Putative linkage signals identified for breast cancer in African American families

Novel breast cancer susceptibility loci under linkage peaks identified in African ancestry consortia

BACKGROUND

Expansion of genome-wide association studies across population groups is needed to improve our understanding of shared and unique genetic contributions to breast cancer. We performed association and replication studies guided by a priori linkage findings from African ancestry (AA) relative pairs.

METHODS

We performed fixed-effect inverse-variance weighted meta-analysis under three significant AA breast cancer linkage peaks (3q26-27, 12q22-23, and 16q21-22) in 9241 AA cases and 10 193 AA controls. We examined associations with overall breast cancer as well as estrogen receptor (ER)-positive and negative subtypes (193,132 SNPs). We replicated associations in the African-ancestry Breast Cancer Genetic Consortium (AABCG).

RESULTS

In AA women, we identified two associations on chr12q for overall breast cancer (rs1420647, OR = 1.15, p = 2.50×10-6; rs12322371, OR = 1.14, p = 3.15×10-6), and one for ER-negative breast cancer (rs77006600, OR = 1.67, p = 3.51×10-6). On chr3, we identified two associations with ER-negative disease (rs184090918, OR = 3.70, p = 1.23×10-5; rs76959804, OR = 3.57, p = 1.77×10-5) and on chr16q we identified an association with ER-negative disease (rs34147411, OR = 1.62, p = 8.82×10-6). In the replication study, the chr3 associations were significant and effect sizes were larger (rs184090918, OR: 6.66, 95% CI: 1.43, 31.01; rs76959804, OR: 5.24, 95% CI: 1.70, 16.16).

CONCLUSION

The two chr3 SNPs are upstream to open chromatin ENSR00000710716, a regulatory feature that is actively regulated in mammary tissues, providing evidence that variants in this chr3 region may have a regulatory role in our target organ. Our study provides support for breast cancer variant discovery using prioritization based on linkage evidence.

Race and genetics versus 'race' in genetics: A systematic review of the use of African ancestry in genetic studies

Social scientists have long understood race to be a social category invented to justify slavery and evolutionary biologists know the socially constructed racial categories do not align with our biological understanding of genetic variation. The completion of the Human Genome Project in 2003 confirmed humans are 99.9% identical at the DNA level and there is no genetic basis for race. A systematic review of the PubMed medical literature published since 2003 was conducted to assess the use of African ancestry to denote study populations in genetic studies categorized as clinical trials, to examine the stated rationale for its use and to assess the use of evolutionary principles to explain human genetic diversity. We searched for papers that included the terms 'African', 'African American' or 'Black' in studies of behavior (20 papers), physiological responses, the pharmacokinetics of drugs and/or disease associations (62 papers), and as a genetic category in studies, including the examination of genotypes associated with life stress, pain, stuttering and drug clearance (126 papers). Of these, we identified 74 studies in which self-reported race alone or in combination with admixture mapping was used to define the study population. However, none of these studies provided a genetic explanation for the use of the self-identified race as a genetic category and only seven proffered evolutionary explanations of their data. The concept of continuous genetic variation was not clearly articulated in any of these papers, presumably due to the paucity of evolutionary science in the college and medical school curricula.

Copy number alterations associated with clinical features in an underrepresented population with breast cancer

Background

As the most incident tumor among women worldwide, breast cancer is a heterogeneous disease. Tremendous efforts have been made to understand how tumor characteristics as histological type, molecular subtype, and tumor microenvironment collectively influence disease diagnosis to treatment, which impact outcomes. Differences between populations and environmental and cultural factors have impacts on the origin and evolution of the disease, as well as the therapeutic challenges that arise due to these factors. We, then, compared copy number variations (CNVs) in mucinous and nonmucinous luminal breast tumors from a Brazilian cohort to investigate major CNV imbalances in mucinous tumors versus non‐mucinous luminal tumors, taking into account their clinical and pathological features.

Methods

48 breast tumor samples and 48 matched control blood samples from Brazilian women were assessed for CNVs by chromosome microarray. Logistic regression and random forest models were used in order to assess CNVs in chromosomal regions from tumors.

Results

CNVs that were identified in chromosomes 1, 5, 8, 17, 19, and 21 classify tumors according to their histological type, ethnicity, disease stage, and familial history.

Conclusion

Copy number alterations described in this study provide a better understanding of the landscape of genomic aberrations in mucinous breast cancers that are associated with clinical features.