Abstract A64: Germline PIK3CA polymorphisms detected by NGS in a small cohort of ER+ breast cancer patients are associated with recurrence while on tamoxifen treatment and ethnicity
Authors: Nunez-Lopez Yury O. , Rangel-Acevedo Leticia , Smith Lon , Weitman Steve , Kuhn John 
Published: October 2015

Abstract
Purpose: Identify DNA variants in the PIK3CA locus in breast cancer patients and assess the association with ethnicity and/or recurrence with tamoxifen treatment.
Methods: We performed targeted next generation sequencing (NGS) of PIK3CA exons and portions of surrounding intronic areas, including an intronic region containing a WDR3 pseudogene, in addition to 2 kb of promoter and 1 kb upstream genomic regions. DNA samples from a total of 27 patients were included in the study: 13 Hispanic and 14 non-Hispanic white (NHW) women with ER+ breast cancer. NGS was performed on an Ion PGM instrument and library preparation using a custom made PIK3CA AmpliSeq panel.
Results: We identified four single nucleotide variants (SNVs) that were exclusive to Hispanic breast cancer patients as compared to NHW patients (23% vs. 0%, respectively, Z score, p = 0.048, FDR = 0.386), and were significantly overrepresented in the Hispanic breast cancer group as compared to the general Hispanic population (1000 Genome Project dataset). Those SNVs were: synonymous rs115746478, intronic rs11918324 and rs3729682, and upstream rs74651987. We also identified four additional variants (all intronic, three SNVs and one small deletion) that were significantly associated with recurrence while receiving tamoxifen: rs2677760 (p = 0.0021, FDR = 0.0337), rs3729679 (p = 0.0021, FDR = 0.0337), rs10576446 (p = 0.0132, FDR = 0.1412), and rs7640662 (p = 0.0324, FDR = 0.2419). Interestingly, rs10576446 and rs7640662 are two intronic mutations separated by only 213 bases that show mutual exclusivity in our breast cancer patient cohort (no allele frequency data is available from the 1000 Genome project for these SNPs). A WDR3 pseudogene lies in this particular PIK3CA intronic region, for which low levels of expressed sequence tags have been reported. Although not statistically significant, rs7640662 showed a trend for ethnic-specificity given by a higher frequency in NHW breast cancer patients as compared with Hispanic patients (21.4% vs. 0.08%).
Conclusion: Our preliminary data suggests that germline DNA variants in non-coding sequences with the potential to change mRNA transcript expression and/or transcript isoform composition may be more prevalent than expected in cancer patients (due to a research bias to analyze variants in coding sequences). The functional significance of these SNVs related to breast cancer is to be determined. (Supported by P30CA054174)
Citation Format: Yury O. Nunez-Lopez, Leticia Rangel-Acevedo, Lon Smith, Steve Weitman, John Kuhn. Germline PIK3CA polymorphisms detected by NGS in a small cohort of ER+ breast cancer patients are associated with recurrence while on tamoxifen treatment and ethnicity. [abstract]. In: Proceedings of the Seventh AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 9-12, 2014; San Antonio, TX. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2015;24(10 Suppl):Abstract nr A64.