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• W2493018502 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. 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. High levels of the expression of the human epidermal growth factor receptor (HER)-2 protein, due to amplification of the HER2 gene (ERBB2), frequently occurs in breast cancers1Slamon D.J. Clark G.M. Wong Sg Levin W.J. Ullrich A. McGuire W.L. Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene.Science. 1987; 235: 177-182Crossref PubMed Scopus (9910) Google Scholar, 2Carlson R.W. Moench S.J. Hammond W.W. Perez E.A. Burstein H.J. Allred D.C. Vogel C.L. Goldstein L.J. Somlo G. Gradishar W.J. Hudis Wa Jahanzeb M. Stark A. Wolff A.C. Press M.F. Winer E.P. Paik S. Ljung B.J. HER2 testing in breast cancer: NCCN task force report and recommendations.J Natl Compr Canc Netw. 2006; 4: S1-S23Crossref PubMed Scopus (76) Google Scholar and gastrointestinal cancers.3Rüschoff J. Hanna W. Bilous M. Hofmann M. Osamura R.Y. Penault-Llorca F. van de Vijver M. Viale G. HER2 testing in gastric cancer: a practical approach.Mod Pathol. 2012; 25: 637-650Crossref PubMed Scopus (413) Google Scholar, 4Zhou Z. Hick D.G. HER2 amplification or overexpression in upper GI tract and breast cancer with clinical diagnosis and treatment.in: Siregar Y. Oncogene and Cancer: From Bench to Clinic. InTech, Rijeka, Croatia2013Crossref Google Scholar The classic methods of measurement of HER2 are immunohistochemistry analysis for protein expression and fluorescence in situ hybridization techniques for gene amplification.5Gown A.M. Goldstein L.C. The knowns and the unknowns in HER2 testing in breast cancer.Am J Clin Pathol. 2011; 136: 5-6Crossref PubMed Scopus (6) Google Scholar The accurate measurements of HER2 amplification levels are important for determining the proper treatment using anti-HER2 therapeutics.4Zhou Z. Hick D.G. HER2 amplification or overexpression in upper GI tract and breast cancer with clinical diagnosis and treatment.in: Siregar Y. Oncogene and Cancer: From Bench to Clinic. InTech, Rijeka, Croatia2013Crossref Google Scholar, 6Ross J.S. Slodkowska E.A. Symmans W.F. Pusztai L. Ravdin P.M. Hortobagyi G.N. The HER-2 receptor and breast cancer: ten years of targeted anti-HER-2 therapy and personalized medicine.Oncologist. 2009; 14: 320-368Crossref PubMed Scopus (904) Google Scholar, 7Valabrega G. Montemurro F. Aglietta M. Trastuzumab: mechanism of action, resistance and future perspectives in HER2-overexpressing breast cancer.Ann Oncol. 2007; 18: 977-984Crossref PubMed Scopus (463) Google Scholar There is a good correlation between the HER2 gene copy numbers and HER2 protein expression using immunohistochemistry analysis and fluorescence in situ hybridization methods when the measurements are carefully performed in clinical breast cancer samples8Press M. Slamon D. Flom K. Park J. Zhou J. Bernstein L. Evaluation of HER-2/neu gene amplification and overexpression: comparison of frequently used assay methods in a molecularly characterized cohort of breast cancer specimens.J Clin Oncol. 2002; 20: 3095-3105Crossref PubMed Scopus (362) Google Scholar and also in breast cancer cell lines.9Szollosi J. Balazs M. Feuerstein B. Benz C. Waldman F. ERBB-2 (HER2/NEU) gene copy number, p185(HER-2) overexpression and intratumor heterogeneity in human breast cancer.Cancer Res. 1995; 55: 5400-5407PubMed Google Scholar An analysis of individual cells from breast cancer cell lines showed a good correlation between a high copy number of chromosome 17 (where the HER2 gene is located) and high HER2 protein expression.9Szollosi J. Balazs M. Feuerstein B. Benz C. Waldman F. ERBB-2 (HER2/NEU) gene copy number, p185(HER-2) overexpression and intratumor heterogeneity in human breast cancer.Cancer Res. 1995; 55: 5400-5407PubMed Google Scholar Recently, real-time quantitative PCR (qPCR) was shown to be a sensitive method of confirming HER2 gene amplification in clinical samples in which immunohistochemistry analytical methods have failed.10Koudelakova V. Berkovcova J. Trojanec R. Vrbkova J. Radova L. Ehrmann J. Kolar Z. Melichar B. Hajduch M. Evaluation of HER2 gene status in breast cancer samples with indeterminate fluorescence in situ hybridization by quantitative real-time PCR.J Mol Diagn. 2015; 17: 446-455Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar There is considerable interest in measuring the amplification of the HER2 gene along with other gene targets in cancer, using quantitative nucleic acid measurement techniques, especially those methods that can screen for panels of mutations to tailor treatments for individual patients.11Simon R. Roychowdhury S. Implementing personalized cancer genomics in clinical trials.Nat Rev Drug Discov. 2013; 12: 358-369Crossref PubMed Scopus (234) Google Scholar Next-generation sequencing (NGS) provides a powerful tool to detect multiple genetic alterations in a quantitative manner. Targeted-amplicon and whole-exome sequencing (WES) technologies for mutation measurements in cancer are becoming more widespread in clinical laboratories. Those NGS assays sequence targeted regions with clinically or biologically relevant genetic loci with high read depth coverage. Therefore, the assay can achieve high sensitivity for detecting somatic mutations in cancer. However, clinically relevant copy number variations (CNVs) are an essential measurement. NGS has shown great promise, and advances in computation methods have occurred,12Wang H. Nettleton D. Ying K. Copy number variation detection using next generation sequencing read counts.BMC Bioinformatics. 2014; 15: 109Crossref PubMed Scopus (66) Google Scholar, 13Pirooznia M. Goes F.S. Zandi P.P. Whole-genome CNV analysis: advances in computational approaches.Front Genet. 2015; 6: 138Crossref PubMed Scopus (108) Google Scholar, 14Guo Y. Sheng Q. Samuels D.C. Lehmann B. Bauer J.A. Pietenpol J. Shyr Y. Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control.Biomed Res Int. 2013; 2013: 915636Crossref PubMed Scopus (38) Google Scholar but these methods have not yet been fully validated using reference materials to confirm the calculations. Recently, the use of whole-genome sequencing (WGS) (at low coverage levels), along with recent advances in computation methods, has allowed for the calculation of CNVs using NGS.13Pirooznia M. Goes F.S. Zandi P.P. Whole-genome CNV analysis: advances in computational approaches.Front Genet. 2015; 6: 138Crossref PubMed Scopus (108) Google Scholar Guidelines on the quality management of NGS in clinical applications have been proposed, including test validation, quality-control procedures, proficiency testing, and the use of reference materials.15Gargis A.S. Kalman L. Berry M.W. Bick D.P. Dimmock D.P. Hambuch T. et al.Assuring the quality of next-generation sequencing in clinical laboratory practice.Nat Biotechnol. 2012; 30: 1033-1036Crossref PubMed Scopus (362) Google Scholar NGS assays intended for clinical oncology applications have been validated using pooled cancer cell lines and clinical samples.16Lih C.J. Sims D.J. Harrington R.D. Polley E.C. Zhao Y. Mehaffey M.G. Forbes T.D. Das B. Walsh W.D. Datta V. Harper K.N. Bouk C.H. Rubinstein L.V. Simon R.M. Conley B.A. Chen A.P. Kummar S. Doroshow J.H. Williams P.M. Analytical validation and application of a targeted next-generation sequencing mutation-detection assay for use in treatment assignment in the NCI-MPACT trial.J Mol Diagn. 2016; 18: 51-67Abstract Full Text Full Text PDF PubMed Scopus (34) Google Scholar, 17Frampton G.M. Fichtenholtz A. Otto G.A. Wang K. Downing S.R. He J. et al.Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.Nat Biotechnol. 2013; 31: 1023-1031Crossref PubMed Scopus (1435) Google Scholar Reference materials are well-characterized samples that are ensured to be homogenous and stable and to accurately reflect the intended analyte. They can be used to ensure that measurement methods are working correctly, to calibrate instruments, to evaluate assay performance, to identify the weaknesses of the measurement process, and to assign values to other materials.18May W. Parris R. Beck C. Fassett J. Greenberg R. Guenther F. Kramer G. Wise S. Gillis T. Colbert J. Gettings R. MacDonald B. Standard Reference Materials®, definitions of terms and modes used at NIST for value-assignment of reference materials for chemical measurements.NIST Special Publication 260-136. 2000; Google Scholar Reference materials are used to improve the confidence and reliability of measurement methods by providing samples that are ensured to have the certified properties for their intended purpose. There are significant challenges in producing reference materials from biological materials, especially cell lines that require a high level of characterization, because of differences in the genomic materials due to the genetic drift that occurs during cell culture. Currently, reference materials for cancer measurements are very limited. A World Health Organization international standard for the BCR-ABL mRNA levels consists of mixtures of cell lines to obtain different levels of the gene fusion mRNA target.19White H.E. Matejtschuk P. Rigsby P. Gabert J. Lin F. Wang Y.L. Branford S. Müller M.C. Beaufils N. Beillard E. Colomer D. Dvorakova D. Ehrencrona H. Goh H.G. El Housni H. Jones D. Kairisto V. Kamel-Reid S. Kim D.W. Langabeer S. Ma E.S.K. Press R.D. Romeo G. Wang L. Zoi K. Hughes T. Saglio G. Hochhaus A. Goldman J.M. Metcalfe P. Cross N.C. Establishment of the first World Health Organization International Genetic Reference Panel for quantitation of BCR-ABL mRNA.Blood. 2010; 116: e111-e117Crossref PubMed Scopus (126) Google Scholar The Genetic Testing Reference Materials coordination program (Centers for Disease Control and Prevention, http://www.cdc.gov/clia/Resources/GetRM, last accessed July 8, 2016) publishes consensus data from interlaboratory measurements on cell lines obtained from cell repositories.20Kalman L.V. Amos Wilson J. Buller A. Dixon L. Edelmann L. Geller L. Highsmith W.E. Holtegaard L. Kornreich R. Rohlfs E.M. Payeur T. Sellers T. Muralidharan K. Characterization of genomic DNA reference materials for genetic testing of disorders common in people of Ashkenazi Jewish decent.J Mol Diagn. 2009; 6: 530-536Abstract Full Text Full Text PDF Scopus (9) Google Scholar, 21Barker S.D. Bale S. Buller A. Das S. Friedman K. Godwin A.K. Grody W. Highsmith E. Kant J. Lyon E. Mao R. Monaghan K.G. Payne D.A. Pratt V.M. Roa B. Schrijver I. Shrimpton A.E. Spector E. Telatar M. Weck K. Zehnbauer B. Booker J. Kalman L.V. Development and characterization of reference materials for MTHFR, SERPINA1, RET, BRCA1, and BRCA2 genetic testing.J Mol Diagn. 2009; 11: 553-561Abstract Full Text Full Text PDF PubMed Scopus (10) Google Scholar, 22Pratt V.M. Everts R.E. Aggarwal P. Beyer B.N. Broeckel U. Epstein-Baak R. Hujsak P. Kornreich R. Liao J. Lorier R. Scott S.A. Smith C.H. Toji L.H. Turner A. Kalman L.V. Characterization of 137 genomic DNA reference materials for 28 pharmacogenetic genes: a GeT-RM collaborative project.J Mol Diagn. 2015; 18: 109-123Abstract Full Text Full Text PDF PubMed Scopus (84) Google Scholar Due to the lack of reference materials, many laboratories produce their own control materials derived from cell lines or limited patient samples on an ad hoc basis. However, these ad hoc materials are not characterized fully, and stability and homogeneity may not have been determined. In this report, we show the utility of the National Institute of Standards and Technology's (NIST) Standard Reference Materials (SRM) 2373 to ensure the quality and improve the confidence of the measurement of HER2 gene amplification using different NGS methods. Details regarding the certification of NIST SRM 2373 are available from the certificate of analysis and an article describing the development and characterization of SRM 2373.23He H.J. Almeida J.L. Lund S. Steffen C.R. Choquette S. Cole K.D. Development of NIST Standard Reference Material 2373: genomic DNA standards for HER2 measurements.Biomol Detect Quantif. 2016; 8: 1-8Crossref PubMed Scopus (15) Google Scholar The cell lines were obtained from the American Type Culture Collection (ATCC) (Manassas, VA) and grown in the NIST laboratories using the recommended culture conditions. The breast cancer cell lines have different sources, hormone sensitivity,24Neve R. Chin K. Fridlyand J. Yeh J. Baehner F. Fevr T. Clark L. Bayani N. Coppe J. Tong F. Speed T. Spellman P. DeVries S. Lapuk A. Wang N. Kuo W. Stilwell J. Pinkel D. Albertson D. Waldman F. McCormick F. Dickson R. Johnson M. Lippman M. Ethier S. Gazdar A. Gray J. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.Cancer Cell. 2006; 10: 515-527Abstract Full Text Full Text PDF PubMed Scopus (2386) Google Scholar and karyotypes25Kytola S. Rummukainen J. Nordgren A. Karhu R. Farnebo F. Isola J. Larsson C. Chromosomal alterations in 15 breast cancer cell lines by comparative genomic hybridization and spectral karyotyping.Genes Chromosomes Cancer. 2000; 28: 308-317Crossref PubMed Scopus (111) Google Scholar, 26Roschke A.V. Tonon G. Gehlhaus K.S. McTyre N. Bussey K.J. Lababidi S. Scudiero D.A. Weinstein J.N. Kirsch I.R. Karyotypic complexity of the NCI-60 drug-screening panel.Cancer Res. 2003; 63: 8634-8647PubMed Google Scholar, 27Davidson J.M. Gorringe K.L. Chin S.F. Orsetti B. Besret C. Courtay-Cahen C. Roberts I. Theillet C. Caldas C. Edwards P.A. Molecular cytogenetic analysis of breast cancer cell lines.Br J Cancer. 2000; 83: 1309-1317Crossref PubMed Scopus (87) Google Scholar, 28Popovici C. Basset C. Bertucci F. Orsetti B. Adelaide J. Mozziconacci M.J. Conte N. Murati A. Ginestier C. Charafe-Jauffret E. Ethier S.P. Lafage-Pochitaloff M. Theillet C. Birnbaum D. Chaffanet M. Reciprocal translocations in breast tumor cell lines: cloning of a t(3;20) that targets the FHIT gene.Genes Chromosomes Cancer. 2002; 35: 204-218Crossref PubMed Scopus (30) Google Scholar (Table 1). The HapMap cell lines CEPH NA12878 (characterized by the Genome in The Bottle consortium29Zook J.M. Chapman B. Wang J. Mittelman D. Hofmann O. Hide W. Salit M.L. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.Nat Biotechnol. 2014; 32: 246-251Crossref PubMed Scopus (472) Google Scholar), Chinese Female (NA18526), and Yoruban (NA18507) were used as reference genomes for the NGS methods. All three HapMap cell lines were obtained from the Coriell Institute for Medical Research (Camden, NJ) and cultured using the recommended culture conditions.Table 1Information for the Five Cell Lines Used in SRM 2373Cell lineMDA-MB-231 component BMDA-MB-361 component CMDA-MB-453 component DBT474 component ESK-BR-3 component ASourcePleural effusionBrain metastasisPericardial effusionInvasive ductal carcinomaPleural effusion metastasisKaryotypeHypotriploid26Roschke A.V. Tonon G. Gehlhaus K.S. McTyre N. Bussey K.J. Lababidi S. Scudiero D.A. Weinstein J.N. Kirsch I.R. Karyotypic complexity of the NCI-60 drug-screening panel.Cancer Res. 2003; 63: 8634-8647PubMed Google ScholarHyperdiploid25Kytola S. Rummukainen J. Nordgren A. Karhu R. Farnebo F. Isola J. Larsson C. Chromosomal alterations in 15 breast cancer cell lines by comparative genomic hybridization and spectral karyotyping.Genes Chromosomes Cancer. 2000; 28: 308-317Crossref PubMed Scopus (111) Google ScholarTetraploid27Davidson J.M. Gorringe K.L. Chin S.F. Orsetti B. Besret C. Courtay-Cahen C. Roberts I. Theillet C. Caldas C. Edwards P.A. Molecular cytogenetic analysis of breast cancer cell lines.Br J Cancer. 2000; 83: 1309-1317Crossref PubMed Scopus (87) Google Scholar, 28Popovici C. Basset C. Bertucci F. Orsetti B. Adelaide J. Mozziconacci M.J. Conte N. Murati A. Ginestier C. Charafe-Jauffret E. Ethier S.P. Lafage-Pochitaloff M. Theillet C. Birnbaum D. Chaffanet M. Reciprocal translocations in breast tumor cell lines: cloning of a t(3;20) that targets the FHIT gene.Genes Chromosomes Cancer. 2002; 35: 204-218Crossref PubMed Scopus (30) Google ScholarHypertriploid25Kytola S. Rummukainen J. Nordgren A. Karhu R. Farnebo F. Isola J. Larsson C. Chromosomal alterations in 15 breast cancer cell lines by comparative genomic hybridization and spectral karyotyping.Genes Chromosomes Cancer. 2000; 28: 308-317Crossref PubMed Scopus (111) Google ScholarHypertriploid25Kytola S. Rummukainen J. Nordgren A. Karhu R. Farnebo F. Isola J. Larsson C. Chromosomal alterations in 15 breast cancer cell lines by comparative genomic hybridization and spectral karyotyping.Genes Chromosomes Cancer. 2000; 28: 308-317Crossref PubMed Scopus (111) Google Scholar (highly modified)TypeBasal24Neve R. Chin K. Fridlyand J. Yeh J. Baehner F. Fevr T. Clark L. Bayani N. Coppe J. Tong F. Speed T. Spellman P. DeVries S. Lapuk A. Wang N. Kuo W. Stilwell J. Pinkel D. Albertson D. Waldman F. McCormick F. Dickson R. Johnson M. Lippman M. Ethier S. Gazdar A. Gray J. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.Cancer Cell. 2006; 10: 515-527Abstract Full Text Full Text PDF PubMed Scopus (2386) Google ScholarLuminal A24Neve R. Chin K. Fridlyand J. Yeh J. Baehner F. Fevr T. Clark L. Bayani N. Coppe J. Tong F. Speed T. Spellman P. DeVries S. Lapuk A. Wang N. Kuo W. Stilwell J. Pinkel D. Albertson D. Waldman F. McCormick F. Dickson R. Johnson M. Lippman M. Ethier S. Gazdar A. Gray J. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.Cancer Cell. 2006; 10: 515-527Abstract Full Text Full Text PDF PubMed Scopus (2386) Google ScholarLuminal24Neve R. Chin K. Fridlyand J. Yeh J. Baehner F. Fevr T. Clark L. Bayani N. Coppe J. Tong F. Speed T. Spellman P. DeVries S. Lapuk A. Wang N. Kuo W. Stilwell J. Pinkel D. Albertson D. Waldman F. McCormick F. Dickson R. Johnson M. Lippman M. Ethier S. Gazdar A. Gray J. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.Cancer Cell. 2006; 10: 515-527Abstract Full Text Full Text PDF PubMed Scopus (2386) Google ScholarLuminal A24Neve R. Chin K. Fridlyand J. Yeh J. Baehner F. Fevr T. Clark L. Bayani N. Coppe J. Tong F. Speed T. Spellman P. DeVries S. Lapuk A. Wang N. Kuo W. Stilwell J. Pinkel D. Albertson D. Waldman F. McCormick F. Dickson R. Johnson M. Lippman M. Ethier S. Gazdar A. Gray J. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.Cancer Cell. 2006; 10: 515-527Abstract Full Text Full Text PDF PubMed Scopus (2386) Google ScholarLuminal B24Neve R. Chin K. Fridlyand J. Yeh J. Baehner F. Fevr T. Clark L. Bayani N. Coppe J. Tong F. Speed T. Spellman P. DeVries S. Lapuk A. Wang N. Kuo W. Stilwell J. Pinkel D. Albertson D. Waldman F. McCormick F. Dickson R. Johnson M. Lippman M. Ethier S. Gazdar A. Gray J. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.Cancer Cell. 2006; 10: 515-527Abstract Full Text Full Text PDF PubMed Scopus (2386) Google ScholarHormone statusTriple negative24Neve R. Chin K. Fridlyand J. Yeh J. Baehner F. Fevr T. Clark L. Bayani N. Coppe J. Tong F. Speed T. Spellman P. DeVries S. Lapuk A. Wang N. Kuo W. Stilwell J. Pinkel D. Albertson D. Waldman F. McCormick F. Dickson R. Johnson M. Lippman M. Ethier S. Gazdar A. Gray J. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.Cancer Cell. 2006; 10: 515-527Abstract Full Text Full Text PDF PubMed Scopus (2386) Google ScholarER positive24Neve R. Chin K. Fridlyand J. Yeh J. Baehner F. Fevr T. Clark L. Bayani N. Coppe J. Tong F. Speed T. Spellman P. DeVries S. Lapuk A. Wang N. Kuo W. Stilwell J. Pinkel D. Albertson D. Waldman F. McCormick F. Dickson R. Johnson M. Lippman M. Ethier S. Gazdar A. Gray J. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.Cancer Cell. 2006; 10: 515-527Abstract Full Text Full Text PDF PubMed Scopus (2386) Google ScholarNegative ER/PR24Neve R. Chin K. Fridlyand J. Yeh J. Baehner F. Fevr T. Clark L. Bayani N. Coppe J. Tong F. Speed T. Spellman P. DeVries S. Lapuk A. Wang N. Kuo W. Stilwell J. Pinkel D. Albertson D. Waldman F. McCormick F. Dickson R. Johnson M. Lippman M. Ethier S. Gazdar A. Gray J. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.Cancer Cell. 2006; 10: 515-527Abstract Full Text Full Text PDF PubMed Scopus (2386) Google ScholarTriple Positive24Neve R. Chin K. Fridlyand J. Yeh J. Baehner F. Fevr T. Clark L. Bayani N. Coppe J. Tong F. Speed T. Spellman P. DeVries S. Lapuk A. Wang N. Kuo W. Stilwell J. Pinkel D. Albertson D. Waldman F. McCormick F. Dickson R. Johnson M. Lippman M. Ethier S. Gazdar A. Gray J. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.Cancer Cell. 2006; 10: 515-527Abstract Full Text Full Text PDF PubMed Scopus (2386) Google ScholarNegative ER24Neve R. Chin K. Fridlyand J. Yeh J. Baehner F. Fevr T. Clark L. Bayani N. Coppe J. Tong F. Speed T. Spellman P. DeVries S. Lapuk A. Wang N. Kuo W. Stilwell J. Pinkel D. Albertson D. Waldman F. McCormick F. Dickson R. Johnson M. Lippman M. Ethier S. Gazdar A. Gray J. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.Cancer Cell. 2006; 10: 515-527Abstract Full Text Full Text PDF PubMed Scopus (2386) Google ScholarNIST-certified ratio1.36.42.917.79.795% uncertainty interval1.1–1.55.7–7.12.6–3.215.9–19.58.7–10.7ER, estrogen receptor status; NIST, National Institute of Standards and Technology; PR, progesterone status; SRM, Standard Reference Material. Open table in a new tab ER, estrogen receptor status; NIST, National Institute of Standards and Technology; PR, progesterone status; SRM, Standard Reference Material. Genomic DNA samples were prepared using the Quick-gDNA MidiPrep kit (catalog number D3100; Zymo Research, Irvine, CA). The DNA samples were treated with bovine pancreatic ribonuclease A before purification to remove the enzyme.23He H.J. Almeida J.L. Lund S. Steffen C.R. Choquette S. Cole K.D. Development of NIST Standard Reference Material 2373: genomic DNA standards for HER2 measurements.Biomol Detect Quantif. 2016; 8: 1-8Crossref PubMed Scopus (15) Google Scholar All purified genomic DNA samples were prepared in buffer (10 mmol/L Tris, 0.1 mmol/L EDTA, pH 8.0) and stored at 4°C. The cell line DNA was authenticated using the AmpFLSTR Identifiler Plus PCR Amplification Kit (catalog number 4427368; Life Technologies, Carlsbad, CA) on a 3500xl Genetic Analyzer with a 36-cm capillary array and POP-4 polymer (Life Technologies). The DNA samples were analyzed both when received from the repository and when the cells were expanded to produce the genomic DNA used for the production of SRM 2373.23He H.J. Almeida J.L. Lund S. Steffen C.R. Choquette S. Cole K.D. Development of NIST Standard Reference Material 2373: genomic DNA standards for HER2 measurements.Biomol Detect Quantif. 2016; 8: 1-8Crossref PubMed Scopus (15) Google Scholar The short tandem repeat markers matched the values documented by ATCC. Cell lines were checked for myoplasma contamination using a PCR kit (Universal Mycoplasma Detection Kit 30-1012K; ATCC). An approximate concentration of the DNA components was determined using absorbance at 260 nm on five replicates (using the value 1 absorbance unit at 260 nm = 50 μg/mL).23He H.J. Almeida J.L. Lund S. Steffen C.R. Choquette S. Cole K.D. Development of NIST Standard Reference Material 2373: genomic DNA standards for HER2 measurements.Biomol Detect Quantif. 2016; 8: 1-8Crossref PubMed Scopus (15) Google Scholar TaqMan assays for HER2 and the four reference genes were developed at NIST23He H.J. Almeida J.L. Lund S. Steffen C.R. Choquette S. Cole K.D. Development of NIST Standard Reference Material 2373: genomic DNA standards for HER2 measurements.Biomol Detect Quantif. 2016; 8: 1-8Crossref PubMed Scopus (15) Google Scholar and validated using the MIME30Bustin S.A. Benes V. Garson J.A. Hellemans J. Huggett J. Kubista M. Mueller R. Nolan T. Pfaffl M.W. Shipley G.L. Vandesompele J. Wittwer C.T. The MIQE Guidelines: minimum Information for publication of quantitative real-time PCR experiments.Clin Chem. 2009; 55: 611-622Crossref PubMed Scopus (10344) Google Scholar and dMIME31Huggett J.F. Foy C.A. Benes V. Emslie K. Garson J.A. Haynes R. Hellemans J. Kubista M. Mueller R.D. Nolan T. Pfaffl M.W. Shipley G.L. Vandesompele J. Wittwer C.T. Bustin S.A. The digital MIQE guidelines: minimum Information for publication of quantitative digital PCR experiments.Clin Chem. 2013; 59: 892-902Crossref PubMed Scopus (594) Google Scholar guidelines. The primers and gene locations are shown in Table 2, and the probes, in Table 3. Black hole quencher 1– and fluorescein amidite–labeled probes were obtained from LGC Biosearch Technologies (Novato, CA). The qPCR measurements were taken using SYBR Green to determine the quantitation cycle using the ABI 7500 PCR System (Life Technologies). A quantitative human genomic DNA standard, SRM 2372 component A (produced from white blood cells from a healthy human male donor), was used to calibrate the standard curves for HER2 and the reference genes.23He H.J. Almeida J.L. Lund S. Steffen C.R. Choquette S. Cole K.D. Development of NIST Standard Reference Material 2373: genomic DNA standards for HER2 measurements.Biomol Detect Quantif. 2016; 8: 1-8Crossref PubMed Scopus (15) Google Scholar The chamber dPCR reactions were run on a BioMark platform (Fluidigm, San Francisco, CA) and the droplet dPCR assays were performed using a Q×100 Droplet Digital PCR System (Bio-Rad, Hercules, CA).Table 2PCR Primer Information for Reference Genes and HER2 Assays Used by MoChaPrimer nameSequencePCR amplicon (bp)Gene nameLocation (GRCh37/hq19 nucleotide number)HER2-2F5′-CTCATCGCTCACAACCAAGT-3′112HER2 (17q12)Exon 7 (chr17:37864601-37864620)HER2-2R5′-GGTCTCCATTGTCTAGCACG-3′(chr17:37864693-37864712)EIF5-F5′-GGCCGATAAATTTTTGGAAATG-3′112EIF5B 2q11.2Intron 1 (chr2:99974140-99974161)EIF5-R5′-GGAGTATCCCCAAAGGCATCT-3′(chr2:99974231-99974251)2PR4-F5′-CGGGTTTGGGTTCAGGTCTT-3′97RPS27A 2p16Intron 4 (chr2:55462316-55462335)2PR4-R5′-TGCTACAATGAAAACATTCAGAAGTCT-3′(chr2:55462386-55462412)R4Q5-F5′-CTCAGAAAAATGGTGGGAATGTT-3′122DCK 4q13.3-q21.1Exon 3 (chr4:71888097-71888119)R4Q5-R5′-GCCATTCAGAGAGGCAAGCT-3′(chr4:71888199-71888218)22C3-F5′-AGGTCTGGTGGCTTCTCCAAT-3′78PMM1 22q13.2Intron 7 (chr22:41973739-41973759)22C3-R5′-CCCCTAAGAGGTCTGTTGTGTTG-3′(chr22:41973682-41973704)MoCha, Molecular Characterization and Clinical Assay Development Laboratory at the Frederick National Laboratory for Cancer Research (Frederick, MD). Open table in a new tab Table 3TaqMan Fluorescent Probe Sequences for HER2 and Reference Gene Assays Used by MoChaProbe nameSequence5′ Label3′ QuencherHER2-2 (BHQ)5′-ACCCAGCTCTTTGAGGACAACTATGC-3′FAMBHQ-1EIF5-P5′-TTCAGCCTTCTCTTCTCATGCAGTTGTCAG-3′FAMBHQ-12PR4-P5′-TTTGTCTACCACTTGCAAAGCTGGCCTTT-3′FAMBHQ-1R4Q5-P5′-CCTTCCAAACATATGCCTGTCTCAGTCGA-3′FAMBHQ-122C3-P5′-CAAATCACCTGAGGTCAAGGCCAGAACA-3′FAMBHQ-1BHQ, black hole quencher; FAM, fluorescein amidite; MoCha, Molecular Characterization and Clinical Assay Development Laboratory at the Frederick National Laboratory for Cancer Research (Frederick, MD). Open table in a new tab MoCha, Molecular Characterization and Clinical Assay Development Laboratory at the Frederick National Laboratory for Cancer Research (Frederick, MD). BHQ, black hole quencher; FAM, fluorescein amidite; MoCha, Molecular Characterization and Clinical Assay Development Laboratory at the Frederick National Laboratory for Cancer Research (Frederick, MD). The SRM23" @default.
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• W2493018502 date "2016-09-01" @default.
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• W2493018502 title "Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next-Generation Sequencing Methods" @default.
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• W2493018502 doi "https://doi.org/10.1016/j.jmoldx.2016.05.008" @default.
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