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J Mol Diagn. 2016 Sep;18(5):753-761. doi: 10.1016/j.jmoldx.2016.05.008. Epub 2016 Jul 25.

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

Author information

1
Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
2
Division of Biosystems and Biomaterials, National Institute of Standards and Technology, Gaithersburg, Maryland.
3
Division of Statistical Engineering, National Institute of Standards and Technology, Gaithersburg, Maryland.
4
Division of Biosystems and Biomaterials, National Institute of Standards and Technology, Gaithersburg, Maryland. Electronic address: kenneth.cole@nist.gov.

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.

PMID:
27455875
PMCID:
PMC5397679
DOI:
10.1016/j.jmoldx.2016.05.008
[Indexed for MEDLINE]
Free PMC Article

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