Experimentally Deduced Criteria for Detection of Clinically Relevant Fusion 3' Oncogenes from FFPE Bulk RNA Sequencing Data.

ABSTRACT: Drugs targeting receptor tyrosine kinase (RTK) oncogenic fusion proteins demonstrate impressive anti-cancer activities. The fusion presence in the cancer is the respective drug prescription biomarker, but their identification is challenging as both the breakpoint and the exact fusion partners are unknown. RNAseq offers the advantage of finding both fusion parts by screening sequencing reads. Paraffin (FFPE) tissue blocks are the most common way of storing cancer biomaterials in biobanks. However, finding RTK fusions in FFPE samples is challenging as RNA fragments are short and their artifact ligation may appear in sequencing libraries. Here, we annotated RNAseq reads of 764 experimental FFPE solid cancer samples, 96 leukemia samples, and 2 cell lines, and identified 36 putative clinically

SUBMITTER: Rabushko E 

PROVIDER: S-EPMC9405289 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature