Related Experiment Video
Updated: Mar 24, 2026
Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
The Pan-Tumor Landscape of Gene Amplifications and Copy Number Amplification Ratio for Established and Emerging
Jessica K Lee1, Julia C F Quintanilha1, Kuei-Ting Chen1
1Foundation Medicine, Inc., Boston, Massachusetts.
Purpose:
Gene copy number (CN) amplifications and protein overexpression are common drug targets, and detection relies on various methodologies, including next-generation sequencing-based CN, immunohistochemistry (IHC), and in situ hybridization (ISH). We investigated the pan-tumor landscape of amplifications and developed AmpRatio, a novel method of CN quantitation.
Experimental Design:
Pan-tumor tissue (N = 486,340) and liquid (N = 85,635) samples underwent hybrid capture-based comprehensive genomic profiling. A genome-wide CN model for each sample was generated to estimate the purity, ploidy, and segment-level CN. AmpRatio was calculated by dividing gene CN/sample ploidy. A US-based deidentified clinicogenomic database was utilized to assess the relationship between ERBB2 AmpRatio and HER2 IHC/FISH and outcomes on anti-HER2 therapies.
Results:
Amplifications with varying degrees of gain were reported in 38.6% of pan-tumor tissue samples, most frequently MYC (5.6%), 11q13 (5.2%), ERBB2 (5.2%), and CCNE1 (3.2%). ERBB2 AmpRatio was associated with HER2 positivity by IHC/FISH in gastroesophageal [overall percent agreement (OPA) 90%] and breast (OPA 95%) cancers. Among patients treated with anti-HER2 therapies, ERBB2 AmpRatio significantly stratified outcomes within the ERBB2-amplified and IHC-defined HER2+ and HER2-low/ultralow populations. High concordance (sensitivity 88%) of amplification detection in liquid biopsy versus tissue was associated with higher AmpRatio and ctDNA tumor fraction ≥20%.
Conclusions:
CN amplifications are prevalent and diverse biomarkers, and AmpRatio is variable across genes and tumor types. ERBB2 AmpRatio is associated with outcomes to HER2-directed therapies and may have utility alongside IHC for clinical decision-making. With the increasing number of therapies targeting amplifications/overexpression, it will be important to define harmonized methods for CN quantification for optimal patient selection.
Insights
Gene copy number amplifications are common drug targets. A new method, AmpRatio, quantifies gene copy number and shows promise in predicting patient outcomes for HER2-directed therapies.
Area of Science:
- Oncology
- Genomics
- Biomarker Discovery
Background:
- Gene copy number (CN) amplifications and protein overexpression are key drug targets.
- Current detection methods include next-generation sequencing (NGS)-based CN, immunohistochemistry (IHC), and in situ hybridization (ISH).
- The pan-tumor landscape of amplifications requires further investigation.
Purpose of the Study:
- To investigate the pan-tumor landscape of gene copy number amplifications.
- To develop and validate AmpRatio, a novel method for quantitative gene copy number analysis.
- To assess the clinical utility of ERBB2 (also known as HER2) AmpRatio in relation to HER2 testing and anti-HER2 therapies.
Main Methods:
- Comprehensive genomic profiling of over 486,000 tissue and 85,000 liquid samples.
- Generation of genome-wide CN models to estimate purity, ploidy, and segment-level CN.
- Calculation of AmpRatio (gene CN/sample ploidy) and assessment of its correlation with HER2 IHC/FISH and patient outcomes.
Main Results:
- Amplifications were found in 38.6% of tissue samples, with MYC, 11q13, ERBB2, and CCNE1 being most frequent.
- ERBB2 AmpRatio demonstrated high agreement with HER2 positivity by IHC/FISH in gastroesophageal and breast cancers.
- ERBB2 AmpRatio significantly stratified outcomes in patients receiving anti-HER2 therapies, including HER2-low/ultralow populations.
Conclusions:
- Gene copy number amplifications are prevalent and diverse biomarkers.
- AmpRatio is a variable but valuable metric across different genes and tumor types.
- ERBB2 AmpRatio shows potential clinical utility alongside IHC for guiding anti-HER2 therapy decisions and patient selection.
Related Concept Videos
02:26Comparing Copy Number Variations and SNPs
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
02:07Tumor Progression
Colon cancer is one of the best-documented examples of tumor progression. Early mutation in the APC gene in colon cells causes a small growth on the colon wall called a polyp. With time, this polyp grows into a benign, pre-cancerous tumor. Further...
02:07Tumor Progression