Project description:We report a detailed characterization of the HPV16 genome in two brain metastases from OPSCC tumors. The use of a target enrichment strategy followed by next generation sequencing (NGS) provided an effective way to identify viral infection in tumor genome, including internal deletions and insertion sites into the host genome. Applying similar strategies to a larger cohort of HPV+ HNSCC brain metastases could help to identify biomarkers that can predict metastasis and/or identify novel therapeutic options.
Project description:Most proteogenomic approaches for mapping single amino acid polymorphisms (SAPs) require construction of a sample-specific database containing protein variants predicted from the next-generation sequencing (NGS) data. We present a new strategy for direct SAP detection without relying on NGS data. Among the 348 putative SAP peptides identified in an industrial yeast strain, 85.6% of SAP sites were validated by genomic sequencing.
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:In this study, we carried out genome-scale CRISPRi modulation combining fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS) to identify genetic determinants for FFAs overproduction in Escherichia coli. The pcnBi (AP) strain that repressed the expression of pcnB produced 2992 mg l FFAs, which was 4.0-fold of the CF (A) strain. To analyze the underlying mechanism of FFAs overproduction, the engineered strain pcnBi and the control strain CF were applied to the transcriptomic and proteomic analyses.