A case-control study to identify molecular risk factors for local recurrence in young breast cancer patients.

[1]  H. Bartelink,et al.  A signature that may be predictive of early vs. late recurrence after radiation treatment (RT) for breast cancer that may inform the biology of early, aggressive recurrences. , 2020, International journal of radiation oncology, biology, physics.

[2]  Nikhil Wagle,et al.  Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer. , 2018, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[3]  M. Fernö,et al.  Response to Radiotherapy After Breast-Conserving Surgery in Different Breast Cancer Subtypes in the Swedish Breast Cancer Group 91 Radiotherapy Randomized Clinical Trial. , 2017, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[4]  P. V. van Diest,et al.  Contemporary Locoregional Recurrence Rates in Young Patients With Early-Stage Breast Cancer. , 2016, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[5]  L. Pierce,et al.  Postoperative Radiotherapy After Breast-Conserving Surgery for Early-Stage Breast Cancer: A Review. , 2016, JAMA oncology.

[6]  M. Reinders,et al.  RUBIC identifies driver genes by detecting recurrent DNA copy number breaks , 2016, Nature Communications.

[7]  R. Finn,et al.  Targeting the cyclin-dependent kinases (CDK) 4/6 in estrogen receptor-positive breast cancers , 2016, Breast Cancer Research.

[8]  Felix Y. Feng,et al.  Development and Validation of a Novel Radiosensitivity Signature in Human Breast Cancer , 2015, Clinical Cancer Research.

[9]  H. Bartelink,et al.  Gene expression profiling to predict the risk of locoregional recurrence in breast cancer: a pooled analysis , 2014, Breast Cancer Research and Treatment.

[10]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[11]  M. Dunning,et al.  Genome-driven integrated classification of breast cancer validated in over 7,500 samples , 2014, Genome Biology.

[12]  A. Frigessi,et al.  Development and Validation of a Gene Profile Predicting Benefit of Postmastectomy Radiotherapy in Patients with High-Risk Breast Cancer: A Study of Gene Expression in the DBCG82bc Cohort , 2014, Clinical Cancer Research.

[13]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[14]  John M S Bartlett,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. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[15]  V. Tjan-Heijnen,et al.  Local recurrence following breast-conserving treatment in women aged 40 years or younger: trends in risk and the impact on prognosis in a population-based cohort of 1143 patients. , 2013, European journal of cancer.

[16]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[17]  F. Markowetz,et al.  The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups , 2012, Nature.

[18]  Emmanuel Barillot,et al.  Search for a Gene Expression Signature of Breast Cancer Local Recurrence in Young Women , 2012, Clinical Cancer Research.

[19]  C. Sotiriou,et al.  Elucidating Prognosis and Biology of Breast Cancer Arising in Young Women Using Gene Expression Profiling , 2012, Clinical Cancer Research.

[20]  P. Watson,et al.  True recurrence versus new primary: an analysis of ipsilateral breast tumor recurrences after breast-conserving therapy. , 2011, International journal of radiation oncology, biology, physics.

[21]  R. Gelber,et al.  Strategies for subtypes—dealing with the diversity of breast cancer: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2011 , 2011, Annals of oncology : official journal of the European Society for Medical Oncology.

[22]  Adam B. Olshen,et al.  Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles , 2011, Bioinform..

[23]  V. Tjan-Heijnen,et al.  Are breast conservation and mastectomy equally effective in the treatment of young women with early breast cancer? Long-term results of a population-based cohort of 1,451 patients aged ≤40 years , 2011, Breast Cancer Research and Treatment.

[24]  T. Nielsen,et al.  Breast cancer subtypes and the risk of local and regional relapse. , 2010, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[25]  S. Paik,et al.  Association between the 21-gene recurrence score assay and risk of locoregional recurrence in node-negative, estrogen receptor-positive breast cancer: results from NSABP B-14 and NSABP B-20. , 2010, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[26]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[27]  M. J. van de Vijver,et al.  Local Recurrence after Breast-Conserving Therapy in Relation to Gene Expression Patterns in a Large Series of Patients , 2009, Clinical Cancer Research.

[28]  A. Bleyer,et al.  Breast cancer before age 40 years. , 2009, Seminars in oncology.

[29]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[30]  A. Nobel,et al.  Supervised risk predictor of breast cancer based on intrinsic subtypes. , 2009, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[31]  Barbara L. Smith,et al.  Breast cancer subtype approximated by estrogen receptor, progesterone receptor, and HER-2 is associated with local and distant recurrence after breast-conserving therapy. , 2008, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[32]  Carsten Peterson,et al.  Gene expression profiling in primary breast cancer distinguishes patients developing local recurrence after breast-conservation surgery, with or without postoperative radiotherapy , 2008, Breast Cancer Research.

[33]  Emmanuel Barillot,et al.  High-resolution mapping of DNA breakpoints to define true recurrences among ipsilateral breast cancers. , 2008, Journal of the National Cancer Institute.

[34]  Daniel Birnbaum,et al.  Integrated profiling of basal and luminal breast cancers. , 2007, Cancer research.

[35]  Howard Y. Chang,et al.  Predicting a local recurrence after breast-conserving therapy by gene expression profiling , 2006, Breast Cancer Research.

[36]  D. Birnbaum,et al.  BMC Cancer , 2003 .

[37]  M. J. van de Vijver,et al.  Gene Expression Profiles of Primary Breast Carcinomas from Patients at High Risk for Local Recurrence after Breast-Conserving Therapy , 2006, Clinical Cancer Research.

[38]  M. Wigler,et al.  Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.

[39]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[40]  L Collette,et al.  Can patient-, treatment- and pathology-related characteristics explain the high local recurrence rate following breast-conserving therapy in young patients? , 2003, European journal of cancer.

[41]  S. Singletary,et al.  Classifying local disease recurrences after breast conservation therapy based on location and histology , 2002, Cancer.

[42]  R. Tibshirani,et al.  Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[43]  J. Peterse,et al.  Differences in risk factors for local and distant recurrence after breast-conserving therapy or mastectomy for stage I and II breast cancer: pooled results of two large European randomized trials. , 2001, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[44]  Christian A. Rees,et al.  Molecular portraits of human breast tumours , 2000, Nature.

[45]  Richard Sylvester,et al.  Long-term results of a randomized trial comparing breast-conserving therapy with mastectomy: European Organization for Research and Treatment of Cancer 10801 trial. , 2000, Journal of the National Cancer Institute.

[46]  M. J. van de Vijver,et al.  Local recurrence after breast-conserving therapy for invasive breast cancer: high incidence in young patients and association with poor survival. , 1998, International journal of radiation oncology, biology, physics.

[47]  D. Horsfall,et al.  EMS1 amplification can occur independently of CCND1 or INT-2 amplification at 11q13 and may identify different phenotypes in primary breast cancer , 1997, Oncogene.

[48]  E. van Limbergen,et al.  Whole-breast irradiation with or without a boost for patients treated with breast-conserving surgery for early breast cancer: 20-year follow-up of a randomised phase 3 trial. , 2015, The Lancet. Oncology.

[49]  H. Bartelink,et al.  Quality indicators for breast cancer: revisiting historical evidence in the context of technology changes. , 2012, Seminars in radiation oncology.

[50]  Bryan Langholz,et al.  Risk set sampling in epidemiologic cohort studies , 1996 .