Additional file 10: Provides sample patient data as an example of
input needed for RFRS sample code and provides sample R code
for running the RFRS algorithm.
Additional file 11: Consists of the R data files for 17-gene and
Additional file 12: Consists of additional R data files which allow
plotting of patients’ RFRS result and determination of predicted
relapse probability for the report file.
Additional file 13: Shows a sample patient report produced by the
Additional file 14: Consists of a complete list of GEO sample
identifiers for training and test datasets combined.
Additional file 15: Consists of additional sample R code to help
reproduce the analysis.
AUC: Area under curve; ER: Estrogen receptor; GEO: Gene Expression
Omnibus; GO: Gene ontology; HER2: Human epidermal growth factor
receptor 2; LN: Lymph node; OOB: Out of bag; RFRS: Random forest relapse
score; ROC: Receiver-operating characteristic.
Cepheid Inc. has licensed from OHSU technology of which OLG, FP, OME,
PTS, and JWG are inventors. The technology is used in this research. This
potential conflict of interest has been reviewed and managed by OHSU.
The remaining authors declare that they have no competing interests.
OLG participated in the design of the study, assembled the data, developed
analysis methods, performed the analysis, and drafted the manuscript. FP,
OME, and LMH participated in the design of the study and helped with
analysis. EAC participated in the design of the study and helped to draft the
manuscript. PTS and JWG conceived of the study, and participated in its
design and coordination and helped to draft the manuscript. All authors
read and approved the final manuscript.
OLG and FP were postdoctoral fellows and LMH was a scientist at Lawrence
Berkeley National Laboratory (LBNL), all under the supervision of PTS and
JWG, during the production of this work. OLG is currently a genome fellow
at the Genome Institute and research assistant professor at Washington
University Medical School. OME is a student at University of California,
Berkeley. LMH is currently a research assistant professor at Oregon Health &
Science University (OHSU). EAC is a medical oncologist and an assistant
professor at University of California, San Francisco School of Medicine. PTS
was a staff scientist at LBNL and is currently an associate professor at OHSU.
JWG was Life Sciences Division director and associate laboratory director for
Biosciences at LBNL, program leader of Breast Oncology and Cancer Genetics
at UCSF Helen Diller Family Comprehensive Cancer Center and a professor at
UCSF. JWG is currently co-director of the Bay Area Breast Cancer Specialized
Program of Research Excellence (SPORE), visiting faculty at LBNL, emeritus
professor at UCSF, director of the OHSU Center for Spatial Systems
Biomedicine (OCSSB), Gordon Moore endowed chair and the department of
Biomedical Engineering chair at OHSU.
OLG was supported by a Fellowship from the Canadian Institutes of Health
Research. EAC was supported by K08 CA137153 . OME was supported by the
NCI ICBP Summer Cancer Research Fellowship program. This work was
supported by the Director, Office of Science, Office of Biological &
Environmental Research, of the U.S. Department of Energy under Contract
No. DE-AC02-05CH11231; U54 CA 112970 and SU2C-AACR-DT0409 to JWG.
The content of the information does not necessarily reflect the position or
the policy of the Government, and no official endorsement should be
Department of Cancer and DNA Damage Responses, Life Sciences Division,
Lawrence Berkeley National Laboratory, One Cyclotron Rd, Berkeley 94720,
Current affiliation: Department of Medicine, Division of Oncology,
The Genome Institute, Washington University, Campus Box 8501, 4444
Forest Park Ave, St. Louis 63108, MO, USA.
Current affiliation: Sequenta Inc.,
400 East Jamie Court, Suite 301, South San Francisco 94080, CA, USA.
Department of Biomedical Engineering, Center for Spatial Systems
Biomedicine, Knight Cancer Institu te, Oregon Health and Science University,
3303 SW Bond Ave, Portland, 97239, OR, USA.
Division of Hematology/
Oncology, University of California San Francisco, 505 Parnassus Avenue, San
Francisco 94143, CA, USA.
Current affiliation: Department of Molecular and
Medical Genetics, Oregon Health and Science University, 3181 SW Sam
Jackson Park Rd, Portland 97239, OR, USA.
Received: 15 March 2013 Accepted: 26 September 2013
Published: 11 October 2013
1. Berry DA, Cronin KA, Plevritis SK, Fryback DG, Clarke L, Zelen M,
Mandelblatt JS, Yakovlev AY, Habbema JD, Feuer EJ: Effect of screening
and adjuvant therapy on mortality from breast cancer. NEnglJMed
2005, 353: 1784 –1792.
2. Early Breast Cancer Trialists’ Collaborative Group: Effects of
chemotherapy and hormonal therapy for early breast cancer on
recurrence and 15- year sur vival: an overview of the ran domised trials.
Lancet 2005 , 365: 1687–1717.
3. Desmedt C, Piette F, Loi S, Wang Y, Lallemand F, Haibe-Kains B, Viale G,
Delorenzi M, Zhang Y, D’Assignies MS: Strong time dependence of the 76-
gene prognostic signature for node-negative breast cancer patients in
the TRANSBIG multicenter independent validation series. Clin Cancer Res
2007, 13:3207 – 3214.
4. Ivshina AV, George J, Senko O, Mow B, Putti TC, Smeds J, Lindahl T, Pawitan
Y, Hall P, Nordgren H, et al: Genetic reclassification of histologic grade
delineates new clinical subtypes of breast cancer. Cancer Res 2006,
5. Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt AM, Gillet C, Ellis P, Harris
A, Bergh J, Foekens JA, Klijn JG, Larsimont D, Buyse M, Bontempi G,
Delorenzi M, Piccart MJ, Sotiriou C: Definition of clinically distinct
molecular subtypes in estrogen receptor-positive breast carcinomas
through genomic grade. J Clin Oncol 2007, 25:1239–1246.
6. Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P,
Klaar S, Liu ET, Bergh J: An expression signature for p53 status in human
breast cancer predicts mutation status, transcriptional effects, and
patient survival. Proc Natl Acad S ci U S A 2005, 102:13550–13555.
7. Schmidt M, Bohm D, von Torne C, Steiner E, Puhl A, Pilch H, Lehr HA,
Hengstler JG, Kolbl H, Gehrmann M: The humoral immune system has a
key prognostic impact in node-negative breast cancer. Cancer Res 2008,
8. Sotiriou C, Wirapati P, Loi S, HarrisA,FoxS,SmedsJ,NordgrenH,Farmer
P, Praz V, Haibe-Ka ins B, Desmedt C, Larsimont D, Cardoso F, Peterse H,
Nuyten D, Buyse M, Van de Vijver MJ, Bergh J, Piccart M, Delorenzi M:
Gene expression profiling in breast cancer: understanding the
molecular basis of histolo gic grade to improve prognosis.
JNatlCancerInst2006 , 98:262–272.
9. Symmans WF, Hatzis C, Sotiriou C, Andre F, Peintinger F, Regitnig P,
Daxenbichler G, Desmedt C, Domont J, Marth C, Delaloge S, Bauernhofer T,
Valero V, Booser DJ, Hortobagyi GN, Pusztai L: Genomic index of sensitivity
to endocrine therapy for breast cancer. J Clin Oncol 2010, 28:4111–4119.
10. Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D,
Timmermans M, Meijer-van Gelder ME, Yu J:
Gene-expression profiles to
predict distant metastasis of lymph-node-negative primary breast
cancer. Lancet 2005, 365:671–679.
11. Zhang Y, Sieuwerts AM, McGreevy M, Casey G, Cufer T, Paradiso A, Harbeck
N, Span PN, Hicks DG, Crowe J, Tubbs RR, Budd GT, Lyons J, Sweep FC,
Schmitt M, Schittulli F, Golouh R, Talantov D, Wang Y, Foekens JA: The 76-
gene signature defines high-risk patients that benefit from adjuvant
tamoxifen therapy. Breast Cancer Res Treat 2009, 116:303–309.
12. Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF,
Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko
M, Ayanbule O, Yefanov A, Soboleva A: NCBI GEO: archive for functional
genomics data sets–10 years on. Nucleic Acids Res 2011, 39:D1005–D1010.
13. Gautier L, Cope L, Bolstad BM, Irizarry RA: affy–analysis of Affymetrix
GeneChip data at the probe level. Bioinformatics 2004, 20:307– 315.
Griffith et al. Genome Medicine 2013, 5:92 Page 13 of 14