Comprehensive somatic genetic alteration profiling for triple-negative breast cancer patients by targeted kinome sequencing

Abstract

Introduction: Triple-negative breast cancer (TNBC) is a heterogeneous, complex disease and due to its aggressiveness, targeted therapy is an unmet need continuously being challenged. Protein kinases are one of the main therapeutic targets with innumerable targeted agents being developed without profound success in TNBC patients. Along with development of targeted therapy predictors of these kinase inhibitors is also an obstacle needed to be overcome. In this study, we investigated targetable or potentially targetable somatic genetic alterations in TNBC, by target kinome sequencing of TNBC cancer tissues. Methods: A total of 247 breast cancer tissues, 59 fresh frozen samples and 188 formalin-fixed paraffin embedded (FFPE) samples, each with a matched normal sample were collected. Targeted sequencing was done by using Agilent SureSelect Human Kinome Panel (612 genes including over 500 kinases) by next-generation sequencing technology. An average of 250x depth coverage was acquired in all sequenced samples. SNP microarray was also done for 46 pairs of frozen tissue samples. Results: A final total of 200 tumor-normal matched tissues were used for targeted sequencing and 170 of these were analyzed as TNBC samples. At least one genetic alteration was identified in 148 cases (87.1%) with a median of four (range 0-137) alterations detected per case. A sum of 719 somatic mutations was found in 256 genes. 412 nonsynonymous single nucleotide variations (SNV) were detected, 279 of these being novel mutations. Copy number variations (CNV) were found in 115 genes from 87 patients. The most frequently altered genes were TP53 in 92 (54.1%) patients, followed by MYC in 20 (11.8%) patients and OBSCN, PIK3CA, each in 16 (9.4%) patients. 83 potentially actionable target genes were identified in 128 (75.3%) patients with more than half of these patients having more than 1 potentially actionable gene aberration. A median of 8 potential genetic alterations were identified in each patient. These target genes were classified into 6 functionally relevant pathways, showing receptor tyrosine kinase/growth factor pathway and PI3K/MTOR pathway being the most frequently dysregulated pathways. Conclusion: Our strategy of targeted kinome sequencing of TNBC cancer tissues to detect cases with alterations in potentially targetable genes is a feasible approach as a cancer panel.