Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer

[1]  Hao Cai,et al.  Individualized identification of disease-associated pathways with disrupted coordination of gene expression , 2016, Briefings Bioinform..

[2]  Eytan Domany,et al.  Pathway‐based personalized analysis of breast cancer expression data , 2015, Molecular oncology.

[3]  A. Ashworth,et al.  Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers. , 2015, Cancer discovery.

[4]  E. Wang,et al.  TUSC4 functions as a tumor suppressor by regulating BRCA1 stability. , 2015, Cancer research.

[5]  A. Børresen-Dale,et al.  A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer , 2014, Molecular oncology.

[6]  Qiang Sun,et al.  Individual-level analysis of differential expression of genes and pathways for personalized medicine , 2015, Bioinform..

[7]  N. McGranahan,et al.  Chromosomal instability selects gene copy-number variants encoding core regulators of proliferation in ER+ breast cancer. , 2014, Cancer research.

[8]  Lana X. Garmire,et al.  A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer , 2014, PLoS Comput. Biol..

[9]  Taesung Park,et al.  Personalized identification of altered pathways in cancer using accumulated normal tissue data , 2014, Bioinform..

[10]  C. Greenwood,et al.  Chromosome-breakage genomic instability and chromothripsis in breast cancer , 2014, BMC Genomics.

[11]  G. Chenevix-Trench,et al.  A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy , 2014, Nucleic acids research.

[12]  D. Durocher,et al.  Mitosis Inhibits DNA Double-Strand Break Repair to Guard Against Telomere Fusions , 2014, Science.

[13]  A. Venkitaraman Cancer Suppression by the Chromosome Custodians, BRCA1 and BRCA2 , 2014, Science.

[14]  Ralph R. Weichselbaum,et al.  DNA Repair Pathway Gene Expression Score Correlates with Repair Proficiency and Tumor Sensitivity to Chemotherapy , 2014, Science Translational Medicine.

[15]  F. D. D. Fagagna A direct role for small non-coding RNAs in DNA damage response. , 2014 .

[16]  D. Sheer,et al.  The role of microhomology in genomic structural variation. , 2014, Trends in genetics : TIG.

[17]  G. Mills,et al.  Genome-wide Transcriptome Profiling of Homologous Recombination DNA Repair , 2014, Nature Communications.

[18]  A. Venkitaraman Tumour Suppressor Mechanisms in the Control of Chromosome Stability: Insights from BRCA2 , 2014, Molecules and cells.

[19]  F. d’Adda di Fagagna A direct role for small non-coding RNAs in DNA damage response. , 2014, Trends in cell biology.

[20]  K. Cimprich,et al.  Causes and consequences of replication stress , 2013, Nature Cell Biology.

[21]  M. Debatisse,et al.  Spontaneous slow replication fork progression elicits mitosis alterations in homologous recombination-deficient mammalian cells , 2013, Proceedings of the National Academy of Sciences.

[22]  A. Aguilera,et al.  Causes of genome instability. , 2013, Annual review of genetics.

[23]  Roman Rouzier,et al.  Genomic Instability: A Stronger Prognostic Marker Than Proliferation for Early Stage Luminal Breast Carcinomas , 2013, PloS one.

[24]  Chris Sander,et al.  The molecular diversity of Luminal A breast tumors , 2013, Breast Cancer Research and Treatment.

[25]  N. McGranahan,et al.  The causes and consequences of genetic heterogeneity in cancer evolution , 2013, Nature.

[26]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[27]  T. Misteli,et al.  Non‐coding RNAs in DNA damage and repair , 2013, FEBS letters.

[28]  A. Nussenzweig,et al.  End-joining, translocations and cancer , 2013, Nature Reviews Cancer.

[29]  J. Reis-Filho,et al.  Taxane benefit in breast cancer—a role for grade and chromosomal stability , 2013, Nature Reviews Clinical Oncology.

[30]  Michal Sheffer,et al.  Pathway-based personalized analysis of cancer , 2013, Proceedings of the National Academy of Sciences.

[31]  A. D’Andrea,et al.  Chromatin Remodeling at DNA Double-Strand Breaks , 2013, Cell.

[32]  Jiri Bartek,et al.  Replication stress links structural and numerical cancer chromosomal instability , 2013, Nature.

[33]  Young Eun Choi,et al.  Charity begins at home: non-coding RNA functions in DNA repair , 2013, Nature Reviews Molecular Cell Biology.

[34]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumours , 2013 .

[35]  A. Vincent-Salomon,et al.  Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation. , 2012, Cancer research.

[36]  A. Malkova,et al.  Microhomology Directs Diverse DNA Break Repair Pathways and Chromosomal Translocations , 2012, PLoS genetics.

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

[38]  H. Ulrich Ubiquitin and SUMO in DNA repair at a glance , 2012, Journal of Cell Science.

[39]  Qin Huang,et al.  Polyploid cells rewire DNA damage response networks to overcome replication stress-induced barriers for tumour progression , 2012, Nature Communications.

[40]  Masaaki Oka,et al.  Luminal A and luminal B (HER2 negative) subtypes of breast cancer consist of a mixture of tumors with different genotype , 2012, BMC Research Notes.

[41]  N. Mailand,et al.  The ubiquitin‐ and SUMO‐dependent signaling response to DNA double‐strand breaks , 2011, FEBS letters.

[42]  E. Yeh,et al.  SUMOylation and de‐SUMOylation in response to DNA damage , 2011, FEBS letters.

[43]  Shiaw-Yih Lin,et al.  DNA damage and breast cancer. , 2011, World journal of clinical oncology.

[44]  Nicolai J. Birkbak,et al.  Relationship of Extreme Chromosomal Instability with Long-term Survival in a Retrospective Analysis of Primary Breast Cancer , 2011, Cancer Epidemiology, Biomarkers & Prevention.

[45]  X. Chen,et al.  Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. , 2011, The Journal of clinical investigation.

[46]  Zoltan Szallasi,et al.  Paradoxical relationship between chromosomal instability and survival outcome in cancer. , 2011, Cancer research.

[47]  Laurent Sansregret,et al.  Gene signatures of genomic instability as prognostic tools for breast cancer. , 2011, Future oncology.

[48]  E. Wiechec Implications of genomic instability in the diagnosis and treatment of breast cancer , 2011, Expert review of molecular diagnostics.

[49]  Nicolai J. Birkbak,et al.  Chromosomal instability confers intrinsic multidrug resistance. , 2011, Cancer research.

[50]  Lincoln Stein,et al.  Reactome: a database of reactions, pathways and biological processes , 2010, Nucleic Acids Res..

[51]  S. Sleijfer,et al.  Patterns and incidence of chromosomal instability and their prognostic relevance in breast cancer subtypes , 2011, Breast Cancer Research and Treatment.

[52]  J. Benítez,et al.  BRCA2 Acts as RAD51 Loader to Facilitate Telomere Replication and Capping , 2010, Nature Structural &Molecular Biology.

[53]  David Haussler,et al.  Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM , 2010, Bioinform..

[54]  D. Compton,et al.  Mechanisms of Chromosomal Instability , 2010, Current Biology.

[55]  T. Halazonetis,et al.  Genomic instability — an evolving hallmark of cancer , 2010, Nature Reviews Molecular Cell Biology.

[56]  J. Lupski,et al.  Mechanisms of change in gene copy number , 2009, Nature Reviews Genetics.

[57]  Thomas J. Hardcastle,et al.  Chromosomal instability determines taxane response , 2009, Proceedings of the National Academy of Sciences.

[58]  S. Gasser,et al.  Crosstalk between histone modifications during the DNA damage response. , 2009, Trends in cell biology.

[59]  Sampsa Hautaniemi,et al.  The gene expression signature of genomic instability in breast cancer is an independent predictor of clinical outcome , 2009, International journal of cancer.

[60]  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.

[61]  J. Holt,et al.  Rad51 overexpression rescues radiation resistance in BRCA2‐defective cancer cells , 2009, Molecular carcinogenesis.

[62]  A. Kauffmann,et al.  Overexpression of DNA repair genes is associated with metastasis: a new hypothesis. , 2008, Mutation research.

[63]  B. Orelli,et al.  RAD51 up-regulation bypasses BRCA1 function and is a common feature of BRCA1-deficient breast tumors. , 2007, Cancer research.

[64]  Z. Szallasi,et al.  A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers , 2006, Nature Genetics.

[65]  A. Nobel,et al.  The molecular portraits of breast tumors are conserved across microarray platforms , 2006, BMC Genomics.

[66]  Thomas Helleday,et al.  Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase , 2005, Nature.

[67]  Alan Ashworth,et al.  Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy , 2005, Nature.

[68]  A. Ashworth,et al.  Hallmarks of 'BRCAness' in sporadic cancers , 2004, Nature Reviews Cancer.

[69]  Jeremy M. Stark,et al.  Rad51 overexpression promotes alternative double-strand break repair pathways and genome instability , 2004, Oncogene.

[70]  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.

[71]  D. Schild,et al.  Mutants of the Five Rad51 Paralogs Recombinational Repair in Knockout Chromosome Instability and Defective , 2022 .

[72]  P. Glazer,et al.  Genomic instability in cancer. , 2001, Novartis Foundation symposium.

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

[74]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..