Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network-Breast Initiative
Christian Brueffer, Johan Vallon-Christersson, Dorthe Grabau, Anna Ehinger, Jari Häkkinen, Cecilia Hegardt, Janne Malina, Yilun Chen, Pär-Ola Bendahl, Jonas Manjer, Martin Malmberg, Christer Larsson, Niklas Loman, Lisa Rydén, Åke Borg, Lao H Saal, Christian Brueffer, Johan Vallon-Christersson, Dorthe Grabau, Anna Ehinger, Jari Häkkinen, Cecilia Hegardt, Janne Malina, Yilun Chen, Pär-Ola Bendahl, Jonas Manjer, Martin Malmberg, Christer Larsson, Niklas Loman, Lisa Rydén, Åke Borg, Lao H Saal
Abstract
Purpose: In early breast cancer (BC), five conventional biomarkers-estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)-are used to determine prognosis and treatment. We aimed to develop classifiers for these biomarkers that were based on tumor mRNA sequencing (RNA-seq), compare classification performance, and test whether such predictors could add value for risk stratification.
Methods: In total, 3,678 patients with BC were studied. For 405 tumors, a comprehensive multi-rater histopathologic evaluation was performed. Using RNA-seq data, single-gene classifiers and multigene classifiers (MGCs) were trained on consensus histopathology labels. Trained classifiers were tested on a prospective population-based series of 3,273 BCs that included a median follow-up of 52 months (Sweden Cancerome Analysis Network-Breast [SCAN-B], ClinicalTrials.gov identifier: NCT02306096), and results were evaluated by agreement statistics and Kaplan-Meier and Cox survival analyses.
Results: Pathologist concordance was high for ER, PgR, and HER2 (average κ, 0.920, 0.891, and 0.899, respectively) but moderate for Ki67 and NHG (average κ, 0.734 and 0.581). Concordance between RNA-seq classifiers and histopathology for the independent cohort of 3,273 was similar to interpathologist concordance. Patients with discordant classifications, predicted as hormone responsive by histopathology but non-hormone responsive by MGC, had significantly inferior overall survival compared with patients who had concordant results. This extended to patients who received no adjuvant therapy (hazard ratio [HR], 3.19; 95% CI, 1.19 to 8.57), or endocrine therapy alone (HR, 2.64; 95% CI, 1.55 to 4.51). For cases identified as hormone responsive by histopathology and who received endocrine therapy alone, the MGC hormone-responsive classifier remained significant after multivariable adjustment (HR, 2.45; 95% CI, 1.39 to 4.34).
Conclusion: Classification error rates for RNA-seq-based classifiers for the five key BC biomarkers generally were equivalent to conventional histopathology. However, RNA-seq classifiers provided added clinical value in particular for tumors determined by histopathology to be hormone responsive but by RNA-seq to be hormone insensitive.
Conflict of interest statement
The following represents disclosure information provided by authors of this manuscript. All relationships are considered compensated. Relationships are self-held unless noted. I = Immediate Family Member, Inst = My Institution. Relationships may not relate to the subject matter of this manuscript. For more information about ASCO's conflict of interest policy, please refer to www.asco.org/rwc or ascopubs.org/po/author-center. Christian BruefferEmployment: SAGA Diagnostics ABJohan Vallon-ChristerssonNo relationship to discloseDorthe GrabauNo relationship to discloseAnna EhingerNo relationship to discloseJari HäkkinenNo relationship to discloseCecilia HegardtNo relationship to discloseJanne MalinaEmployment: Unilabs Honoraria: AstraZenecaYilun ChenNo relationship to disclosePär-Ola BendahlNo relationship to discloseJonas ManjerNo relationship to discloseMartin MalmbergNo relationship to discloseChrister LarssonHonoraria: Lilly (I) Research Funding: Diamyd Medical AB (I) Travel, Accommodations, Expenses: Lilly (I)Niklas LomanHonoraria: AstraZeneca Consulting or Advisory Role: AmgenLisa RydénResearch Funding: RocheÅke BorgHonoraria: Roche, AstraZeneca Travel, Accommodations, Expenses: Roche, AstraZenecaLao H. SaalEmployment: SAGA Diagnostics AB Leadership: SAGA Diagnostics AB Stock and Other Ownership Interests: SAGA Diagnostics AB Patents, Royalties, Other Intellectual Property: Patent filed for methods related to ultrasensitive quantification of nucleotide sequence variants.
© 2018 by American Society of Clinical Oncology.
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References
- Gradishar WJ, Anderson BO, Blair SL, et al. : Breast cancer, version 3.2014. J Natl Compr Canc Netw 12:542-590, 2014
- Senkus E, Kyriakides S, Ohno S, et al. : Primary breast cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol 26:v8-v30, 2015
- Hammond MEH, Hayes DF, Dowsett M, et al. : American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer. J Clin Oncol 28:2784-2795, 2010
- Press MF, Sauter G, Bernstein L, et al. : Diagnostic evaluation of HER-2 as a molecular target: An assessment of accuracy and reproducibility of laboratory testing in large, prospective, randomized clinical trials. Clin Cancer Res 11:6598-6607, 2005
- Perez EA, Suman VJ, Davidson NE, et al. : HER2 testing by local, central, and reference laboratories in specimens from the North Central Cancer Treatment Group N9831 intergroup adjuvant trial. J Clin Oncol 24:3032-3038, 2006
- Rydén L, Haglund M, Bendahl P-O, et al. : Reproducibility of human epidermal growth factor receptor 2 analysis in primary breast cancer: A national survey performed at pathology departments in Sweden. Acta Oncol 48:860-866, 2009
- Ekholm M, Grabau D, Bendahl P-O, et al. : Highly reproducible results of breast cancer biomarkers when analysed in accordance with national guidelines: A Swedish survey with central re-assessment. Acta Oncol 54:1040-1048, 2015
- Wolff AC, Hammond MEH, Hicks DG, et al. : Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update. J Clin Oncol 31:3997-4013, 2013
- Dowsett M, Nielsen TO, A’Hern R, et al. : Assessment of Ki67 in breast cancer: Recommendations from the International Ki67 in Breast Cancer working group. J Natl Cancer Inst 103:1656-1664, 2011
- Polley MYC, Leung SCY, McShane LM, et al. : An international Ki67 reproducibility study. J Natl Cancer Inst 105:1897-1906, 2013
- Gnant M, Thomssen C, Harbeck N: St Gallen/Vienna 2015: A brief summary of the consensus discussion. Breast Care (Basel) 10:124-130, 2015
- Rakha EA, Reis-Filho JS, Baehner F, et al. : Breast cancer prognostic classification in the molecular era: The role of histological grade. Breast Cancer Res 12:207, 2010
- van ’t Veer LJ, Dai H, van de Vijver MJ, et al. : Gene expression profiling predicts clinical outcome of breast cancer. Nature 415:530-536, 2002
- Saal LH, Johansson P, Holm K, et al. : Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity. Proc Natl Acad Sci USA 104:7564-7569, 2007
- Parker JS, Mullins M, Cheang MC, et al. : Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 27:1160-1167, 2009
- Roepman P, Horlings HM, Krijgsman O, et al. : Microarray-based determination of estrogen receptor, progesterone receptor, and HER2 receptor status in breast cancer. Clin Cancer Res 15:7003-7011, 2009
- Saal LH, Vallon-Christersson J, Häkkinen J, et al. : The Sweden Cancerome Analysis Network Breast (SCAN-B) initiative: A large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine. Genome Med 7:20, 2015
- Häkkinen J, Nordborg N, Månsson O, et al. : Implementation of an open source software solution for laboratory information management and automated RNAseq data analysis in a large-scale cancer genomics initiative using BASE with extension package Reggie. bioRxiv doi: 10.1101/038976 [epub on February 6, 2016]
- Tibshirani R, Hastie T, Narasimhan B, et al. : Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 99:6567-6572, 2002
- Huang W, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44-57, 2009
- Cicchetti DV, Feinstein AR: High agreement but low kappa: II. Resolving the paradoxes. J Clin Epidemiol 43:551-558, 1990
- Viera AJ, Garrett JM: Understanding interobserver agreement: The kappa statistic. Fam Med 37:360-363, 2005
- Bastani M, Vos L, Asgarian N, et al. : A machine learned classifier that uses gene expression data to accurately predict estrogen receptor status. PLoS One 8:e82144, 2013
- Kun Y, How LC, Hoon TP, et al. : Classifying the estrogen receptor status of breast cancers by expression profiles reveals a poor prognosis subpopulation exhibiting high expression of the ERBB2 receptor. Hum Mol Genet 12:3245-3258, 2003
- Viale G, Slaets L, Bogaerts J, et al. : High concordance of protein (by IHC), gene (by FISH; HER2 only), and microarray readout (by TargetPrint) of ER, PgR, and HER2: Results from the EORTC 10041/BIG 03-04 MINDACT trial. Ann Oncol 25:816-823, 2014
- Wilson TR, Xiao Y, Spoerke JM, et al. : Development of a robust RNA-based classifier to accurately determine ER, PR, and HER2 status in breast cancer clinical samples. Breast Cancer Res Treat 148:315-325, 2014
- Cieslik M, Chugh R, Wu YM, et al. : The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing. Genome Res 25:1372-1381, 2015
- Roychowdhury S, Iyer MK, Robinson DR, et al. : Personalized oncology through integrative high-throughput sequencing: A pilot study. Sci Transl Med 3:111ra121, 2011
- Cardoso F, van’t Veer LJ, Bogaerts J, et al. : 70-Gene signature as an aid to treatment decisions in early-stage breast cancer. N Engl J Med 375:717-729, 2016
- Boiesen P, Bendahl PO, Anagnostaki L, et al. : Histologic grading in breast cancer: Reproducibility between seven pathologic departments. Acta Oncol 39:41-45, 2000
- Lowery AJ, Miller N, Devaney A, et al. : MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer. Breast Cancer Res 11:R27, 2009
- Rantalainen M, Klevebring D, Lindberg J, et al. : Sequencing-based breast cancer diagnostics as an alternative to routine biomarkers. Sci Rep 6:38037, 2016
- Dhondalay GK, Tong DL, Ball GR: Estrogen receptor status prediction for breast cancer using artificial neural network. Proc Int Conf Mach Learn Cybern 2:727-731, 2011
- Paik S, Shak S, Tang G, et al. : A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 351:2817-2826, 2004
- Ivshina AV, George J, Senko O, et al. : Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res 66:10292-10301, 2006
- Sotiriou C, Wirapati P, Loi S, et al. : Gene expression profiling in breast cancer: Understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 98:262-272, 2006
Source: PubMed