title: Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next-Generation Sequencing Methods.
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.
authors.affiliation: Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
authors.forename: Chih-Jian
authors.initials: CJ
authors.lastname: Lih
authors.affiliation: Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
authors.forename: Han
authors.initials: H
authors.lastname: Si
authors.affiliation: Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
authors.forename: Biswajit
authors.initials: B
authors.lastname: Das
authors.affiliation: Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
authors.forename: Robin D
authors.initials: RD
authors.lastname: Harrington
authors.affiliation: Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
authors.forename: Kneshay N
authors.initials: KN
authors.lastname: Harper
authors.affiliation: Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
authors.forename: David J
authors.initials: DJ
authors.lastname: Sims
authors.affiliation: Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
authors.forename: Paul M
authors.initials: PM
authors.lastname: McGregor
authors.affiliation: Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
authors.forename: Corinne E
authors.initials: CE
authors.lastname: Camalier
authors.affiliation: Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
authors.forename: Andrew Y
authors.initials: AY
authors.lastname: Kayserian
authors.affiliation: Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
authors.forename: P Mickey
authors.initials: PM
authors.lastname: Williams
authors.affiliation: Division of Biosystems and Biomaterials, National Institute of Standards and Technology, Gaithersburg, Maryland.
authors.forename: Hua-Jun
authors.initials: HJ
authors.lastname: He
authors.affiliation: Division of Biosystems and Biomaterials, National Institute of Standards and Technology, Gaithersburg, Maryland.
authors.forename: Jamie L
authors.initials: JL
authors.lastname: Almeida
authors.affiliation: Division of Statistical Engineering, National Institute of Standards and Technology, Gaithersburg, Maryland.
authors.forename: Steve P
authors.initials: SP
authors.lastname: Lund
authors.affiliation: Division of Biosystems and Biomaterials, National Institute of Standards and Technology, Gaithersburg, Maryland.
authors.forename: Steve
authors.initials: S
authors.lastname: Choquette
authors.affiliation: Division of Biosystems and Biomaterials, National Institute of Standards and Technology, Gaithersburg, Maryland. Electronic address: kenneth.cole@nist.gov.
authors.forename: Kenneth D
authors.initials: KD
authors.lastname: Cole
mesh_terms: D045744:Cell Line, Tumor; D059472:Exome; D005260:Female; D005784:Gene Amplification; D018628:Gene Dosage; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods / Q000592:standards; D006801:Humans; D008297:Male; D009369:Neoplasms / Q000175:diagnosis / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics*; D012015:Reference Standards
chemical_list: D018719:Erb-b2 Receptor Tyrosine Kinases