BA2 - High-dimensional genotype in relation to breast cancer and WHI clinical trial interventions

Investigator Names and Contact Information

Ross Prentice (rprentic@whi.org)

Introduction/Intent

Breast cancer is among the three leading causes of cancer death in US women. At least 20%, perhaps as much as one-third of breast cancer is thought to be attributable to inherited factors. Breast cancer is a multifactorial polygenic disease and theoretical data, as well as results from previous studies, suggest that numerous common genetic variants resulting in moderate associations contribute substantially to overall occurrence of these cancers. The first stage of a genome-wide scan study using 360,000 common single nucleotide polymorphisms (SNPs) involving 1000 breast cancer cases and pair-matched controls has been completed, and a second stage involving 800 breast cancer cases and pair-matched controls, and 10,000 SNPs selected using first stage data, has also been completed using specimens from the WHI observational study. The study proposed here will provide an additional major study for the selection of breast cancer-related SNPs from among these 10,000, and will provide an opportunity to examine the effect of disease-related SNPs on the breast cancer hazard ratios arising from each component of the WHI clinical trial.

Recent advancements in genotyping technology have allowed genome-wide studies of this type to become feasible, and present a logical and critical next step to further explore the impact of genetic variants in this disease and to elucidate intervention effects in the WHI clinical trial. The SNP markers in the present study will be genotyped using the high-throughput Affymetrix GeneChip microarray platform with the chips already designed by Perlegen Sciences. The genotyping will be performed at the state-of-the-art facilities of Perlegen Sciences and the genotype, clinical outcome, and other research data will be analyzed in a collaborative fashion by investigators at the Fred Hutchinson Cancer Research Center and at Perlegen, with the help of WHI consultants. The elimination of false positive findings is a major consideration in high-dimensional genotyping studies of this type. For the multistage designs proposed the overall significance level will be chosen as 0.0000025 for breast cancer, leaving an expected total of only 0.9 false positive findings. Equally important, these studies will be sufficiently powered to establish moderate associations between genotypes and cancer risk, and to identify moderate associations between genotypes and WHI clinical trial intervention effects. We expect that results will identify new candidate pathways and help to elucidate the effects of interventions studied in the WHI clinical trial. These findings can also be expected to improve our understanding of the genetic susceptibility and molecular mechanisms of breast carcinogenesis, potentially leading to improved screening and preventive strategies for a very common cancer in postmenopausal women.

This proposal seeks to identify aspects of genotype that relate to the risk of breast cancer, and aspects of genotype that relate to the magnitude of intervention effects on breast cancer in the Women’s Health Initiative (WHI) randomized controlled clinical trial (CT). An ongoing genome-wide scan of breast cancer cases (as well as coronary heart disease and stroke cases) and matched controls in the WHI cohorts, being carried out as a collaborative study between Perlegen Sciences and the WHI, underlies the specific objectives as follows:

  1. To further assess the relationship between breast cancer risk and the 10,000 single nucleotide polymorphisms (SNPs) that have been identified in the first stage of the ongoing Perlegen-WHI collaborative study of breast cancer, through application to the 2,242 breast cancer cases in the WHI clinical trial, and to pair-matched controls, and

  2. To examine interactions of the effects of each of the four interventions studied in the WHI clinical trial (estrogen plus progestin; estrogen-alone; low-fat dietary pattern; calcium and vitamin D supplementation) with these 10,000 SNPs, using the same breast cancer cases and matched controls.

Results/Findings

Some of the publications related to this ancillary study are: 846, 1045, 1055, 1070, 1104. For a complete, up-to-date list of WHI papers related to this ancillary study, please use the searchable Papers section of this website.

Related Papers

Variation in the FGFR2 gene and the effects of postmenopausal hormone therapy on invasive breast cancer

Ross Prentice et al., 2009/10 PubMed #19861516 MSID: 846
Breast cancer concern is a major reason for the recent marked reduction in use of postmenopausal hormone therapy, although equally effective means of controlling menopausal symptoms are lacking. Single nucleotide polymorphisms (SNP) in the fibroblast growth factor receptor 2 (FGFR2) gene are substantially associated with postmenopausal breast cancer risk and could influence hormone therapy effects.We interrogated eight SNPs in intron 2 of the FGFR2 gene for 2,166 invasive breast cancer cases fro...
Keywords: None Provided
Related Studies: BA2

Genetic variants in the MRPS30 region and postmenopausal breast cancer risk

Ying Huang et al., 2011/6 PubMed #21702935 MSID: 1070
Genome-wide association studies have identified several genomic regions that are associated with breast cancer risk, but these provide an explanation for only a small fraction of familial breast cancer aggregation. Genotype by environment interactions may contribute further to such explanation, and may help to refine the genomic regions of interest.We examined genotypes for 4,988 SNPs, selected from recent genome-wide studies, and four randomized hormonal and dietary interventions among 2,166 wo...
Keywords: None Provided
Related Studies: BA2

Pooled versus individual genotyping in a breast cancer genome-wide association study

Ying Huang et al., 2010/9 PubMed #20718042 MSID: 1104
We examine the measurement properties of pooled DNA odds ratio estimates for 7,357 single nucleotide polymorphisms (SNPs) genotyped in a genome-wide association study of postmenopausal breast cancer. This study involved DNA pools formed from 125 cases or 125 matched controls. Individual genotyping for these SNPs subsequently came available for a substantial majority of women included in seven pool pairs, providing the opportunity for a comparison of pooled DNA and individual odds ratio estimates...
Keywords: Gwas; Dna Pooling
Related Studies: BA2, M3, W7

Variation in the FGFR2 gene and the effect of a low-fat dietary pattern on invasive breast cancer

Ross Prentice et al., 2010/1 PubMed #20056625 MSID: 1045
The Women's Health Initiative dietary modification (DM) trial provided suggestive evidence of a benefit of a low-fat dietary pattern on breast cancer risk, with stronger evidence among women whose baseline diet was high in fat. Single nucleotide polymorphisms (SNP) in the FGFR2 gene relate strongly to breast cancer risk and could influence intervention effects.All 48,835 trial participants were postmenopausal and ages 50 to 79 years at enrollment (1993-1998). We interrogated eight SNPs in intron...
Keywords: None Provided
Related Studies: BA2

Assessment of clinical validity of a breast cancer risk model combining genetic and clinical information

Matthew Mealiffe et al., 2010/10 PubMed #20956782 MSID: 1055
The Gail model is widely used for the assessment of risk of invasive breast cancer based on recognized clinical risk factors. In recent years, a substantial number of single-nucleotide polymorphisms (SNPs) associated with breast cancer risk have been identified. However, it remains unclear how to effectively integrate clinical and genetic risk factors for risk assessment.Seven SNPs associated with breast cancer risk were selected from the literature and genotyped in white non-Hispanic women in a...
Keywords: Keywords: Breast Cancer; Snp; Snp Risk Model; Gail Model; Breast Cancer Risk
Related Studies: BA2

Case-only approach to identifying markers predicting treatment effects on the relative risk scale

James Dai et al., 2017/9 PubMed #28960244 MSID: 3140
Retrospectively measuring markers on stored baseline samples from participants in a randomized controlled trial (RCT) may provide high quality evidence as to the value of the markers for treatment selection. Originally developed for approximating gene-environment interactions in the odds ratio scale, the case-only method has recently been advocated for assessing gene-treatment interactions on rare disease endpoints in randomized clinical trials. In this article, the case-only approach is shown t...
Keywords: Interaction; Precision Medicine; Predictive Biomarker; Treatment Selection; Randomized Trial
Related Studies: BA2

A breast cancer susceptibility locus is associated with pre-clinical autoantibodies to MRPS30 protein in postmenopausal women subsequently diagnosed with breast cancer

Approved Proposal, Hanash, Samir et al., 2017/12 MSID: 3517
Keywords: Mrps30 Protein; Autoantibody; Mrps30 Snps; Breast Cancer; Early Detection; Risk Assessment
Related Studies: 403, BA2