P2-07-01: Copy Number Variants in Early-Onset-Breast Cancer.

Abstract

Abstract Background: Copy number variants (CNVs) are known to contribute to the risk for development of immune diseases, neurological disorders and to a lesser extent cancer. Many CNVs do not directly involve gene sequences. CHL1, a cell adhesion molecule with homology to L1CAM, is down-regulated in a large proportion of breast cancer. A deletion CNV immediately 5’ of the CHL1 transcriptional start site has been described. The CHL1 CNV's role in breast cancer risk has not previously been explored. Material and Methods: 50 research subjects recruited to the Washington University/Siteman Cancer Center Young Women's Breast Cancer Program (YWBCP) were selected for a CNV discovery study. These women were diagnosed breast cancer < age 40, tested negative for BRCA1/2 mutations and have a negative family history for breast cancer. The selection criteria enriched for de novo mutations. Comparative genomic hybridization (CGH) analyses were undertaken using the NimbleGen 2.1 million oligonucleotide array. DNA copy number was compared between proband and each of her parents to identify potential deletions or amplifications in the daughter relative to both parents (de novo changes). PCR was used to confirm a subset of the CGH-predicted differences in copy number. Chi-square test was used to determine statistical significances of CNV occurrences near the CHL1 gene between women with breast cancer and control cases. Results: aCGH data analysis has been completed for 25 YWBC trios (patients and parents). 247 differences in copy number in the breast cancer cases relative to their parents were identified (1-18 putative de novo CNVs per case). 91% of the observed changes were deletions and 9% were amplifications. One proband showed an 11,560 bp deletion 5’ of the CHL1 gene that was not seen in her parents. Conventional PCR confirmed a homozygous deletion of a ∼3 kb region in the patient, in the region of a known CNV with a reported frequency of ∼3%. Testing an additional 368 early-onset breast cancer cases for the CHL1 deletion revealed 25 additional homozygous deletions (6.8%). The deletion was present in 9 of 197 controls (4.5%). qPCR studies revealed the parents of the patient with the CHL1 deletion each carried a single copy of the CNV, making de novo copy number change in the proband very unlikely. Deletion specific assays for the CHL1 CNV are being used to test CNV genotypes in an extended case-control study. Discussion: CHL1 expression has previously been shown to be down-regulated in primary breast tumors. Our preliminary analysis of YWBC cases and controls indicates the CHL1 regulatory region CNV is unlikely to be associated with risk for early-onset breast cancer. Additional candidate de novo copy number changes seen in the genomes of patients with early-onset breast cancer are being evaluated to determine their roles as genetic risk factors. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-07-01.