Benign polymorphisms in the BRCA genes with linkage disequilibrium is associated with cancer characteristics

Abstract

Germline pathogenic mutation of the BRCA gene increases the prevalence of breast cancer. Reports on the benign variants of BRCA genes are limited. However, the definition of these variants might be altered with the accumulation of clinical evidence. Therefore, in the present study, we focused on benign single nucleotide polymorphisms (SNPs) of BRCA genes. Linkage disequilibrium was calculated from whole genome sequencing of the BRCA genes obtained from 500 healthy controls and 49 breast cancer patients. Sanger sequencing was used to confirm the mutation. The linkage disequilibrium was noted for seven and three SNPs in the BRCA1 and BRCA2 genes, respectively. Breast cancer with BRCA1/2 linkage disequilibrium was not correlated with a personal history of benign diseases or family history of cancer. Nevertheless, breast cancer with BRCA1 linkage disequilibrium was correlated with high tumor-infiltrating lymphocytes and positive extensive intraductal components. The patients with BRCA1 linkage disequilibrium tended to have worse disease-specific survival. Cancers with BRCA2 linkage disequilibrium are associated with a lower ratio of grade III cancer. Moreover, patients with BRCA2 linkage disequilibrium tended to have better overall survival. In conclusion, linkage disequilibrium from benign SNPs of the BRCA genes potentially affects cancer characteristics.

Keywords: BRCA1/2 genes; benign variants; breast cancer; linkage disequilibrium; polymorphism.

FIGURE 1

The linkage disequilibrium (LD) structures of (SNVs) in the BRCA1/2 genes from 500 healthy controls and 49 breast cancer patients. Each SNV is listed and located, representing the physical positions in the units of base pairs. The LD coefficient (D′) is shown unless D′ = 1. The white square represents the case of D′ < 1 and logarithm of the odds (LOD) < 2; purple describes the case of D′ = 1 and LOD < 2; and bright red depicts the case of D′ = 1 and LOD ≥ 2. The LD blocks within each gene are labeled in an inverted triangle based on Gabriel's method. (A) BRCA1 in 500 healthy controls. (B) BRCA2 in 500 healthy controls. (C) BRCA1 in 49 breast cancer patients. (D) BRCA2 in 49 breast cancer patients.

FIGURE 2

Heatmap and clustering of p‐values for 21 single nucleotide variants (SNVs) of the BRCA1/2 genes (n = 49 patients with breast cancer). The p‐values were calculated by logistic regression between the SNVs and pathological factors, including tumor size, histological grade, extensive intraductal component (EIC), lymphatic tumor emboli (LTE), lymph node (LN) metastasis, intrinsic subtype, estrogen receptor (ER), progesterone receptor, and human epidermal growth factor receptor 2 (HER2) or grade. For the intrinsic subtype, those with hormone receptor‐positive/HER2‐negative cancer was treated as the reference group, and their data were compared with those with HER2‐enriched and tripe negative breast cancer. A p < 0.05 was defined as significant, and these values are shown in dark red.

FIGURE 3

Pathological findings of 49 breast cancer patients, comparing the data between those with wild‐type genes and those with BRCA1 linkage disequilibrium. (A) Tumor‐infiltrating lymphocytes. (B) Extensive intraductal components. (C) Lymphatic tumor emboli. (D) Histological differentiation and grade. (E) Tumor stage. (F) Lymph node metastasis. (G) Extranodal extension. (H) Tumor–nodal–metastasis stage. (I) Subtype, defined as hormone receptor‐positive, HER2‐negative (HR⁺, HER2⁻), HER2‐enriched, and triple negative breast cancer (TNBC).

FIGURE 4

Pathological findings of 49 breast cancer patients, comparing the data between those with the wild‐type gene and those with the BRCA2 linkage disequilibrium. (A) Tumor‐infiltrating lymphocytes. (B) Extensive intraductal components. (C) Lymphtic tumor emboli. (D) Histological differentiation and grade. (E) Tumor stage. (F) Lymph node metastasis. (G) Extranodal extension. (H) Tumor–nodal–metastasis stage. (I) Subtype, defined as hormone receptor‐positive, HER2‐negative (HR⁺, HER2⁻), HER2‐enriched, and triple negative breast cancer (TNBC).

FIGURE 5

Kaplan–Meier curve of recurrence‐free survival and overall survival. Correlation of (A) BRCA1 exonic mutation (p = 0.7728), (B) BRCA2 exonic mutation (p = 0.9683), (C) BRCA1 linkage disequilibrium (p = 0.4069), and (D) BRCA2 linkage disequilibrium (p = 0.5070) with the disease‐free survival of breast cancer patients.

FIGURE 6

Kaplan–Meier curve of overall survival. Correlation of (A) BRCA1 exonic mutation (p = 0.3034), (B) BRCA2 exonic mutation (p = 0.9963), (C) BRCA1 linkage disequilibrium (p = 0.6490), and (D) BRCA2 linkage disequilibrium (p = 0.3483) with the overall survival of breast cancer patients.