Neoantigens derived from differential mutations of invasive ductal carcinomas with axillary lymph node metastasis

Abstract

Abstract Invasive ductal carcinomas (IDCs) are the most common breast cancer type. It was reported that almost 80% of breast cancers are IDCs. IDCs can be treated by immunotherapy using neoantigens. Therefore, common neoantigens that are specific for ductal carcinomas should be determined. We aimed to determine differential expression of neoantigens for IDCs in the presence or absence of axillary lymph node metastasis. DNA was isolated from paraffin-embedded (FFPE) tissue specimens by using GeneRead DNA FFPE Kit. QIAseq Targeted DNA panel for human breast cancer was used for sequencing of isolated tumor DNA. Next generation sequencing was performed using a Illumina MiSeq. Total exons of 93 genes were studied. A bioinformatic analysis was conducted by a platform-specific pipeline software (Qiagen Clinical Insight-AnalyseTM and Clinical Insight-InterpretTM). We found significant variations in several genes for individuals with or without axillary lymph node metastasis. In particular, variations in CDKN2A and PIK3R1genes were quite interesting to determine individual neoantigens of ductal carcinomas as potential immunotherapy targets. Currently, these findings are still under further investigations. Based on these findings, we concluded that NGS analysis is a very powerful technology in determination of specific neoantigens of individuals with ductal carcinomas. Also NGS can be used to discover new genes related to axillary lymph node metastasis for ductal carcinomas. Supported by Gazi University BAP.