Breast tumors from CHEK2 1100delC-mutation carriers: genomic landscape and clinical implications

[1]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..

[2]  L. O’Driscoll.  Gene Expression Profiling , 2011, Methods in Molecular Biology.

[3]  J. Murnane,et al.  Telomere loss as a mechanism for chromosome instability in human cancer. , 2010, Cancer research.

[4]  Päivi Heikkilä,et al.  Subtyping of Breast Cancer by Immunohistochemistry to Investigate a Relationship between Subtype and Short and Long Term Survival: A Collaborative Analysis of Data for 10,159 Cases from 12 Studies , 2010, PLoS medicine.

[5]  I. Petersen,et al.  The CHK2–BRCA1 tumour suppressor pathway ensures chromosomal stability in human somatic cells , 2010, Nature Cell Biology.

[6]  David Haussler,et al.  The UCSC Genome Browser database: update 2010 , 2009, Nucleic Acids Res..

[7]  Stephen Fox,et al.  Subtypes of familial breast tumours revealed by expression and copy number profiling , 2010, Breast Cancer Research and Treatment.

[8]  M. Ringnér,et al.  Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics , 2010, Breast Cancer Research.

[9]  Jari Häkkinen,et al.  BASE - 2nd generation software for microarray data management and analysis , 2009, BMC Bioinformatics.

[10]  R. Gelber,et al.  Thresholds for therapies: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2009 , 2009, Annals of oncology : official journal of the European Society for Medical Oncology.

[11]  David Pellman,et al.  A Mechanism Linking Extra Centrosomes to Chromosomal Instability , 2009, Nature.

[12]  Hanns Hatt,et al.  Activation of an Olfactory Receptor Inhibits Proliferation of Prostate Cancer Cells* , 2009, The Journal of Biological Chemistry.

[13]  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.

[14]  A. Ashworth,et al.  Family History, Genetic Testing, and Clinical Risk Prediction: Pooled Analysis of CHEK2*1100delC in 1,828 Bilateral Breast Cancers and 7,030 Controls , 2009, Cancer Epidemiology Biomarkers & Prevention.

[15]  G. Smyth,et al.  Microarray background correction: maximum likelihood estimation for the normal–exponential convolution , 2008, Biostatistics.

[16]  Chris Mungall,et al.  AmiGO: online access to ontology and annotation data , 2008, Bioinform..

[17]  N. Crawford,et al.  The origins of breast cancer prognostic gene expression profiles. , 2009, Cancer research.

[18]  Yehudit Hasin,et al.  High-Resolution Copy-Number Variation Map Reflects Human Olfactory Receptor Diversity and Evolution , 2008, PLoS genetics.

[19]  Carlos Caldas,et al.  High-resolution array CGH clarifies events occurring on 8p in carcinogenesis , 2008, BMC Cancer.

[20]  Steinar Lundgren,et al.  CHEK2 Mutations Affecting Kinase Activity Together With Mutations in TP53 Indicate a Functional Pathway Associated with Resistance to Epirubicin in Primary Breast Cancer , 2008, PloS one.

[21]  Gianluca Bontempi,et al.  Biological Processes Associated with Breast Cancer Clinical Outcome Depend on the Molecular Subtypes , 2008, Clinical Cancer Research.

[22]  B. Trask,et al.  Extensive copy-number variation of the human olfactory receptor gene family. , 2008, American journal of human genetics.

[23]  M. A. van de Wiel,et al.  Weighted clustering of called array CGH data. , 2008, Biostatistics.

[24]  Päivi Heikkilä,et al.  NAD(P)H:quinone oxidoreductase 1 NQO1*2 genotype (P187S) is a strong prognostic and predictive factor in breast cancer , 2008, Nature Genetics.

[25]  Gianluca Bontempi,et al.  Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen , 2008, BMC Genomics.

[26]  E. Leygue,et al.  Expression of small breast epithelial mucin (SBEM) protein in tissue microarrays (TMAs) of primary invasive breast cancers , 2008, Histopathology.

[27]  Olga Anczuków,et al.  Does the nonsense‐mediated mRNA decay mechanism prevent the synthesis of truncated BRCA1, CHK2, and p53 proteins? , 2008, Human mutation.

[28]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[29]  M. Cole,et al.  Turning the Tables: Myc Activates Wnt in Breast Cancer , 2007, Cell cycle.

[30]  Johan Staaf,et al.  Normalization of array-CGH data: influence of copy number imbalances , 2007, BMC Genomics.

[31]  L. Vosshall,et al.  Genetic variation in a human odorant receptor alters odour perception , 2007, Nature.

[32]  Yutaka Matsuda,et al.  Autocrine WNT signaling contributes to breast cancer cell proliferation via the canonical WNT pathway and EGFR transactivation , 2007, Breast Cancer Research.

[33]  Gordon K. Smyth,et al.  A comparison of background correction methods for two-colour microarrays , 2007, Bioinform..

[34]  Johan Staaf,et al.  High‐resolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridization , 2007, Genes, chromosomes & cancer.

[35]  Wessel N. van Wieringen,et al.  CGHcall: calling aberrations for array CGH tumor profiles , 2007, Bioinform..

[36]  J. Davis.  Bioinformatics and Computational Biology Solutions Using R and Bioconductor , 2007 .

[37]  E. S. Venkatraman,et al.  A faster circular binary segmentation algorithm for the analysis of array CGH data , 2007, Bioinform..

[38]  M. A. van de Wiel,et al.  CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss , 2007, Cancer informatics.

[39]  David Haussler,et al.  The UCSC genome browser database: update 2007 , 2006, Nucleic Acids Res..

[40]  J. Peterse,et al.  Breast cancer survival and tumor characteristics in premenopausal women carrying the CHEK2*1100delC germline mutation. , 2006, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[41]  J. Klijn,et al.  Identification of women with an increased risk of developing radiation-induced breast cancer: a case only study , 2007, Breast Cancer Research.

[42]  I. Campbell,et al.  Genetic and Epigenetic Analysis of CHEK2 in Sporadic Breast, Colon, and Ovarian Cancers , 2006, Clinical Cancer Research.

[43]  Ajay N. Jain,et al.  Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. , 2006, Cancer cell.

[44]  Joshy George,et al.  Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. , 2006, Cancer research.

[45]  H. Nevanlinna,et al.  The CHEK2 gene and inherited breast cancer susceptibility , 2006, Oncogene.

[46]  R. Eeles,et al.  Rare germ line CHEK2 variants identified in breast cancer families encode proteins that show impaired activation. , 2006, Cancer research.

[47]  D. Lancet,et al.  Widespread ectopic expression of olfactory receptor genes , 2006, BMC Genomics.

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

[49]  M. J. van de Vijver,et al.  Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. , 2006, Journal of the National Cancer Institute.

[50]  Jeong Hoon Kim,et al.  Differential Use of Functional Domains by Coiled-coil Coactivator in Its Synergistic Coactivator Function with β-Catenin or GRIP1* , 2006, Journal of Biological Chemistry.

[51]  T. Eberlein.  A Multigene Assay to Predict Recurrence of Tamoxifen-Treated, Node-Negative Breast Cancer , 2006 .

[52]  L. Holmberg,et al.  Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts , 2005, Breast Cancer Research.

[53]  H. Beug,et al.  Molecular requirements for epithelial-mesenchymal transition during tumor progression. , 2005, Current opinion in cell biology.

[54]  P. Hall,et al.  An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[55]  Rafael A. Irizarry,et al.  Bioinformatics and Computational Biology Solutions using R and Bioconductor , 2005 .

[56]  J. Foekens,et al.  Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer , 2005, The Lancet.

[57]  Päivi Heikkilä,et al.  Correlation of CHEK2 protein expression and c.1100delC mutation status with tumor characteristics among unselected breast cancer patients , 2005, International journal of cancer.

[58]  Peter Devilee,et al.  Comparative genomic hybridization profiles in human BRCA1 and BRCA2 breast tumors highlight differential sets of genomic aberrations. , 2005, Cancer research.

[59]  Gordon K. Smyth,et al.  limma: Linear Models for Microarray Data , 2005 .

[60]  M. Cronin,et al.  A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. , 2004, The New England journal of medicine.

[61]  S. Geisler,et al.  Alternative splicing and mutation status of CHEK2 in stage III breast cancer , 2004, Oncogene.

[62]  O. Watanabe,et al.  Expression of twist and wnt in human breast cancer. , 2004, Anticancer research.

[63]  M. Schutte,et al.  Tumour characteristics and prognosis of breast cancer patients carrying the germline CHEK2*1100delC variant , 2004, Journal of Medical Genetics.

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

[65]  P. Mombaerts,et al.  A Contextual Model for Axonal Sorting into Glomeruli in the Mouse Olfactory System , 2004, Cell.

[66]  Nazneen Rahman,et al.  CHEK2*1100delC and susceptibility to breast cancer: a collaborative analysis involving 10,860 breast cancer cases and 9,065 controls from 10 studies. , 2004, American journal of human genetics.

[67]  K. Sossey-Alaoui,et al.  CLCA2 tumour suppressor gene in 1p31 is epigenetically regulated in breast cancer , 2004, Oncogene.

[68]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[69]  J. Reed,et al.  Bcl-2 Gene Family and Related Proteins in Mammary Gland Involution and Breast Cancer , 1999, Journal of Mammary Gland Biology and Neoplasia.

[70]  Jorma Isola,et al.  Patterns of chromosomal imbalances defines subgroups of breast cancer with distinct clinical features and prognosis. A study of 305 tumors by comparative genomic hybridization. , 2003, Cancer research.

[71]  J. Klijn,et al.  The CHEK2*1100delC variant acts as a breast cancer risk modifier in non-BRCA1/BRCA2 multiple-case families. , 2003, Cancer research.

[72]  Terry Speed,et al.  Normalization of cDNA microarray data. , 2003, Methods.

[73]  R. Tibshirani,et al.  Repeated observation of breast tumor subtypes in independent gene expression data sets , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[74]  T. Speed,et al.  Statistical issues in cDNA microarray data analysis. , 2003, Methods in molecular biology.

[75]  M. Katoh,et al.  WNT and FGF gene clusters (review). , 2002, International journal of oncology.

[76]  R. Eeles,et al.  CHEK2 variants in susceptibility to breast cancer and evidence of retention of the wild type allele in tumours , 2002, British Journal of Cancer.

[77]  M. Ringnér,et al.  Impact of DNA amplification on gene expression patterns in breast cancer. , 2002, Cancer research.

[78]  O. Kallioniemi,et al.  A CHEK2 genetic variant contributing to a substantial fraction of familial breast cancer. , 2002, American journal of human genetics.

[79]  R. DePinho,et al.  Connecting chromosomes, crisis, and cancer. , 2002, Science.

[80]  S. Gruvberger,et al.  BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data , 2002, Genome Biology.

[81]  L. Murphy,et al.  Identification of a novel breast- and salivary gland-specific, mucin-like gene strongly expressed in normal and tumor human mammary epithelium. , 2002, Cancer research.

[82]  Yudong D. He,et al.  Gene expression profiling predicts clinical outcome of breast cancer , 2002, Nature.

[83]  Van,et al.  A gene-expression signature as a predictor of survival in breast cancer. , 2002, The New England journal of medicine.

[84]  S. Firestein.  How the olfactory system makes sense of scents , 2001, Nature.

[85]  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.

[86]  A. Levine,et al.  Surfing the p53 network , 2000, Nature.

[87]  K Holli,et al.  Population-based study of BRCA1 and BRCA2 mutations in 1035 unselected Finnish breast cancer patients. , 2000, Journal of the National Cancer Institute.

[88]  Alexander Kinev,et al.  BRCA1 Is Associated with a Human SWI/SNF-Related Complex Linking Chromatin Remodeling to Breast Cancer , 2000, Cell.

[89]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[90]  J. Levine,et al.  Surfing the p53 network , 2000, Nature.

[91]  K. Isselbacher,et al.  Heterozygous germ line hCHK2 mutations in Li-Fraumeni syndrome. , 1999, Science.

[92]  A. Gruber,et al.  Molecular cloning and transmembrane structure of hCLCA2 from human lung, trachea, and mammary gland. , 1999, American journal of physiology. Cell physiology.

[93]  J. Jónasson,et al.  Loss of heterozygosity at chromosome 1p in different solid human tumours: association with survival , 1999, British Journal of Cancer.

[94]  W. Kuo,et al.  High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays , 1998, Nature Genetics.

[95]  W. Dreyer,et al.  The area code hypothesis revisited: olfactory receptors and other related transmembrane receptors may function as the last digits in a cell surface code for assembling embryos. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[96]  A. Harris,et al.  Compartment switching of WNT-2 expression in human breast tumors. , 1996, Cancer research.

[97]  D. Pinkel,et al.  Comparative Genomic Hybridization for Molecular Cytogenetic Analysis of Solid Tumors , 2022 .

[98]  B. Ljung,et al.  Heterogeneity for allelic loss in human breast cancer. , 1992, Journal of the National Cancer Institute.