1.56] and younger women of either race [OR = 1.35, 95% CI 1.02-1.78) and the ATGT haplotype in Whites (OR = 1.30, 95% CI 1.15-1.46). Recent GWAS hits for breast cancer in Europeans and Whites (i.e. women of European descent) thus showed evidence of replication among AAs and Whites in the CBCS. Several new haplotypes were associated with breast cancer in AA and younger women, particularly the FGFR2 GTGT haplotype. These results highlight the need to conduct GWAS among younger women and in a variety of racial-ethnic populations.
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Affiliation(s)
- Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106-5065, USA.
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386
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Shi J, Long J, Gao YT, Lu W, Cai Q, Wen W, Zheng Y, Yu K, Xiang YB, Hu FB, Zheng W, Shu XO. Evaluation of genetic susceptibility loci for obesity in Chinese women. Am J Epidemiol 2010; 172:244-54. [PMID: 20616199 DOI: 10.1093/aje/kwq129] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recent genome-wide association (GWA) studies have identified 18 genetic loci for obesity. Using directly observed and imputed GWA genotyping data on approximately 5,000 Chinese women (1996-2007), the authors evaluated 17 single nucleotide polymorphisms (SNPs) that represent 17 distinct obesity loci. Two SNPs near the BAT2 and MC4R genes and 3 SNPs within the FTO, SEC16B, and SH2B1 genes were significantly associated with body mass index (weight (kg)/height (m)(2)), body weight, and the prevalence of obesity. The per-allele increase in body mass index ranged from 0.16 units (BAT2) to 0.38 units (SH2B1). Odds ratios for obesity ranged from 1.46 (95% confidence interval (CI): 1.12, 1.92) for BAT2 to 2.16 (95% CI: 1.39, 3.37) for MC4R. A genetic risk score calculated by summing the number of risk-increasing alleles that each woman carried at these 5 loci was significantly associated with the prevalence of obesity. Women carrying 5 or more risk alleles had a 3.13-fold (95% CI: 2.06, 4.77) higher prevalence of obesity than women carrying 1 or no risk alleles. Results from this study extend some previous GWA findings to Chinese women and show the need for additional studies to identify susceptibility loci in Chinese and other Asian populations.
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Affiliation(s)
- Jiajun Shi
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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387
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Boada M, Antunez C, López-Arrieta J, Caruz A, Moreno-Rey C, Ramírez-Lorca R, Morón FJ, Hernández I, Mauleón A, Rosende-Roca M, Martínez-Lage P, Marín J, Tárraga L, Alegret M, Pedrajas JR, Urda N, Royo JL, Saez ME, Gayán J, González-Pérez A, Real LM, Ruiz A, Galán JJ. Estrogen receptor alpha gene variants are associated with Alzheimer's disease. Neurobiol Aging 2010; 33:198.e15-24. [PMID: 20674091 DOI: 10.1016/j.neurobiolaging.2010.06.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 05/19/2010] [Accepted: 06/21/2010] [Indexed: 11/19/2022]
Abstract
The present research is aimed at assessing the role of 3 estrogen receptor alpha (ESR1) gene variants in late onset Alzheimer's disease (AD) susceptibility. One thousand one hundred thirteen unrelated late onset sporadic AD patients, 1109 healthy controls and 121 neurologically healthy elderly controls were used to carry out case-control genetic association studies with ESR1 rs3844508, rs2234693, and ESR1 noncoding deletion 1 (ESR1-NCD1) polymorphisms. Thirty-five healthy male samples were used for molecular analyses. The rs2234693 polymorphism is associated with AD in our population (odds ratio [OR], 1.29; p = 0.008). The rs3844508 marker confers protection against AD in males (OR, 0.57; p = 0.001) and the deletion ESR1-NCD1 is a risk factor for AD in women (OR, 1.67; p < 0.001). Molecular analyses on ESR1-NCD1 indicate that this deletion confers a higher response to estradiol activity on ESR1 receptor and it is also associated with differential expression of ESR1 isoforms. Our results support the involvement of ESR1 gene in AD and point to the existence of sexual dimorphism for ESR1 markers. In addition, carriers of ESR1-NCD1 deletion could overrespond to estradiol action.
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Affiliation(s)
- Mercé Boada
- ACE Foundation, Catalan Institute of Applied Neurosciences, Barcelona, Spain
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388
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Stacey SN, Sulem P, Zanon C, Gudjonsson SA, Thorleifsson G, Helgason A, Jonasdottir A, Besenbacher S, Kostic JP, Fackenthal JD, Huo D, Adebamowo C, Ogundiran T, Olson JE, Fredericksen ZS, Wang X, Look MP, Sieuwerts AM, Martens JWM, Pajares I, Garcia-Prats MD, Ramon-Cajal JM, de Juan A, Panadero A, Ortega E, Aben KKH, Vermeulen SH, Asadzadeh F, van Engelenburg KCA, Margolin S, Shen CY, Wu PE, Försti A, Lenner P, Henriksson R, Johansson R, Enquist K, Hallmans G, Jonsson T, Sigurdsson H, Alexiusdottir K, Gudmundsson J, Sigurdsson A, Frigge ML, Gudmundsson L, Kristjansson K, Halldorsson BV, Styrkarsdottir U, Gulcher JR, Hemminki K, Lindblom A, Kiemeney LA, Mayordomo JI, Foekens JA, Couch FJ, Olopade OI, Gudbjartsson DF, Thorsteinsdottir U, Rafnar T, Johannsson OT, Stefansson K. Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus. PLoS Genet 2010; 6:e1001029. [PMID: 20661439 PMCID: PMC2908678 DOI: 10.1371/journal.pgen.1001029] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 06/16/2010] [Indexed: 12/31/2022] Open
Abstract
We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor α (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case∶control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively). Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2×10−3), African (OR = 1.35, P = 0.014), and Asian (OR = 1.23, P = 2.9×10−4) population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9×10−7), was without significant heterogeneity between ancestries (Phet = 0.36) and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268), which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping. In genome-wide association studies of disease susceptibility, there is no particular expectation that a genotyped SNP showing an association is itself a pathogenic variant. Rather, it is more likely that a SNP giving a signal does so because it is in linkage disequilibrium (LD) with a pathogenic variant. When the analysis is shifted to a population of another ancestry, the tagging relationship between the genotyped SNP and the pathogenic variant may be disrupted, due to differing patterns of LD between populations. Thus, it is not straightforward to determine whether a susceptibility locus identified in one ancestral population is also associated with risk in another. Moreover, the differing patterns of LD between ancestral populations can be used to gain resolution in genetic mapping. We refer to this approach as ancestry-shift refinement mapping. Here, we apply it to a breast cancer risk variant near the estrogen receptor α gene that was initially described in a Chinese population. We show that the tagging relationship between the originally described SNP rs2046210 and the pathogenic variant(s) is not maintained in Europeans and Africans. We identify a SNP, rs9397435, that is associated with breast cancer risk in populations of Asian, European, and African ancestry.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - James D. Fackenthal
- Department of Medicine and Center for Clinical Cancer Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Dezheng Huo
- Department of Medicine and Center for Clinical Cancer Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Clement Adebamowo
- Division of Oncology, Department of Surgery, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Oyo, Nigeria
| | - Temidayo Ogundiran
- Division of Oncology, Department of Surgery, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Oyo, Nigeria
| | - Janet E. Olson
- Department of Laboratory Medicine and Pathology and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Zachary S. Fredericksen
- Department of Laboratory Medicine and Pathology and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Maxime P. Look
- Department of Medical Oncology, Erasmus MC Rotterdam, Josephine Nefkens Institute and Cancer Genomics Center, Rotterdam, The Netherlands
| | - Anieta M. Sieuwerts
- Department of Medical Oncology, Erasmus MC Rotterdam, Josephine Nefkens Institute and Cancer Genomics Center, Rotterdam, The Netherlands
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Rotterdam, Josephine Nefkens Institute and Cancer Genomics Center, Rotterdam, The Netherlands
| | - Isabel Pajares
- Division of Medical Oncology, University Hospital, Zaragoza, Spain
| | | | - Jose M. Ramon-Cajal
- Divisions of Surgical Pathology and Gynecology, San Jorge Hospital, Huesca, Spain
| | - Ana de Juan
- Division of Medical Oncology, Marques de Valdecilla University Hospital, Santander, Spain
| | - Angeles Panadero
- Division of Medical Oncology, Hospital Ciudad de Coria, Coria, Spain
| | - Eugenia Ortega
- Division of Medical Oncology, University Hospital, Lérida, Spain
| | - Katja K. H. Aben
- Comprehensive Cancer Centre IKO, Nijmegen, The Netherlands
- Department of Epidemiology, Biostatistics and Health Technology Assessment, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Sita H. Vermeulen
- Department of Epidemiology, Biostatistics and Health Technology Assessment, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Fatemeh Asadzadeh
- Department of Epidemiology, Biostatistics and Health Technology Assessment, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | | - Sara Margolin
- Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Environmental Science, China Medical University, Taichung, Taiwan
| | - Pei-Ei Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden
| | - Per Lenner
- Department of Oncology, Norrlands University Hospital, Umeå, Sweden
| | - Roger Henriksson
- Department of Oncology, Norrlands University Hospital, Umeå, Sweden
| | - Robert Johansson
- Department of Oncology, Norrlands University Hospital, Umeå, Sweden
| | - Kerstin Enquist
- Department of Public Health and Clinical Medicine/Nutritional Research, Umeå University, Umeå, Sweden
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine/Nutritional Research, Umeå University, Umeå, Sweden
| | - Thorvaldur Jonsson
- Departments of Oncology, Surgery, and The Cancer Center, Landspitali-University Hospital, Reykjavik, Iceland
| | - Helgi Sigurdsson
- Departments of Oncology, Surgery, and The Cancer Center, Landspitali-University Hospital, Reykjavik, Iceland
| | - Kristin Alexiusdottir
- deCODE Genetics, Reykjavik, Iceland
- Departments of Oncology, Surgery, and The Cancer Center, Landspitali-University Hospital, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Lambertus A. Kiemeney
- Comprehensive Cancer Centre IKO, Nijmegen, The Netherlands
- Department of Epidemiology, Biostatistics and Health Technology Assessment, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Department of Urology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Jose I. Mayordomo
- Division of Medical Oncology, University Hospital, Zaragoza, Spain
- Health Science Institute, Nanotechnology Institute of Aragon, Zaragoza, Spain
| | - John A. Foekens
- Department of Medical Oncology, Erasmus MC Rotterdam, Josephine Nefkens Institute and Cancer Genomics Center, Rotterdam, The Netherlands
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Olufunmilayo I. Olopade
- Department of Medicine and Center for Clinical Cancer Genetics, University of Chicago, Chicago, Illinois, United States of America
| | | | | | | | - Oskar T. Johannsson
- Departments of Oncology, Surgery, and The Cancer Center, Landspitali-University Hospital, Reykjavik, Iceland
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Canzian F, Cox DG, Setiawan VW, Stram DO, Ziegler RG, Dossus L, Beckmann L, Blanché H, Barricarte A, Berg CD, Bingham S, Buring J, Buys SS, Calle EE, Chanock SJ, Clavel-Chapelon F, DeLancey JOL, Diver WR, Dorronsoro M, Haiman CA, Hallmans G, Hankinson SE, Hunter DJ, Hüsing A, Isaacs C, Khaw KT, Kolonel LN, Kraft P, Le Marchand L, Lund E, Overvad K, Panico S, Peeters PHM, Pollak M, Thun MJ, Tjønneland A, Trichopoulos D, Tumino R, Yeager M, Hoover RN, Riboli E, Thomas G, Henderson BE, Kaaks R, Feigelson HS. Comprehensive analysis of common genetic variation in 61 genes related to steroid hormone and insulin-like growth factor-I metabolism and breast cancer risk in the NCI breast and prostate cancer cohort consortium. Hum Mol Genet 2010; 19:3873-84. [PMID: 20634197 DOI: 10.1093/hmg/ddq291] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
There is extensive evidence that increases in blood and tissue concentrations of steroid hormones and of insulin-like growth factor I (IGF-I) are associated with breast cancer risk. However, studies of common variation in genes involved in steroid hormone and IGF-I metabolism have yet to provide convincing evidence that such variants predict breast cancer risk. The Breast and Prostate Cancer Cohort Consortium (BPC3) is a collaboration of large US and European cohorts. We genotyped 1416 tagging single nucleotide polymorphisms (SNPs) in 37 steroid hormone metabolism genes and 24 IGF-I pathway genes in 6292 cases of breast cancer and 8135 controls, mostly Caucasian, postmenopausal women from the BPC3. We also imputed 3921 additional SNPs in the regions of interest. None of the SNPs tested was significantly associated with breast cancer risk, after correction for multiple comparisons. The results remained null when cases and controls were stratified by age at diagnosis/recruitment, advanced or nonadvanced disease, body mass index, with or without in situ cases; or restricted to Caucasians. Among 770 estrogen receptor-negative cases, an SNP located 3' of growth hormone receptor (GHR) was marginally associated with increased risk after correction for multiple testing (P(trend) = 1.5 × 10(-4)). We found no significant overall associations between breast cancer and common germline variation in 61 genes involved in steroid hormone and IGF-I metabolism in this large, comprehensive study. Although previous studies have shown that variations in these genes can influence endogenous hormone levels, the magnitude of the effect of single SNPs does not appear to be sufficient to alter breast cancer risk.
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Affiliation(s)
- Federico Canzian
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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390
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Wang X, Pankratz VS, Fredericksen Z, Tarrell R, Karaus M, McGuffog L, Pharaoh PD, Ponder BA, Dunning AM, Peock S, Cook M, Oliver C, Frost D, Sinilnikova OM, Stoppa-Lyonnet D, Mazoyer S, Houdayer C, Hogervorst FB, Hooning MJ, Ligtenberg MJ, Spurdle A, Chenevix-Trench G, Schmutzler RK, Wappenschmidt B, Engel C, Meindl A, Domchek SM, Nathanson KL, Rebbeck TR, Singer CF, Gschwantler-Kaulich D, Dressler C, Fink A, Szabo CI, Zikan M, Foretova L, Claes K, Thomas G, Hoover RN, Hunter DJ, Chanock SJ, Easton DF, Antoniou AC, Couch FJ. Common variants associated with breast cancer in genome-wide association studies are modifiers of breast cancer risk in BRCA1 and BRCA2 mutation carriers. Hum Mol Genet 2010; 19:2886-97. [PMID: 20418484 PMCID: PMC2893806 DOI: 10.1093/hmg/ddq174] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 04/21/2010] [Indexed: 12/19/2022] Open
Abstract
Recent studies have identified single nucleotide polymorphisms (SNPs) that significantly modify breast cancer risk in BRCA1 and BRCA2 mutation carriers. Since these risk modifiers were originally identified as genetic risk factors for breast cancer in genome-wide association studies (GWASs), additional risk modifiers for BRCA1 and BRCA2 may be identified from promising signals discovered in breast cancer GWAS. A total of 350 SNPs identified as candidate breast cancer risk factors (P < 1 x 10(-3)) in two breast cancer GWAS studies were genotyped in 3451 BRCA1 and 2006 BRCA2 mutation carriers from nine centers. Associations with breast cancer risk were assessed using Cox models weighted for penetrance. Eight SNPs in BRCA1 carriers and 12 SNPs in BRCA2 carriers, representing an enrichment over the number expected, were significantly associated with breast cancer risk (P(trend) < 0.01). The minor alleles of rs6138178 in SNRPB and rs6602595 in CAMK1D displayed the strongest associations in BRCA1 carriers (HR = 0.78, 95% CI: 0.69-0.90, P(trend) = 3.6 x 10(-4) and HR = 1.25, 95% CI: 1.10-1.41, P(trend) = 4.2 x 10(-4)), whereas rs9393597 in LOC134997 and rs12652447 in FBXL7 showed the strongest associations in BRCA2 carriers (HR = 1.55, 95% CI: 1.25-1.92, P(trend) = 6 x 10(-5) and HR = 1.37, 95% CI: 1.16-1.62, P(trend) = 1.7 x 10(-4)). The magnitude and direction of the associations were consistent with the original GWAS. In subsequent risk assessment studies, the loci appeared to interact multiplicatively for breast cancer risk in BRCA1 and BRCA2 carriers. Promising candidate SNPs from GWAS were identified as modifiers of breast cancer risk in BRCA1 and BRCA2 carriers. Upon further validation, these SNPs together with other genetic and environmental factors may improve breast cancer risk assessment in these populations.
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Affiliation(s)
- Xianshu Wang
- Department of Laboratory Medicine and Pathology and
| | | | | | - Robert Tarrell
- Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Mary Karaus
- Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Lesley McGuffog
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | | | | | | | - Susan Peock
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - Margaret Cook
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - Clare Oliver
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - Debra Frost
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - EMBRACE
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - Olga M. Sinilnikova
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | - Dominique Stoppa-Lyonnet
- INSERM U509, Service de Génétique Oncologique, Institut Curie, Université Paris-Descartes, Paris, France
| | - Sylvie Mazoyer
- Equipe labellisée LIGUE 2008, UMR5201 CNRS, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Claude Houdayer
- INSERM U509, Service de Génétique Oncologique, Institut Curie, Université Paris-Descartes, Paris, France
| | - GEMO
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
- INSERM U509, Service de Génétique Oncologique, Institut Curie, Université Paris-Descartes, Paris, France
| | - Frans B.L. Hogervorst
- Department of Pathology, Family Cancer Clinic, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maartje J. Hooning
- Department of Medical Oncology, Rotterdam Family Cancer Clinic, Erasmus, The Netherlands
| | | | - HEBON
- Department of Pathology, Family Cancer Clinic, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Amanda Spurdle
- Queensland Institute of Medical Research, Brisbane, QLD 4029, Australia
| | | | - kConFab
- kConFab (Kathleen Cunningham Foundation Consortium for Research into Familial Breast Cancer), Peter MacCallum Cancer Institute, Melbourne, VIC 3002, Australia
| | - Rita K. Schmutzler
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Barbara Wappenschmidt
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Christoph Engel
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Alfons Meindl
- Department of Obstetrics and Gynaecology, Klinikum rechts der Isar, Technical University, Munich, Germany
| | | | | | | | | | | | | | | | | | - Michal Zikan
- Department of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Kathleen Claes
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Gilles Thomas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David J. Hunter
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA and
| | - Stephen J. Chanock
- Advanced Technology Center, National Cancer Institute, Gaithersburg, MD, USA
| | - Douglas F. Easton
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - Antonis C. Antoniou
- Department of Public Health and Primary Care, Cancer Research UK Genetic Epidemiology Unit and
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology and
- Health Sciences Research, Mayo Clinic, Rochester, MN, USA
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391
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Long J, Cai Q, Shu XO, Qu S, Li C, Zheng Y, Gu K, Wang W, Xiang YB, Cheng J, Chen K, Zhang L, Zheng H, Shen CY, Huang CS, Hou MF, Shen H, Hu Z, Wang F, Deming SL, Kelley MC, Shrubsole MJ, Khoo US, Chan KYK, Chan SY, Haiman CA, Henderson BE, Le Marchand L, Iwasaki M, Kasuga Y, Tsugane S, Matsuo K, Tajima K, Iwata H, Huang B, Shi J, Li G, Wen W, Gao YT, Lu W, Zheng W. Identification of a functional genetic variant at 16q12.1 for breast cancer risk: results from the Asia Breast Cancer Consortium. PLoS Genet 2010; 6:e1001002. [PMID: 20585626 PMCID: PMC2891809 DOI: 10.1371/journal.pgen.1001002] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 05/25/2010] [Indexed: 11/18/2022] Open
Abstract
Genetic factors play an important role in the etiology of breast cancer. We carried out a multi-stage genome-wide association (GWA) study in over 28,000 cases and controls recruited from 12 studies conducted in Asian and European American women to identify genetic susceptibility loci for breast cancer. After analyzing 684,457 SNPs in 2,073 cases and 2,084 controls in Chinese women, we evaluated 53 SNPs for fast-track replication in an independent set of 4,425 cases and 1,915 controls of Chinese origin. Four replicated SNPs were further investigated in an independent set of 6,173 cases and 6,340 controls from seven other studies conducted in Asian women. SNP rs4784227 was consistently associated with breast cancer risk across all studies with adjusted odds ratios (95% confidence intervals) of 1.25 (1.20−1.31) per allele (P = 3.2×10−25) in the pooled analysis of samples from all Asian samples. This SNP was also associated with breast cancer risk among European Americans (per allele OR = 1.19, 95% CI = 1.09−1.31, P = 1.3×10−4, 2,797 cases and 2,662 controls). SNP rs4784227 is located at 16q12.1, a region identified previously for breast cancer risk among Europeans. The association of this SNP with breast cancer risk remained highly statistically significant in Asians after adjusting for previously-reported SNPs in this region. In vitro experiments using both luciferase reporter and electrophoretic mobility shift assays demonstrated functional significance of this SNP. These results provide strong evidence implicating rs4784227 as a functional causal variant for breast cancer in the locus 16q12.1 and demonstrate the utility of conducting genetic association studies in populations with different genetic architectures. Breast cancer is one of the most common malignancies among women worldwide. Genetic factors play an important role in the etiology of breast cancer. To identify genetic susceptibility loci for breast cancer, we performed a genome-wide association study in 15,468 breast cancer cases and 13,001 controls. A single nucleotide polymorphism (SNP) rs4784227 located on chromosome 16q12.1, a previously-reported region for breast cancer risk, was found to be associated with breast cancer risk. The association of this SNP with breast cancer risk remained highly significant in Asians after adjusting all previously-reported SNPs in this region. In vitro biochemical experiments using both luciferase reporter and electrophoretic mobility shift assays confirmed the functional importance of this SNP. Our results demonstrate the importance of conducting genetic association studies in populations with different genetic backgrounds to identify functional variants.
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Affiliation(s)
- Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Shimian Qu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Chun Li
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Ying Zheng
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Kai Gu
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Wenjing Wang
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Jiarong Cheng
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Lina Zhang
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | | | - Ming-Feng Hou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Nanjing Medical University, Nanjing, China
| | - Furu Wang
- Department of Epidemiology and Biostatistics, Nanjing Medical University, Nanjing, China
| | - Sandra L. Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Mark C. Kelley
- Division of Surgical Oncology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Martha J. Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Ui Soon Khoo
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Kelvin Y. K. Chan
- Division of Surgical Oncology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Sum Yin Chan
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Motoki Iwasaki
- Epidemiology and Prevention Division, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo, Japan
| | - Yoshio Kasuga
- Department of Surgery, Nagano Matsushiro General Hospital, Nagano, Japan
| | - Shoichiro Tsugane
- Epidemiology and Prevention Division, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Kazuo Tajima
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center Central Hospital, Nagoya, Japan
| | - Bo Huang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jiajun Shi
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Guoliang Li
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Wei Lu
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail:
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Ding SL, Yu JC, Chen ST, Hsu GC, Hsu HM, Ho JY, Lin YH, Chang CC, Fann CS, Cheng CW, Wu PE, Shen CY. Diverse Associations between ESR1 Polymorphism and Breast Cancer Development and Progression. Clin Cancer Res 2010; 16:3473-84. [DOI: 10.1158/1078-0432.ccr-09-3092] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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393
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Travis RC, Reeves GK, Green J, Bull D, Tipper SJ, Baker K, Beral V, Peto R, Bell J, Zelenika D, Lathrop M. Gene-environment interactions in 7610 women with breast cancer: prospective evidence from the Million Women Study. Lancet 2010; 375:2143-51. [PMID: 20605201 PMCID: PMC2890858 DOI: 10.1016/s0140-6736(10)60636-8] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Information is scarce about the combined effects on breast cancer incidence of low-penetrance genetic susceptibility polymorphisms and environmental factors (reproductive, behavioural, and anthropometric risk factors for breast cancer). To test for evidence of gene-environment interactions, we compared genotypic relative risks for breast cancer across the other risk factors in a large UK prospective study. METHODS We tested gene-environment interactions in 7610 women who developed breast cancer and 10 196 controls without the disease, studying the effects of 12 polymorphisms (FGFR2-rs2981582, TNRC9-rs3803662, 2q35-rs13387042, MAP3K1-rs889312, 8q24-rs13281615, 2p-rs4666451, 5p12-rs981782, CASP8-rs1045485, LSP1-rs3817198, 5q-rs30099, TGFB1-rs1982073, and ATM-rs1800054) in relation to prospectively collected information about ten established environmental risk factors (age at menarche, parity, age at first birth, breastfeeding, menopausal status, age at menopause, use of hormone replacement therapy, body-mass index, height, and alcohol consumption). FINDINGS After allowance for multiple testing none of the 120 comparisons yielded significant evidence of a gene-environment interaction. By contrast with previous suggestions, there was little evidence that the genotypic relative risks were affected by use of hormone replacement therapy, either overall or for oestrogen-receptor-positive disease. Only one of the 12 polymorphisms was correlated with any of the ten other risk factors: carriers of the high-risk C allele of MAP3K1-rs889312 were significantly shorter than non-carriers (mean height 162.4 cm [95% CI 162.1-162.7] vs 163.1 cm [162.9-163.2]; p=0.01 after allowance for multiple testing). INTERPRETATION Risks of breast cancer associated with low-penetrance susceptibility polymorphisms do not vary significantly with these ten established environmental risk factors. FUNDING Cancer Research UK and the UK Medical Research Council.
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Affiliation(s)
- Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, UK.
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394
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Zhang L, Zhang W, Chen K. Search for cancer risk factors with microarray-based genome-wide association studies. Technol Cancer Res Treat 2010; 9:107-21. [PMID: 20218734 DOI: 10.1177/153303461000900201] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Large-scale genome-wide association studies (GWASs) have emerged as a powerful approach to identify genetic polymorphisms that are associated with risk of developing cancer and other complex diseases. Currently, microarrays are the genotype screening technology of choice in GWASs because they permit interrogation of more than one-million single-nucleotide polymorphisms (SNPs) at the same time. Many novel loci and genetic variants have been identified as markers of cancer risk in a series of recent reports. With improvement of microarray technologies, population-based GWASs coupled with more quantitative validation methods are poised to reveal, in a systematic manner, numerous small changes in complex genetic networks that in combination can have a major impact on a patient's risk of developing cancer. Here, we review recent advancement in GWAS in the search and identification of cancer risk factors.
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Affiliation(s)
- Lina Zhang
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
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395
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Varghese JS, Easton DF. Genome-wide association studies in common cancers—what have we learnt? Curr Opin Genet Dev 2010; 20:201-9. [DOI: 10.1016/j.gde.2010.03.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 03/18/2010] [Accepted: 03/19/2010] [Indexed: 01/31/2023]
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396
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Lin J, Zee RYL, Liu KY, Zhang SM, Lee IM, Manson JE, Giovannucci E, Buring JE, Cook NR. Genetic variation in sex-steroid receptors and synthesizing enzymes and colorectal cancer risk in women. Cancer Causes Control 2010; 21:897-908. [PMID: 20148360 PMCID: PMC2873149 DOI: 10.1007/s10552-010-9518-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 01/28/2010] [Indexed: 01/21/2023]
Abstract
OBJECTIVES Several lines of evidence have suggested that female hormones may lower the risk for developing colorectal cancer. However, the mechanisms by which sex hormones affect colorectal cancer development remain unknown. We sought to determine whether the association may be under genetic control by evaluating genetic variation in estrogen receptors (ESR1 and ESR2), progesterone receptor (PGR), aromatase cytochrome 450 enzyme (CYP19A1), and 17 beta-hydroxysteroid dehydrogenase type 2 gene (HSD17B2). METHODS We included 158 incident cases of colorectal cancer and 563 randomly chosen control subjects from 28,345 women in the Women's Health Study aged 45 or older who provided blood samples and had no history of cancer or cardiovascular disease at baseline in 1993. All cases and controls were Caucasians of European descent. A total of 63 tagging and putative functional SNPs in the 5 genes were included for analysis. Unconditional logistic regression was used to estimate odds ratio (ORs) and 95% confidence intervals (CIs). RESULTS There was no association between variation in ESR1, ESR2, PGR, CYP19A1 and HSD17B2 and colorectal cancer risk after correction for multiple comparisons (p values after correction > or =0.25). There was also no association with any of the haplotypes examined (p > or = 0.15) and no evidence of joint effects of variants in the 5 genes (p > or = 0.51). CONCLUSION Our data offer insufficient support for an association between variation in ESR1, ESR2, PGR, CYP19A1, and HSD17B2 and risk for developing colorectal cancer.
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Affiliation(s)
- Jennifer Lin
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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397
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Ye C, Beeghly-Fadiel A, Lu W, Long J, Shu XO, Gao YT, Zheng W, Cai Q. Two-stage case-control study of DNMT-1 and DNMT-3B gene variants and breast cancer risk. Breast Cancer Res Treat 2010; 121:765-9. [PMID: 19798569 PMCID: PMC3493111 DOI: 10.1007/s10549-009-0569-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 09/20/2009] [Indexed: 11/29/2022]
Abstract
Aberrant DNA methylation of CpG islands is a common epigenetic alteration found in cancers. DNA methylation is typically mediated by DNA methyltransferases (DNMTs). Only two studies have evaluated DNMT-1 and/or DNMT-3B gene polymorphisms in relation to breast cancer risk, and results have been inconsistent. We comprehensively evaluated genetic variations in the DNMT-1 and DNMT-3B genes with breast cancer risk among the participants of the Shanghai Breast Cancer Study, a large-scale, two-stage, case-control study. Of the 25 SNPs in the DNMT-1 and DNMT-3B genes analyzed, only one (rs8101866) reached a normal significance level (P = 0.042). This association, however, was no longer statistically significant after adjustment for multiple comparisons. Our data suggest that there is no apparent association of common DNMT-1 and DNMT-3B polymorphisms with the risk of breast cancer among Chinese women.
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Affiliation(s)
- Chuanzhong Ye
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Wei Lu
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Xiao Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
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398
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Antoniou AC, Chenevix-Trench G. Common genetic variants and cancer risk in Mendelian cancer syndromes. Curr Opin Genet Dev 2010; 20:299-307. [DOI: 10.1016/j.gde.2010.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/23/2010] [Accepted: 03/23/2010] [Indexed: 02/07/2023]
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399
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Turnbull C, Ahmed S, Morrison J, Pernet D, Renwick A, Maranian M, Seal S, Ghoussaini M, Hines S, Healey CS, Hughes D, Warren-Perry M, Tapper W, Eccles D, Evans DG, Hooning M, Schutte M, van den Ouweland A, Houlston R, Ross G, Langford C, Pharoah PDP, Stratton MR, Dunning AM, Rahman N, Easton DF. Genome-wide association study identifies five new breast cancer susceptibility loci. Nat Genet 2010; 42:504-7. [PMID: 20453838 PMCID: PMC3632836 DOI: 10.1038/ng.586] [Citation(s) in RCA: 564] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 04/09/2010] [Indexed: 12/13/2022]
Abstract
Breast cancer is the most common cancer in women in developed countries. To identify common breast cancer susceptibility alleles, we conducted a genome-wide association study in which 582,886 SNPs were genotyped in 3,659 cases with a family history of the disease and 4,897 controls. Promising associations were evaluated in a second stage, comprising 12,576 cases and 12,223 controls. We identified five new susceptibility loci, on chromosomes 9, 10 and 11 (P = 4.6 x 10(-7) to P = 3.2 x 10(-15)). We also identified SNPs in the 6q25.1 (rs3757318, P = 2.9 x 10(-6)), 8q24 (rs1562430, P = 5.8 x 10(-7)) and LSP1 (rs909116, P = 7.3 x 10(-7)) regions that showed more significant association with risk than those reported previously. Previously identified breast cancer susceptibility loci were also found to show larger effect sizes in this study of familial breast cancer cases than in previous population-based studies, consistent with polygenic susceptibility to the disease.
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MESH Headings
- Breast Neoplasms/genetics
- Chromosomes, Human, Pair 10
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 6
- Chromosomes, Human, Pair 8
- Chromosomes, Human, Pair 9
- Female
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Genotype
- Humans
- Polymorphism, Single Nucleotide
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Affiliation(s)
- Clare Turnbull
- Section of Cancer Genetics, The Institute of Cancer Research, Sutton, Surrey, UK
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400
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Ioannidis JPA, Castaldi P, Evangelou E. A compendium of genome-wide associations for cancer: critical synopsis and reappraisal. J Natl Cancer Inst 2010; 102:846-58. [PMID: 20505153 DOI: 10.1093/jnci/djq173] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Since 2007, genome-wide association (GWA) studies have identified numerous well-supported, novel genetic risk loci for common cancers; however, there are concerns that this technology is reaching its limits. We provide an overview of GWA-identified genetic associations with solid tumors. We simulated the distribution of population risk alleles for colorectal, prostate, testicular, and thyroid cancers based on genetic variants identified in GWA studies. We also evaluated whether statistical power to detect typical genetic effects could be improved with studies performing GWA analyses of all available samples rather than multistage designs. Fifty-six eligible articles yielded 92 eligible associations between cancer phenotypes and genetic variants with a median per-allele odds ratio (OR) of 1.22 (interquartile range = 1.15-1.36). Half of the associations pertained to prostate, colorectal, or breast cancer. Individuals at the upper quartile of simulated risk had only 2.1- to 4.2-fold higher relative risk than those in the lower quartile. Comprehensive evaluation of currently available samples with GWA platforms would yield few additional variants with per-allele OR = 1.4, but many more variants with OR = 1.2 could be detected; statistical power to detect weak associations (OR = 1.07) would still be negligible. The GWA approach is effective in identifying common genetic variants with moderate effect; however, identifying loci with very small effects and rare variants will require major new efforts. At present, the utility of GWA-identified risk loci in risk stratification for cancer is limited.
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Affiliation(s)
- John P A Ioannidis
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina 45110, Greece.
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