breast cancer phenotype

Aliases

BC, BRCA1-associated breast cancer, BRCA2-associated breast cancer, breast, breast cancer, breast cancer cells, breast cancer risk, breast cancer susceptibility, breast cancers, breast carcinoma, invasive breast cancer

Related entities (1)

Mentioned in (204)

Papers in which this entity is mentioned.

• A guide to transcriptomic deconvolution in cancer. (2026)
• Comprehensive repertoire of the chromosomal alteration and mutational signatures across 16 cancer types. (2026)
• Artificial Intelligence agents for biological research: a survey. (2026)
• Whole-genome landscapes of 1,364 breast cancers. (2026)
• Whole genome sequencing approach to assess homologous recombination deficiency in a pan-cancer cohort. (2026)
• Nanopore-based cell-free DNA fragmentation and methylation profiles from the cerebral spinal fluid of patients with lung cancer brain metastases. (2025)
• FET fusion oncoproteins disrupt physiologic DNA repair and create a targetable opportunity for ATR inhibitor therapy. (2025)
• Rapid brain tumor classification from sparse epigenomic data. (2025)
• Chromosomal instability as a driver of cancer progression. (2025)
• Functional analysis of cancer-associated germline risk variants. (2025)
• Three-dimensional genome landscape of primary human cancers. (2025)
• Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond. (2025)
• High-Parameter Spatial Multi-Omics through Histology-Anchored Integration (2025)
• Transcription start sites experience a high influx of heritable variants fueled by early development. (2025)
• Tumor-informed deep sequencing of ctDNA detects minimal residual disease and predicts relapse in osteosarcoma. (2024)
• Principles and methods for transferring polygenic risk scores across global populations. (2024)
• CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. (2024)
• Transient loss of Polycomb components induces an epigenetic cancer fate. (2024)
• Recent advances in polygenic scores: translation, equitability, methods and FAIR tools. (2024)
• Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme. (2024)
• Analysis of 10,478 cancer genomes identifies candidate driver genes and opportunities for precision oncology. (2024)
• The Application of Long-Read Sequencing to Cancer. (2024)
• A New Era of Data-Driven Cancer Research and Care: Opportunities and Challenges. (2024)
• ENPP1 Immunobiology as a Therapeutic Target. (2023)
• Combination of genomic instability score and TP53 status for prognosis prediction in lung adenocarcinoma. (2023)
• A Novel Tissue-Free Method to Estimate Tumor-Derived Cell-Free DNA Quantity Using Tumor Methylation Patterns. (2023)
• Comprehensive repertoire of the chromosomal alteration and mutational signatures across 16 cancer types from 10,983 cancer patients (2023)
• GCparagon: evaluating and correcting GC biases in cell-free DNA at the fragment level. (2023)
• Predicting tumour content of liquid biopsies from cell-free DNA. (2023)
• Heritable defects in telomere and mitotic function selectively predispose to sarcomas. (2023)
• Biobank-scale methods and projections for sparse polygenic prediction from machine learning. (2023)
• Machine learning for genetics-based classification and treatment response prediction in cancer of unknown primary. (2023)
• Osteoclasts in Osteosarcoma: Mechanisms, Interactions, and Therapeutic Prospects. (2023)
• Polygenic scoring accuracy varies across the genetic ancestry continuum. (2023)
• Towards understandings of serine/arginine-rich splicing factors. (2023)
• RNA splicing dysregulation and the hallmarks of cancer. (2023)
• Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. (2022)
• At the dawn: cell-free DNA fragmentomics and gene regulation. (2022)
• Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking. (2022)
• Genome-wide mutational signatures in low-coverage whole genome sequencing of cell-free DNA. (2022)
• Explainable multiview framework for dissecting spatial relationships from highly multiplexed data. (2022)
• Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data. (2022)
• Variant interpretation using population databases: Lessons from gnomAD. (2022)
• Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. (2022)
• Single-cell genomic variation induced by mutational processes in cancer. (2022)
• Circulating Tumor DNA as a Biomarker in Patients With Stage III and IV Wilms Tumor: Analysis From a Children's Oncology Group Trial, AREN0533. (2022)
• Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology. (2021)
• Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA. (2021)
• Nanopore sequencing technology, bioinformatics and applications. (2021)
• Application of third-generation sequencing in cancer research. (2021)
• Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing. (2021)
• Evaluating the transcriptional fidelity of cancer models. (2021)
• A practical guide to cancer subclonal reconstruction from DNA sequencing. (2021)
• Therapeutic Implications of Germline Testing in Patients With Advanced Cancers. (2021)
• Integrative reconstruction of cancer genome karyotypes using InfoGenomeR. (2021)
• Detection and characterization of lung cancer using cell-free DNA fragmentomes. (2021)
• kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing. (2021)
• Macrophage Polarization States in the Tumor Microenvironment. (2021)
• Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. (2021)
• Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity. (2021)
• Polygenic risk scores: from research tools to clinical instruments. (2020)
• DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers. (2020)
• Immuno-genomic landscape of osteosarcoma. (2020)
• Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring. (2020)
• Pan-cancer analysis of whole genomes. (2020)
• Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases. (2020)
• Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. (2020)
• Inferring structural variant cancer cell fraction. (2020)
• Emerging Roles of SRSF3 as a Therapeutic Target for Cancer. (2020)
• Pan-cancer landscape of homologous recombination deficiency. (2020)
• Single-cell RNA landscape of intratumoral heterogeneity and immunosuppressive microenvironment in advanced osteosarcoma. (2020)
• Cancer PRSweb: An Online Repository with Polygenic Risk Scores for Major Cancer Traits and Their Evaluation in Two Independent Biobanks. (2020)
• Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers. (2020)
• Neoadjuvant checkpoint blockade for cancer immunotherapy. (2020)
• Comprehensive germline genomic profiles of children, adolescents and young adults with solid tumors. (2020)
• Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. (2020)
• Polygenic prediction via Bayesian regression and continuous shrinkage priors. (2019)
• CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers. (2019)
• Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. (2019)
• Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy. (2019)
• Tumor mutational burden standardization initiatives: Recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions. (2019)
• The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment. (2019)
• Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study. (2019)
• Germline variants associated with leukocyte genes predict tumor recurrence in breast cancer patients. (2019)
• Association of BRCA1- and BRCA2-deficiency with mutation burden, expression of PD-L1/PD-1, immune infiltrates, and T cell-inflamed signature in breast cancer. (2019)
• Genome-Informed Targeted Therapy for Osteosarcoma. (2019)
• Structural variant calling: the long and the short of it. (2019)
• Genome-wide cell-free DNA fragmentation in patients with cancer. (2019)
• RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. (2019)
• Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing (2019)
• Pan-cancer whole-genome analyses of metastatic solid tumours. (2019)
• The Cancer Spliceome: Reprograming of Alternative Splicing in Cancer. (2018)
• Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. (2018)
• Detection of Somatic Structural Variants Enables Quantification and Characterization of Circulating Tumor DNA in Children With Solid Tumors. (2018)
• A fast detection of fusion genes from paired-end RNA-seq data. (2018)
• Quantification of subclonal selection in cancer from bulk sequencing data. (2018)
• Widespread Selection for Oncogenic Mutant Allele Imbalance in Cancer. (2018)
• Enhanced detection of circulating tumor DNA by fragment size analysis. (2018)
• Genome doubling shapes the evolution and prognosis of advanced cancers. (2018)
• Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. (2018)
• Personal Cancer Genome Reporter: variant interpretation report for precision oncology. (2018)
• Comprehensive Cancer-Predisposition Gene Testing in an Adult Multiple Primary Tumor Series Shows a Broad Range of Deleterious Variants and Atypical Tumor Phenotypes. (2018)
• Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes (2018)
• Sensitivity to sequencing depth in single-cell cancer genomics. (2018)
• SvABA: genome-wide detection of structural variants and indels by local assembly. (2018)
• Patterns and mechanisms of structural variations in human cancer. (2018)
• Picky comprehensively detects high-resolution structural variants in nanopore long reads. (2018)
• Thymic involution and rising disease incidence with age. (2018)
• Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome (2017)
• ClonEvol: clonal ordering and visualization in cancer sequencing. (2017)
• OncoKB: A Precision Oncology Knowledge Base. (2017)
• SVclone: inferring structural variant cancer cell fraction (2017)
• HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures. (2017)
• The evolution of tumour phylogenetics: principles and practice. (2017)
• Universal Patterns of Selection in Cancer and Somatic Tissues. (2017)
• ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data. (2017)
• Integrative clustering of multi-level 'omic data based on non-negative matrix factorization algorithm. (2017)
• Patient-derived xenografts undergo mouse-specific tumor evolution. (2017)
• Integrated analysis of gene expression and copy number identified potential cancer driver genes with amplification-dependent overexpression in 1,454 solid tumors. (2017)
• Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. (2017)
• GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly. (2017)
• CScape: a tool for predicting oncogenic single-point mutations in the cancer genome. (2017)
• Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. (2017)
• A method to reduce ancestry related germline false positives in tumor only somatic variant calling. (2017)
• Puberty and structural brain development in humans. (2017)
• ReMixT: clone-specific genomic structure estimation in cancer. (2017)
• Interaction of glycosphingolipids GD3 and GD2 with growth factor receptors maintains breast cancer stem cell phenotype. (2017)
• Copy-number signatures and mutational processes in ovarian carcinoma (2017)
• Fast and Accurate Genomic Analyses using Genome Graphs (2017)
• Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin. (2016)
• B lymphocytes and cancer: a love-hate relationship. (2016)
• Visualizing tumor evolution with the fishplot package for R. (2016)
• Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer-Associated Genes in Families Affected by Breast Cancer. (2016)
• Association of germline variants in the APOBEC3 region with cancer risk and enrichment with APOBEC-signature mutations in tumors. (2016)
• Fragment Length of Circulating Tumor DNA. (2016)
• DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution. (2016)
• Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers. (2016)
• Landscape of somatic mutations in 560 breast cancer whole-genome sequences. (2016)
• The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies. (2016)
• An Fgf-Shh signaling hierarchy regulates early specification of the zebrafish skull. (2016)
• Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. (2016)
• APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication. (2016)
• Development and clinical application of an integrative genomic approach to personalized cancer therapy. (2016)
• GenVisR: Genomic Visualizations in R. (2016)
• Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data. (2016)
• Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. (2016)
• Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets. (2015)
• Design and bioinformatics analysis of genome-wide CLIP experiments. (2015)
• Clock-like mutational processes in human somatic cells. (2015)
• The landscape of long noncoding RNAs in the human transcriptome. (2015)
• Oncogenic fusion protein EWS-FLI1 is a network hub that regulates alternative splicing. (2015)
• Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays. (2014)
• RADIA: RNA and DNA integrated analysis for somatic mutation detection. (2014)
• Genome-wide analysis of noncoding regulatory mutations in cancer. (2014)
• PVT1 dependence in cancer with MYC copy-number increase. (2014)
• Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads. (2014)
• Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. (2014)
• Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma. (2014)
• Long noncoding RNA EWSAT1-mediated gene repression facilitates Ewing sarcoma oncogenesis. (2014)
• Clonal evolution in hematological malignancies and therapeutic implications. (2014)
• Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. (2014)
• The genomic landscape of the Ewing Sarcoma family of tumors reveals recurrent STAG2 mutation. (2014)
• Inferring tumour purity and stromal and immune cell admixture from expression data. (2013)
• Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. (2013)
• Cancer genome landscapes. (2013)
• THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. (2013)
• Prioritizing Potentially Druggable Mutations with dGene: An Annotation Tool for Cancer Genome Sequencing Data. (2013)
• Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. (2013)
• Ewing sarcoma protein: a key player in human cancer. (2013)
• A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks. (2013)
• Signatures of mutational processes in human cancer. (2013)
• Effects of alcohol on the endocrine system. (2013)
• Emerging landscape of oncogenic signatures across human cancers. (2013)
• DGIdb: mining the druggable genome. (2013)
• RNA splicing: a new player in the DNA damage response. (2013)
• An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. (2013)
• Differential expression profiles of glycosphingolipids in human breast cancer stem cells vs. cancer non-stem cells. (2013)
• Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy. (2013)
• Pan-cancer patterns of somatic copy number alteration. (2013)
• Absolute quantification of somatic DNA alterations in human cancer. (2012)
• High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. (2012)
• Myeloid cells in tumor inflammation. (2012)
• Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. (2012)
• Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma. (2012)
• Mutational processes molding the genomes of 21 breast cancers. (2012)
• Microsatellites with macro-influence in ewing sarcoma. (2012)
• Novel mutations target distinct subgroups of medulloblastoma. (2012)
• AID/APOBEC cytosine deaminase induces genome-wide kataegis. (2012)
• Patient-derived tumour xenografts as models for oncology drug development. (2012)
• Massive genomic rearrangement acquired in a single catastrophic event during cancer development. (2011)
• BRCA1 and BRCA2: different roles in a common pathway of genome protection. (2011)
• Outlier-Based Differential Expression Analysis in Proteomics Studies. (2011)
• Functional consequences of developmentally regulated alternative splicing. (2011)
• Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. (2011)
• Mechanisms and consequences of alternative polyadenylation. (2011)
• Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. (2011)
• Allele-specific copy number analysis of tumors. (2010)
• Integrative analysis of the melanoma transcriptome. (2010)
• rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. (2010)
• Recurring mutations found by sequencing an acute myeloid leukemia genome. (2009)
• Fewer permutations, more accurate P-values. (2009)
• 3' end mRNA processing: molecular mechanisms and implications for health and disease. (2008)
• Model-based analysis of ChIP-Seq (MACS). (2008)
• Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results. (2008)

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