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Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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%...

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Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

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Estimating copy number using next-generation sequencing to determine ERBB2 amplification status.

Kohei Nakamura^1,2,3, Eriko Aimono⁴, Junna Oba⁴

¹Genomics Unit, Keio Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjukuku, Tokyo, 160-8582, Japan. knakamura320@keio.jp.

Medical Oncology (Northwood, London, England)

|March 12, 2021

Summary

Next-generation sequencing (NGS) can accurately estimate Erb-b2 receptor tyrosine kinase 2 (ERBB2) gene copy number in breast cancer. This NGS-based method shows high concordance with current diagnostic tests, potentially improving HER2-negative diagnoses.

Keywords:

Breast cancer ERBB2 Gene copy number Immunohistochemistry Next-generation sequencing

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Published on: December 15, 2017

Area of Science:

Oncology
Genomics
Cancer Diagnostics

Background:

Accurate assessment of Erb-b2 receptor tyrosine kinase 2 (ERBB2) amplification is crucial for guiding anti-HER2 therapy in breast and gastric cancers.
Current methods, immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), have limitations, including potential false-negative results for ERBB2 amplification.

Purpose of the Study:

To evaluate the utility of next-generation sequencing (NGS) for estimating ERBB2 gene copy number (CN) in diverse cancer types.
To compare NGS-derived ERBB2 CN estimates with established IHC and FISH results.

Main Methods:

Gene profiling of 160 cancer-related genes was performed on 90 breast and 19 non-breast cancer tissue samples.
ERBB2 copy number (CN) was measured using NGS and subsequently estimated by adjusting for tumor cell histological proportion.
NGS-estimated ERBB2 CN was compared against combined IHC/FISH scores.

Main Results:

An ERBB2-estimated CN of 3.2 or higher derived from NGS showed 98.4% concordance with combined IHC/FISH results in breast cancer cases.
This concordance was not consistently observed in non-breast cancer tissues.
NGS offers a potential method to refine ERBB2 CN assessment, addressing equivocal results from current diagnostics.

Conclusions:

NGS-based estimation of ERBB2 CN is a promising diagnostic approach for anti-HER2 therapy selection in breast cancer.
Further prospective clinical trials are warranted to validate NGS as a reliable diagnostic test for ERBB2 amplification.