MYC Copy Number Detection in Clinical Samples Using a Digital DNA-Hybridization and Detection Method

Area of Science:

• Molecular Pathology
• Cancer Genomics
• Biotechnology

Background:

• Formalin-fixed, paraffin-embedded (FFPE) tissues are standard for clinical pathology archiving.
• Nucleic acids from FFPE samples are often fragmented and chemically modified, complicating genomic analysis.
• Existing methods for copy number alteration (CNA) detection in FFPE samples are often low-plex, lack robustness, or are resource-intensive.

Purpose of the Study:

• To introduce and validate the NanoString nCounter v2 Cancer Copy Number Assay for FFPE samples.
• To provide a robust, reproducible method for assessing CNAs in 87 cancer-relevant genes from FFPE tissues.
• To address the limitations of current CNA detection methods in challenging FFPE clinical samples.

Main Methods:

• Utilized the NanoString nCounter System, a medium-plex platform designed for FFPE sample compatibility.
• Employed a hybridization-based approach using molecular barcoded probes directly on FFPE-derived DNA.
• Incorporated single-molecule imaging without amplification steps to minimize bias and detect hundreds of unique molecules.

Main Results:

• The nCounter v2 Cancer Copy Number Assay demonstrated high robustness and reproducibility with FFPE-derived DNA.
• The assay successfully profiled the copy number status of 87 genes frequently altered in cancer.
• The method effectively overcomes common challenges associated with fragmented and modified nucleic acids in FFPE samples.

Conclusions:

• The NanoString nCounter v2 Cancer Copy Number Assay is a reliable and efficient tool for CNA profiling in FFPE clinical specimens.
• This assay provides a valuable solution for genomic analysis of archival FFPE cancer samples, including assessment of genes like MYC.
• The technology offers an improved approach for cancer genomics research and diagnostics using FFPE material.