Abstract B21: Targeted next-generation sequencing of hotspots in cancer genes in normal-tumor breast cancer patients of African ancestry reveals novel and known mutations
Authors: Ricks-Santi Luisel , McDonald John , Brown Cha'Tonya , Prince Latiffany , Abbas Muneer , Dunston Georgia 
Published: May 2016

Introduction: Genomic profiling of primary tumors and their concomitant normal tissues has provided critical information about the mechanisms associated with carcinogenesis. Furthermore, while comprehensive analysis of breast tumors have yielded actionable findings, breast cancer (BCa) remains one of the most common cancers worldwide and BCa incidences and mortality rates vary by population reflecting health disparities resulting from socioeconomic and biologic factors. Given that African American (AA) BCa cases often display distinctly worse clinicopathological features, we hypothesize that interrogating tumors from AAs could significantly aid in understanding the drivers of BCa carcinogenesis specifically in this population. These findings would aid in the identification of significantly mutated genes leading to the development of interventions for improved drug targeting of tumors in these populations with African Ancestry that display an increase propensity for harboring these previously unknown somatic variants. Methods: For this study, DNA from 16 normal and tumor tissue pairs from the “African American Familial Breast Cancer Study” (AAFBC) were utilized. Using targeted next generation sequencing (NGS) technologies, libraries for the Ion AmpliSeq™Cancer Hotspot Panel v2 (CHPv2) panel were created using 20ng of DNA and each sample was assigned a unique barcode. The CHPv2 is a commercially available primer pool for targeted NGS that amplifies 207 regions within 50 oncogenes for a total of 31kb. The resulting libraries were quantified and pooled with unequal volumes to allow varying depth of coverage between the matched tumor and normal pairs. The samples were sequenced on the Ion Personal Genome Machine™ (PGM™) System with a 316v2 chip. Sequence data from the PGM was processed using the Ion Torrent Suite v4 software package. Single nucleotide variants (SNVs), multi-nucleotide polymorphisms (MNPs), insertions or deletions were identified using Torrent Variant Caller Plugin v.4.6.0.7. Results: Sequencing resulted in 3,241,580 total usable reads with an average length of 126bp. The average coverage was 667x for tumor tissues and 165x for matched normal tissues. There were 88 unique variants representing 528 total variants with an average of 16.5 variants per sample. Of these, there were 52 germline variants that were expressed by both the normal and tumor samples. Five of these variants displayed a loss of one allele resulting in one homozygous (FGFR3) and 4 heterozygous mutations (PDGFRA, STK11 and ERBB4). The remaining 36 variants were somatic mutations of which 20 were novel and 16 have been described previously. The coding consequences were 56% missense mutations, 28% synonymous mutations, 8% frameshifts and 6% in-frame deletions. The most common coding mutations found in at least 3 patients were in TP53, SMARCB1, CDKN2A, NOTCH1 and PIK3CA.

Citation Format: Luisel Ricks-Santi, John McDonald, Cha'Tonya Brown, Latiffany Prince, Muneer Abbas, Georgia Dunston. Targeted next-generation sequencing of hotspots in cancer genes in normal-tumor breast cancer patients of African ancestry reveals novel and known mutations. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr B21.