Jump to: Authorized Access | Attribution | Authorized Requests

Study Description

The genome-wide association study (GWAS) includes participants enrolled into two different studies. The first study, the San Francisco Bay Area Cancer Study (SFBCS) is a population-based case-control study of breast cancer conducted in the San Francisco Bay Area and included women ages 35-79 years from three racial/ethnic groups: Non-Hispanic whites, African Americans, and Hispanics/Latinas. For the GWAS, only Hispanic/Latina women were included. Women diagnosed with invasive breast cancer between 1995 and 2002 were identified through the Greater Bay Area Cancer Registry. Controls were identified by random digit dialing and were frequency-matched to cases by age in 5 year increments and by race/ethnicity. Hispanic/Latina ethnicity was assessed by self-report. 175 Hispanic/Latina cases and 307 Hispanic/Latina controls from the SFBCS had given adequate consent and provided biospecimens that were used in the GWAS to be included in this data submission.

The second study is the Northern California site of the Breast Cancer Family Registry (NC-BCFR). This population-based family study recruited breast cancer cases ages 18-64 years diagnosed from 1995-2009 that were identified through the Greater Bay Area Cancer Registry. Cases included all women at increased genetic susceptibility for breast cancer who met one or more of the following criteria: (a) being diagnosed with breast cancer at age <35 years; b) having a personal history of ovarian cancer or childhood cancer; (c) being diagnosed with two different breast cancers (bilateral breast cancers), with the first one diagnosed at age <50 years; and d) having one or more first-degree relatives with breast cancer, ovarian cancer or childhood cancer. Cases not meeting these criteria were randomly sampled and racial/ethnic minorities were oversampled. Controls were recruited by random digit dialing and were matched by 5-year age increments and by race/ethnicity. For the current GWAS only Latina/Hispanic cases and controls were included. Latina/Hispanic ethnicity was assessed by self-report. 631 Hispanic/Latina cases and 61 Hispanic/Latina controls from the NC-BCFR had given adequate consent and provided biospecimens that were used in the GWAS to be included in this data submission.

  • Study Design:
    • Case-Control
  • Study Type:
    • Case-Control
  • dbGaP estimated ancestry using GRAF-pop
Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. The site also contains data dictionaries, variable summaries, documents, and truncated analyses, whenever available.

Study Inclusion/Exclusion Criteria

Inclusion Criteria:
Cases:
San Francisco Bay Area Cancer Study: Women who are of self-reported Latina/Hispanic ethnicity with invasive breast cancer who lived in the 5 Bay Area Counties (San Francisco, San Mateo, Alameda, Santa Clara, Marin) ages 35-79. Cases were identified through the San Francisco Bay Area Cancer Registry

Northern California Breast Cancer Family Registry: Women who are of self-reported Latina/Hispanic ethnicity who lived in the 5 Bay Area Counties (San Francisco, San Mateo, Alameda, Santa Clara, Marin) diagnosed with invasive breast cancer and had at least one of the following criteria: family history of at least one first degree relative with breast cancer, personal diagnosis of breast cancer at age 35 or younger, personal diagnosis of bilateral breast cancer. Cases were identified through the San Francisco Bay Area Cancer Registry

Exclusion Criteria:
Cases were excluded if their physician reported that they had a contraindication to participation in a research study, if they could not complete the informed consent or the questionnaire in English or Spanish
Northern California Breast Cancer Family Registry:

Controls:
Controls were excluded if their physician reported that they had a contraindication to participation in a research study, if they could not complete the informed consent or the questionnaire in English or Spanish

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Whole Genome Genotyping Affymetrix AFFY_6.0 934940 52074
Study History

The San Francisco Bay Area Cancer Study recruited cases and controls between 199X and 200X. The Cancer Family Registry recruited cases and controls between 199X and 200X.

The SFBCS was used to demonstrate that ancestry is associated with breast cancer risk (Fejerman et al Cancer Research 2008). The investigators used 106 ancestry informative markers to infer genetic ancestry for all of the women in the study. They found that European ancestry was associated with higher risk of breast cancer while Indigenous American ancestry was associated with lower risk.

The GWAS was performed on stored biospecimens between 2008 and 2010. The first analysis of the GWAS data used an admixture mapping approach to identify loci at which ancestry was associated with risk (Fejerman et al Hum Mol Genetics 2012). This analysis also included Hispanic/Latina women from the Multi-ethnic cohort which are not included in this dbGAP submission. The investigators identified 6q25 as a locus by admixture mapping. The investigators then fine mapped this region and replicated in additional datasets (Fejerman et al Nature Communications 2014). They found two SNPs in linkage disequilibrium at 6q25 that were associated with breast cancer risk. The minor allele for these SNPs was only common in women with some Indigenous American ancestry and was highly protective for breast cancer. In addition, the investigators replicated several previously identified SNPs associated with breast cancer at different loci in other populations, although only SNPs at the TOX3 locus met the criteria for genome wide significance.

Selected publications
Diseases/Traits Related to Study (MeSH terms)
Links to Related Resources
Authorized Data Access Requests
See research articles citing use of the data from this study
Study Attribution
Feedback