Association of the NuMA region on chromosome 11q13 with breast cancer susceptibility

Abstract

The development of breast cancer is a complex process that involves multiple genes at many stages, from initial cell cycle dysregulation to disease progression. To identify genetic variations that influence this process, we conducted a large-scale association study using a collection of German cases and controls and >25,000 SNPs located within 16,000 genes. One of the loci identified was located on chromosome 11q13 [odds ratio (OR)=1.85, P=0.017]. The initial association was subsequently tested in two independent breast cancer collections. In both sample sets, the frequency of the susceptibility allele was increased in the cases (OR=1.6, P=0.01). The susceptibility allele was also associated with an increase in cancer family history (P=0.1). Fine mapping showed that the region of association extends approximately 300 kb and spans several genes, including the gene encoding the nuclear mitotic apparatus protein (NuMA). A nonsynonymous SNP (A794G) in NuMA was identified that showed a stronger association with breast cancer risk than the initial marker SNP (OR=2.8, P=0.005 initial sample; OR=2.1, P=0.002 combined). NuMA is a cell cycle-related protein essential for normal mitosis that is degraded in early apoptosis. NuMA-retinoic acid receptor alpha fusion proteins have been described in acute promyelocytic leukemia. Although the potential functional relevance of the A794G variation requires further biological validation, we conclude that variations in the NuMA gene are likely responsible for the observed increased breast cancer risk.

Fig. 1.

Schematic presentation of genome-wide association study from pool-based initial screen to replicated candidate genes. Phases 1 and 2 are conducted by using DNA pools yielding allele frequencies, and all subsequent steps involve genotyping of individual samples. hME, homogeneous Mass-EXTEND. See Results for more details.

Fig. 2.

Distribution of discovery and replication P values for the 52 SNPs selected from the third phase (genotype confirmation) of the large-scale association study. The inner plot shows the P values (–log₁₀ transformed) comparing allele frequencies between cases and controls in the discovery sample (x-axis, two-sided test) versus the comparison in the combined replication samples (y-axis, one-sided test based on effect observed in the discovery sample). The top and right outer margins show the univariate distributions of the discovery and replication P values, respectively. An arrow points to the result for marker rs673478. The result for the NuMA nonsynonymous variation rs3750913 identified during subsequent fine mapping is indicated as a bold +.

Fig. 3.

Association fine mapping of breast cancer susceptibility region on chromosome 11q13. (A) One hundred sixty public domain SNPs in a 100-kb window around the initial marker SNP (arrow) were compared between pools of cases and controls. Sixty-four of 160 SNPs were significant at P = 0.05 (horizontal dashed line). The nonsynonymous A794G SNP in exon 16 of NuMA is indicated (+). The x-axis corresponds to their chromosomal position, the y-axis to the test P values (–log₁₀ scale). The continuous dark line presents the results of a goodness-of-fit test for an excess of significance (compared with 0.05) in a 10-kb sliding window assessed at 1-kb increments. The continuous light gray line is the result of a nonlinear smoothing function showing a weighted average of the P values across the region. The darkness of each point corresponds to the minor allele frequency of each SNP in the control sample (see legend below graph). The LocusLink gene annotations for NCBI genome build 34 are included. (B) Estimates of LD from HapMap CEPH30 data in a 300-kb region encompassing NuMA. Estimates of LD(|D′| and r²) are represented as gray-scale ranging from white (LD = 0) to black (LD = 1) at increments of 0.1. SNP locations are indicated as downward tick marks in the ruler above. The marker SNP rs673478 location is marked (arrow).