Cancer Diagnostics: Targeted Gene Panels for Next Generation of Sequencing | DiaCarta, Inc.

Cancer Diagnostics: Targeted Gene Panels for Next Generation of Sequencing

by | Sep 11, 2018 | Blog

Genome-wide next-generation of sequencing (NGS), such as whole genome sequencing (WGS) and whole exome sequencing (WES) has been used for germline and somatic mutation studies. However, due to the high cost and turnaround time, these NGS methods have not been widely used clinically for cancer diagnostics. On contrast, NGS using targeted gene panels is popular for simultaneous gene mutation detection across different cancer types, including lung cancer, colon cancer, breast cancer, and many others.

The Advantage of NGS Using Targeted Gene Panels

The gene panels contain the known genes whose mutations are associated with certain types of cancer. Targeted sequencing using these cancer gene panels reduce the sequencing depth by 500- to 1000-fold and improve sequencing sensitivity for variant allele frequency (VAF) from 20 to 25% for Sanger sequencing to 5% for NGS. In addition, thousands of samples can be processed for a single run and results are available within 1 to 2 days. While one can argue that only limited information is obtained from targeted gene panel NGS, not all the sequencing information is needed to get clinically relevant data. Multiple gene panels are designed to provide necessary information needed for special clinical diagnostics.

CLIA-certified Pan Cancer Panel NGS for ctDNA and FFPE samples

All the clinical testing performed on human (except for clinical trials and basic research) in the United States are regulated by federal regulatory Standards, CLIA (Clinical Laboratory Improvement Amendments). With the CLIA-certified Optiseq pan-cancer panel, more than 2900 mutation positions (hotspots) within 65 genes can be detected at as low as 1% VAF from circulating tumor DNA (ctDNA) or formalin-fixed paraffin-embedded (FFPE) samples, covering mutations commonly seen in different cancer types. From this panel test report, oncologists learn accurate and actionable information to guide therapies for advanced cancer patients.

XNA technology for targeted gene panel achieves sensitivity at 0.25% VAF

General gene panels reach detection at 5% VAF sensitivity, addition of XNA technology allows detection limit to go down to 0.25% VAF, enriching mutations by 30-fold and reducing sequencing depth. XNA technology selectively amplifies the mutant sequence while suppressing the wildtype sequence amplification, thereby enriching rare mutations in cancer tissue samples. With the designed Opti-seq NGS cancer Nano Panel V2, mutations in 13 amplicons and 17 hotspots of 7 genes can be easily detected without regular deep sequencing. 

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Next-generation sequencing (NGS) is a powerful tool that has seen a fast increase in clinical labs although only a few NGS tests have been approved by the FDA. However, there have been a lot of debate on if variants from NGS sequencing should be confirmed either by Sanger sequencing, the gold standard, or other techniques such as quantitative PCR, or the combination, or other methods.

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