Abstract 2280: Targeted massively parallel sequencing identifies a limited number of clinically actionable variants in women with early onset breast cancer.
Authors: Maxwell Kara N. , Wubbenhorst Bradley , Letrero Richard , D'Andrea Kurt , Powers Jacqueline , Stopfer Jill E. , Domchek Susan M. , Nathanson Katherine L. 
Published: August 2014

Abstract
Approximately 5-10% of breast cancers are likely attributable to single gene mutations. Multiple breast cancer susceptibility genes have been identified; however, there is insufficient information on the clinical benefit of testing for variants in many of these genes outside of BRCA1, BRCA2, TP53 and PTEN. To obtain further information on the spectrum of variants in breast cancer susceptibility genes, we performed massively parallel sequencing using targeted capture of 28 known or proposed breast cancer susceptibility genes in over 250 patients with breast cancer diagnosed under age 40, negative clinical BRCA1 and BRCA2 testing and no personal or family history of ovarian cancer. Sixty-five percent of the patients had a family history of breast cancer. Breast cancers were triple negative in 26% of the patients; 70% of the patients presented with Stage II or greater disease. Positive control mutations in BRCA1, BRCA2, PALB2, CHEK2, MSH2 and BRCC3 were identified using the targeted panel. In analysis of the first 98 study patients, 46+/8 total variants were identified on average per patient with a median read depth of 131. Of the 4,483 total variants identified in the 98 patients, ten variants that are known to be or are likely functionally significant were identified in ten patients (10%). One patient had the CHEK2 1100delC mutation, and another the known deleterious TP53 mutation, P151T. Four of the functionally significant variants are novel frameshift or nonsense mutations in ATM, BRIP1, BARD1 and MRE11A. Four variants predicted to affect splicing, located within the first two nucleotides within the intron, were identified in CHEK2 (3) and MUTYH (1) and are therefore likely to be functionally significant. In addition, 29 patients (29%) were found to carry 27 variants predicted to be deleterious missense variants by multiple variant calling software programs and found at less than 1% frequency in the control population, but are of unclear functional significance as they are either novel or functionally untested. These potentially deleterious variants were identified in ATM (4), RAD50 (3), BRCA2 (3), BARD1 (2), BRCA1 (2), MLH1 (2), NBS (2), BRIP1 (1), CHEK2 (1), MCPH1 (1), MRE11A (1), MSH6 (1), PMS1 (1), and PMS2 (1). These data show that massively parallel sequencing has the ability to identify multiple potentially causative variants in known breast cancer susceptibility genes in patients who present with early onset breast cancer. However, only rare patients, 1% in our initial sample, which will be reported in full, have actionable mutations given current clinical management guidelines. Given the difficulty in determining the functional significance of novel variants, outside of truncating mutations, there is a great deal of uncertainty about how these findings can be translated into improvements in patient care.
Citation Format: Kara N. Maxwell, Bradley Wubbenhorst, Richard Letrero, Kurt D'Andrea, Jacqueline Powers, Jill E. Stopfer, Susan M. Domchek, Katherine L. Nathanson. Targeted massively parallel sequencing identifies a limited number of clinically actionable variants in women with early onset breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2280. doi:10.1158/1538-7445.AM2013-2280