Tumor profiling

GV20 Oncotherapy has extensive experience in genomics technology, development of the novel computational algorithm, it has the ability to perform RNA-seq, DNA-seq, ATAC-seq, and TCR-seq to cancer patients. RNA-Seq can be used to measure gene expression and the abundance of tumor infiltrated immune cell; DNA-seq is used to detect tumor mutation type and mutation frequency; ATAC-seq is a rapid and sensitive technique to assess genome-wide chromatin accessibility; TCR-seq allows identifying T cell repertoire; GV20 Oncotherapy has the ability to integrate multiple cancer genomics datasets to investigate cancer pathogenesis, invasion, and metastasis.

T cell repertoire

TRUST is a computational method to infer the complementarity-determining region 3 (CDR3) sequences of tumor-infiltrating T cells. GV20 Oncotherapy uses TRUST to identify CDR3 sequence from bulk tumor RNA-Seq data. TRUST totally processed 9,142 RNA-seq samples across 29 cancer types and identified over 600,000 CDR3 sequences, including 15% that were full length. Based on identified CDR3 sequence, We observed a strong association between T cell diversity and tumor mutation load and identified three potential immunogenic somatic mutations on the basis of their co-occurrence with CDR3 sequences. Mutations in MUC4, PRAMEF4, MUC5B gene were predicted to result in peptides binding strongly to both MHC class I and class II molecules, that might be potential therapeutic targets.

Tumor-Infiltrating immune cell

Understanding the interactions between tumor and the host immune system is critical to finding prognostic biomarkers, reducing drug resistance, and immunotherapy. Tumor bulk RNA-Seq data generally are used to estimate abundance of tumor infiltrated immune cell, which enables to investigate the interaction between malignant cells and the host immune system and identify prognostic biomarkers of immune therapy. GV20 Oncotherapy use TIMER To analyze tumor-infiltrating immune cells in over 10,000 RNA-seq samples across 23 cancer types from The Cancer Genome Atlas (TCGA) and find immune infiltrates associate much more strongly with patient clinical features, viral infection status, and cancer genetic alterations.