Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers

[1]  Steven J. M. Jones,et al.  Pan-cancer analysis of whole genomes , 2020, Nature.

[2]  Mathieu Lupien,et al.  Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks. , 2020, Molecular cell.

[3]  M. Gerstein,et al.  exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling. , 2019, Cell systems.

[4]  S. Vacher,et al.  Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer , 2018, Breast Cancer Research.

[5]  W. Woodward,et al.  Inflammatory breast cancer biology: the tumour microenvironment is key , 2018, Nature Reviews Cancer.

[6]  E. Lander,et al.  A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer , 2017, Nature Genetics.

[7]  W. Woodward,et al.  Inflammatory breast cancer: a proposed conceptual shift in the UICC-AJCC TNM staging system. , 2017, The Lancet. Oncology.

[8]  Shantao Li,et al.  Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations , 2017, PLoS genetics.

[9]  W. Woodward,et al.  Identification of frequent somatic mutations in inflammatory breast cancer , 2017, Breast Cancer Research and Treatment.

[10]  S. Elledge,et al.  Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy , 2017, Science.

[11]  Roland Eils,et al.  Complex heatmaps reveal patterns and correlations in multidimensional genomic data , 2016, Bioinform..

[12]  P. Park,et al.  Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants , 2016, Nucleic acids research.

[13]  David C. Jones,et al.  Landscape of somatic mutations in 560 breast cancer whole genome sequences , 2016, Nature.

[14]  P. Levine,et al.  Importance of hereditary and selected environmental risk factors in the etiology of inflammatory breast cancer: a case-comparison study , 2016, BMC Cancer.

[15]  Jaroslav Bendl,et al.  PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions , 2016, PLoS Comput. Biol..

[16]  B. Taylor,et al.  deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution , 2016, Genome Biology.

[17]  Ole Lund,et al.  Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing , 2016, Journal of Clinical Microbiology.

[18]  James Y. Zou Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[19]  P. Stephens,et al.  Comprehensive genomic profiling of inflammatory breast cancer cases reveals a high frequency of clinically relevant genomic alterations , 2015, Breast Cancer Research and Treatment.

[20]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[21]  A. Feily,et al.  Inflammatory Breast Carcinoma Presenting with Two Different Patterns of Cutaneous Metastases: Carcinoma Telangiectaticum and Carcinoma Erysipeloides. , 2015, The Journal of clinical and aesthetic dermatology.

[22]  W. Woodward,et al.  Inflammation Mediated Metastasis: Immune Induced Epithelial-To-Mesenchymal Transition in Inflammatory Breast Cancer Cells , 2015, PloS one.

[23]  Mingming Jia,et al.  COSMIC: exploring the world's knowledge of somatic mutations in human cancer , 2014, Nucleic Acids Res..

[24]  Kevin Y. Yip,et al.  FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer , 2014, Genome Biology.

[25]  Obi L. Griffith,et al.  SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution , 2014, PLoS Comput. Biol..

[26]  Shankar Vembu,et al.  PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors , 2015, Genome Biology.

[27]  Lovelace J. Luquette,et al.  Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes , 2013, Cell.

[28]  H. van Dam,et al.  The regulation of TGF-β/SMAD signaling by protein deubiquitination , 2014, Protein & Cell.

[29]  K. Baggerly,et al.  Comparison of molecular subtype distribution in triple-negative inflammatory and non-inflammatory breast cancers , 2013, Breast Cancer Research.

[30]  Hongen Zhang,et al.  RCircos: an R package for Circos 2D track plots , 2013, BMC Bioinformatics.

[31]  Nicholas B. Larson,et al.  PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data , 2013, Bioinform..

[32]  Lovelace J. Luquette,et al.  Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes , 2013, Cell.

[33]  E. Mroz,et al.  MATH, a novel measure of intratumor genetic heterogeneity, is high in poor-outcome classes of head and neck squamous cell carcinoma. , 2013, Oral oncology.

[34]  F. Bertucci,et al.  Uncovering the Molecular Secrets of Inflammatory Breast Cancer Biology: An Integrated Analysis of Three Distinct Affymetrix Gene Expression Datasets , 2013, Clinical Cancer Research.

[35]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[36]  Wendy S. W. Wong,et al.  Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs , 2012, Bioinform..

[37]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[38]  Y. Qi,et al.  Different gene expressions are associated with the different molecular subtypes of inflammatory breast cancer , 2011, Breast Cancer Research and Treatment.

[39]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[40]  C. Deng,et al.  Smad4 loss in mice causes spontaneous head and neck cancer with increased genomic instability and inflammation. , 2009, The Journal of clinical investigation.

[41]  E. Birney,et al.  Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.

[42]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[43]  Zhi Hu,et al.  An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer. , 2008, Cancer research.

[44]  S. Devesa,et al.  Trends in inflammatory breast carcinoma incidence and survival: the surveillance, epidemiology, and end results program at the National Cancer Institute. , 2005, Journal of the National Cancer Institute.

[45]  Yibang Chen,et al.  Interaction of TRAF6 with MAST205 Regulates NF-κB Activation and MAST205 Stability* , 2004, Journal of Biological Chemistry.

[46]  N. Takahashi,et al.  Protocadherin LKC, a new candidate for a tumor suppressor of colon and liver cancers, its association with contact inhibition of cell proliferation. , 2002, Carcinogenesis.

[47]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[48]  M. Rahbar,et al.  Case Control Study of Prognostic Markers and Disease Outcome in Inflammatory Carcinoma Breast: A Unique Clinical Experience , 2001, The breast journal.

[49]  A. Buzdar,et al.  Inflammatory breast carcinoma incidence and survival , 1998, Cancer.

[50]  G. Bonadonna,et al.  Natural history and survival of inoperable breast cancer treated with radiotherapy and radiotherapy followed by radical mastectomy , 1976, Cancer.

[51]  A. Chinnaiyan,et al.  Supplementary Figure S3 , 2012 .

[52]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..