Abstract 2090: A biomarker development for NSCLC patients based on pattern identification of traditional Korean medicine: A pilot study

Abstract

Abstract Background: In the study, we studied a biomarker development for lung cancer based on the pattern identification for the personalized Korean medicine. Methods: We recruited a total of 30 subjects including 4 Xu, 11 Stasis, and 15 not assigned group. Using the tissue sample of the subjects, we performed a whole exome sequencing to examine the genetic differences among three groups. Subjects were composed of normal and cancer tissues to identify cancer specific polymorphisms. A total of seven in silico analyses (GERP++, SIFT, LRT, Mutation Assessor, Mutation Taster, PhyloP and PolyPhen2 HDIV) were performed to predict functional role of significant SNPs. Results: The exome sequencing identified among 23,490 SNPs germline variants, 12 variants showed significant frequency differences between Xu and Stasis groups (P < 0.0005). As similar, 18 and 10 variants were identified in analysis for Xu vs. Gentleness group and Stasis vs. Gentleness group, respectively (P < 0.001). Our exome sequencing also found 8,792 lung cancer specific variants and among the groups identified 6, 34, and 12 variants which showed significant allele frequency differences in the comparison groups; Xu vs. Stasis, Xu vs. Gentleness group, and Stasis vs. Gentleness group. As a result of PCA analysis, in germline data set, Xu group was divided from other groups. Analysis using somatic variants also showed similar result. And in gene ontology analysis using pattern identification variants, we found genes like as FUT3, MYCBPAP, and ST5 were related to tumorigenicity, tumor metastasis, carbohydrate biosynthetic were showed most significant association (P = 0.004) in comparison between Xu and Stasis. Other significant SNPs for two groups (Xu vs. Gentleness group and Stasis vs. Gentleness group) were responsible for eye morphogenesis and olfactory receptor activity (P < 0.01). Classification of somatic pattern identification variants showed close relationship in multicellular organism reproduction, anion-anion antiporter activity, and GTPase regulator activity (P < 0.02). Conclusions: Taken together, our study suggests that this is first attempt to explore the specific variants discovery in whole exome regions for development of lung cancer biomarker based on pattern identification of Korean Traditional Medicine. Our study identified 40 variants in 29 genes in association with germline difference of pattern identification groups and 52 variants in 47 genes in somatic cancer tissues. Citation Format: Ji Hye Kim, Myeong-Sun Kim, Sooyeon Kang, Yu-Jeong Choi, Seo Yeon Lee, Sukjoong Oh, Seong-Gyu Ko. A biomarker development for NSCLC patients based on pattern identification of traditional Korean medicine: A pilot study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2090.