Gene Expression Detection Assay for Cancer Clinical Use

Narrandes, Shavira; Xu, Wayne

Several studies have used next-generation sequencing (NGS) technologies for cancer gene analysis and/or signature development. For example, one study used NGS to analyze 21-genes, including the BRCA1 and BRCA2 tumor suppressor genes, associated with breast and ovarian cancers. 52 NGS was also used to determine the instability and examine the pathogenic properties of and clinical impact resulting from the large number of somatic microdeletions at exon 19 affecting the Epidermal Growth Factor Receptor (EGFR) in NSCLCs. 53 By selecting 33 patients with leukemia and designing amplicons targeting RUNX1, CEBPA, CBL, NRAS, KRAS, DNMT3A, EZH2, and TP53, one study analyzed the robustness of the PCR amplification strategies and GS FLX Titanium and Illumina MiSeq amplicon-deep sequencing platforms. The aim was to evaluate the technologies for their routine clinical use in characterizing and monitoring diseases using individual patient assays. MiSeq could detect TP53 variants and a 24-base pair insertion-deletion, conferring a predictive characteristic of the assay to detect residual disease and identify mutations for the assignment of treatments. 54 The MiSeq RNA-Seq technique was also used to assess the purpose of tumor-educated blood platelets (TEPs) in systemic and local responses in tumor growth. Using a total of 283 platelet samples (228 patients with localized and metastasized tumors and 55 non-disease individuals), mutated KRAS and EGFR in plasma DNA and platelet RNA was detected. Blood-based onco-signatures can be derived from TEP mRNA profiles to examine tissue biomarkers for the stratification of patients into low-and high-risk groups and the selection of their therapies. Although the clinical relevance of blood platelets in the molecular diagnosis of patients presenting with several types of cancer was established, systemic factors such as chronic disease or transient disease states and/or non-cancerous diseases could have affected the TEP mRNA profile, prompting their further validation in blood-based therapy selection, longitudinal studies, and disease recurrence monitoring. 55