Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next- Generation Sequencing Methods

Published

September 1, 2016

Author(s)

Chih-Jian Lih, Robin D. Harrington, Kneshay Harper, David J. Sims, Paul McGregor, Corinne Camalier, Han Si, Biswajit Das, P. M. Williams, Hua-Jun He, Jamie L. Almeida, Steven Lund, Steven J. Choquette, Kenneth D. Cole

Abstract

The National Institute of Standards and Technology (NIST) Standard Reference Materials 2373 is a set of genomic DNA samples prepared from five breast cancer cell lines with certified values for the ratio of the HER2 gene copy number to the copy numbers of reference genes determined by real-time quantitative PCR and digital PCR. Targeted-amplicon, whole-exome, and whole-genome sequencing measurements were used with the reference material to compare the performance of both the laboratory steps and the bioinformatic approaches of the different methods using a range of amplification ratios. Although good reproducibility was observed in each next-generation sequencing method, slightly different HER2 copy numbers associated with platform-specific biases were obtained. This study clearly demonstrates the value of Standard Reference Materials 2373 as reference material and as a calibrator for evaluating assay performance as well as for increasing confidence in reporting HER2 amplification for clinical applications.

Citation

Journal of Molecular Diagnostics

Volume

18

Issue

5

Pub Type

Journals

Download Paper

https://doi.org/10.1016/j.jmoldx.2016.05.008

Local Download

Keywords

Cancer, cell line, reference material, breast cancer, HER2, ERBB2, gene, amplification, measurement, Standard Reference Material

Citation

Lih, C. , Harrington, R. , Harper, K. , Sims, D. , McGregor, P. , Camalier, C. , Si, H. , Das, B. , Williams, P. , He, H. , Almeida, J. , Lund, S. , Choquette, S. and Cole, K. (2016), Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next- Generation Sequencing Methods, Journal of Molecular Diagnostics, [online], https://doi.org/10.1016/j.jmoldx.2016.05.008, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=919591 (Accessed April 23, 2024)