Clinical Application of Targeted Next Generation Sequencing for Colorectal Cancers

Abstract

Promising targeted therapy and personalized medicine are making molecular profiling of tumours a priority. For colorectal cancer (CRC) patients, international guidelines made RAS (KRAS and NRAS) status a prerequisite for the use of anti-epidermal growth factor receptor agents (anti-EGFR). Daily, new data emerge on the theranostic and prognostic role of molecular biomarkers, which is a strong incentive for a validated, sensitive and broadly available molecular screening test in order to implement and improve multi-modal therapy strategy and clinical trials. Next generation sequencing (NGS) has begun to supplant other technologies for genomic profiling. Targeted NGS is a method that allows parallel sequencing of thousands of short DNA sequences in a single test offering a cost-effective approach for detecting multiple genetic alterations with a minimum amount of DNA. In the present review, we collected data concerning the clinical application of NGS technology in the setting of colorectal cancer.

Formalin-fixed paraffin-embedded sample conditions for deep next generation sequencing

“…First of all, one of the major limitations of NGS is the cost. 29 At this time, whole-genome sequencing costs several to ten thousand US dollars per sample, depending on the vendor. When we begin to analyze every sample, the cost will be astronomical.…”

Next generation sequencing‐based gene panel tests for the management of solid tumors

“…Although NGS‐based gene panel testing has the potential to change daily oncology practice, there are many issues to be addressed before it effectively saves cancer patients. One of the major issues of NGS remains the high cost . The NGS‐based gene panel tests cost several thousand US dollars per sample, depending on the vendor, and WES or whole genome sequencing cost more.…”

“…One of the major issues of NGS remains the high cost. 67 The NGS-based gene panel tests cost several thousand US dollars per sample, depending on the vendor, and WES or whole genome sequencing cost more. Another major issue of NGS-based precision medicine strategies is lack of treatment.…”

A practical guide for ancillary studies in pulmonary cytologic specimens

“… However, the yield and performance of these tests depends on 2 main factors: 1) the number of tumor cells (usually >100) and 2) the percentage of tumor cells (key factor for reducing false‐negative in molecular studies where the tumoral DNA is mixed with normal DNA). The limit of detection depends on the sensitivity of the analysis used; respective limits of detection are 10% to 20% for Sanger sequencing, 1% to 8% for NGS, and 1% to 5% for real‐time PCR …”

“…The limit of detection depends on the sensitivity of the analysis used; respective limits of detection are 10% to 20% for Sanger sequencing, 1% to 8% for NGS, and 1% to 5% for real-time PCR. 21 Several limitations in cytology specimens can lead to false-negative results. The first pass in an FNA is often used for diagnostic smears, whereas subsequent passes often contain fewer tumor cells and more blood.…”