Getting to know Next Generation Sequencing

May 25th, 2017

Next Generation Sequencing (NGS), which is becoming more widely known as Comprehensive Genomic Profiling by Massively Parallel Sequencing (CGP), will significantly contribute to targeted therapies and precision medicine. We provide a brief snapshot of what NGS/CGP is, how it works, where it is being used, the potential difficulties and what’s on the horizon.

What is Next Generation Sequencing?

• Next Generation Sequencing (NGS) is becoming more widely known as Comprehensive Genomic Profiling by Massively Parallel Sequencing (CGP)
• NGS/CGP testing will significantly contribute to targeted therapy
• Multiple genes are analysed simultaneously so there is the potential to detect all mutations in a patient specimen
• The four steps of NGS/CGP are:
  • DNA extraction
  • Library prep
  • DNA sequencing
  • Bioinformatics
• A machine reads the DNA and provides a sequence of bases. Sequences from patient samples are compared to known references

Where is NGS/CGP being incorporated?

• NGS/CGP uses the same methodology to screen for a variety of cancer genes (a panel)
• NGS/CGP is being adopted for NSCLC due to the complexity of the driver and resistance mutation tied to therapy options (Figure 1)
• NCCN and ESMO guidelines support broad molecular testing (e.g., NGS/CGP) in non-small cell lung cancer (NSCLC)

Figure 1. Mutations driving NSCLC.

What is the current situation with NGS/CGP in labs?

• There are two distinct groups of NGS/CGP panels emerging:
  • Smaller, ~50 gene panels that are built with known actionable biomarkers
  • Larger, 500+ gene panels to whole exome sequencing
• NGS/CGP is largely centralized to large commercial reference labs and academic institutions
• Many US labs are adopting NGS/CGP – Illumina and ThermoFisher platforms dominate the clinical space (Figure 2)
• EGFR and ALK, along with ROS1 and MET, are commonly part of lung NGS/CGP cancer panels
• Some laboratories do not include ALK in panels as they have a more cost-efficient test validated for ALK

Figure 2. NGS market share of top 20 NGS somatic mutation panel offering laboratories. (*Market share is based on a blended mix of Medicare datasets of different biomarkers performed by NGS.)

Difficulties associated with NGS/CGP

• Turnaround times are lengthy as NGS/CGP is a more complex and labour intensive methodology compared with single gene tests and may exceed the therapeutic window, e.g., in AML
• NGS/CGP diffusion is currently limited to key cancer and reference labs
• Reflex strategy may be required to account for low quality or quantity of DNA
• Coverage of sequencing panels still varies between insurers and may be restricted

What’s coming up?

• The requirement for BRAF testing and sequencing of other genes in the test panel will be a major driver for the adoption of NGS/CGP
• Platform suppliers and the FDA are striving for NGS to become part of therapeutic labels
• Leading pharma and diagnostic companies will embrace NGS/CGP to address key treatment and support their own pipeline and strategic goals