Abstract LB-287: Racial disparity in the TP53 mutation spectra in triple-negative breast cancers: Validation with TCGA data
Authors: Putcha* Balananda-Dhurjati Kumar , Hebert-Magee* Shantel , Jadhav Trafina , Frost Andra R. , Eltoum Isam-Eldin , Manne Upender 
Published: May 2015

Abstract
Background: Triple-negative (negative for estrogen receptor, progesterone receptor, and HER-2 receptor) breast cancers (TNBCs) are aggressive, difficult to treat, and more likely to recur compared to other subtypes. TNBCs are more commonly found in African American (AA) than Caucasian (CA) patients. Since The Cancer Genome Atlas (TCGA) and other studies have reported a higher incidence of mutations in the TP53 gene in TNBCs, we sequenced p53 in TNBCs collected from AAs and CAs by use of a NextGen sequencing platform (Personal Genome Machine, PGM of Ion Torrent) to assess whether genetic variants in TP53 vary based on patient race.
Methods: Genomic DNA was extracted from 18 (10 AAs and 8 CAs) macro-dissected TNBC tumors and their matching normal tissues. Primers were designed using the Ion AmpliseqTM designer (Life Technologies) for a panel of non-silent somatic mutations (PIK3CA, TP53, MAP3K1, MAP2k4, GATA3, MLL3, CDH1, PTEN, PIK3R1, and AKT1) as well as missense point mutations (SF3B1, CDKN1B, RB1, AFF2, NF1, PTPN22, and PTPRD) reported in the TCGA breast cohort study. Using 10 ng of DNA from each sample, 1,541 target sequences were obtained from this panel of genes. Each target sequence was ∼100 bp. These sequences were amplified, and DNA libraries were generated using a protocol recommended by the manufacturer (Ion Torrent, Life Technologies). Samples were barcoded with the Ion Xpress Barcode Adapters, multiplexed for emulsion PCR on Ion OneTouch-2, and sequenced on a PGM sequencer (Life Technologies). Sequencing was performed on 318 chips, and the data were processed using the Ion reporter 4.0 (Life Technologies). Tumor-normal pairs were compared, and the variants were called and further filtered by the Ingenuity variant analysis plug-in. Cancer-driver variants, as identified by Ingenuity, were analyzed according to patient race and molecular subtype. Statistical analyses were performed using the Mann-Whitney or Fisher Exact probability test. Furthermore, we validated our findings with the TCGA data (NIH) using the cBio portal. The TNBC status of TCGA cases was determined based on the clinical data available on the TCGA data portal.
Results: In the panel of genes, cumulative mutations and mutation frequencies of individual genes were not significantly different between AAs and CAs. However, the number of cases with TP53 mutations was higher in CAs (7 of 8, 88%) as compared to AAs (3 of 10, 33%) (p=0.027). Of note, 6 of 7 TNBCs of CAs had mutations in the DNA-binding domain (DBD) of TP53. In contrast, all three TNBCs of AAs had mutations both within and outside the DBD of TP53. Analyses of TCGA data on TNBCs suggested that the frequency of TP53 mutations between CAs (28 of 40, 70%) and AAs (3 of 9, 33%) (p=0.058) was similar to the mutation frequency observed in our analyses.
Conclusion: In TNBCs, the TP53 mutation frequency, especially in the DBD, is higher in CA patients relative to AA patients.
These studies were supported by the Charles Barkley Foundation and by NIH 2U54-CA118948.
Citation Format: Balananda-Dhurjati Kumar Putcha*, Shantel Hebert-Magee*, Trafina Jadhav, Andra R. Frost, Isam-Eldin Eltoum, Upender Manne. Racial disparity in the TP53 mutation spectra in triple-negative breast cancers: Validation with TCGA data. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-287. doi:10.1158/1538-7445.AM2014-LB-287