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Integrative deep-sequencing analysis of cancer samples: discoveries and clinical challenges

D Roukos
2013 The Pharmacogenomics Journal  
platforms to provide valid deep-sequencing data with WGS, whole-exome sequencing and RNA-seq in clinical samples in a short time has resulted in the new era of clinical cancer genome. 1 Genomic heterogeneity  ...  Here, I discuss the results of the first published studies with deep-sequencing and transcriptomic analysis data of clinical samples from roughly 2400 breast cancer and 1125 medulloblastoma patients.  ...  CONFLICT OF INTEREST The author declares no conflict of interest.  ... 
doi:10.1038/tpj.2012.51 pmid:23296155 fatcat:ixorenutmvcd3pvfhqag6r5keq

Stratification of Breast Cancer by Integrating Gene Expression Data and Clinical Variables

Zongzhen He, Junying Zhang, Xiguo Yuan, Jianing Xi, Zhaowen Liu, Yuanyuan Zhang
2019 Molecules  
Clinical data is another promising source. In this study, clinical variables are utilized and integrated to gene expressions for the stratification of breast cancer.  ...  Breast cancer is a heterogeneous disease. Although gene expression profiling has led to the definition of several subtypes of breast cancer, the precise discovery of the subtypes remains a challenge.  ...  Materials and Methods Data Preprocessing The Cancer Genome Atlas (TCGA) RNA-Seq data and clinical information of breast carcinoma were downloaded from the University of California Santa Cruz (UCSC) cancer  ... 
doi:10.3390/molecules24030631 fatcat:knmneqsmjnbh7bg6jlctsqa37q

Analysis of H3K4me3-ChIP-Seq and RNA-Seq data to understand the putative role of miRNAs and their target genes in breast cancer cell lines

Aneesh Kotipalli, Ruma Banerjee, Sunitha Manjari Kasibhatla, Rajendra Joshi
2021 Genomics & Informatics  
Acknowledgments The authors thank the BRAF facility of C-DAC for HPC infrastructure. The authors would also like to deeply thank Dr. Janaki C.H. for her scientific review and critical comments.  ...  The workflow for ChIP-Seq and RNA-Seq data integration is depicted in Fig. 1B .  ...  using ChIP-Seq-RNA-Seq integrated analysis No.  ... 
doi:10.5808/gi.21020 fatcat:5wj5vpm7kvd63heu5j72ngqopq

Single-cell RNA-seq dissects the intratumoral heterogeneity of triple negative breast cancer based on gene regulatory networks

Shunheng Zhou, Yu-e Huang, Haizhou Liu, Xu Zhou, Mengqin Yuan, Fei Hou, Lihong Wang, Wei Jiang
2021 Molecular Therapy: Nucleic Acids  
Triple-negative breast cancer (TNBC) is a subtype of breast cancer with high intratumoral heterogeneity.  ...  In conclusion, the construction of GRNs based on scRNA-seq data could help us to dissect the intratumoral heterogeneity and identify the critical genes of TNBC.  ...  Hence, traditional analysis of breast cancer based on bulk RNA-seq would be quite insufficient.  ... 
doi:10.1016/j.omtn.2020.12.018 pmid:33575114 pmcid:PMC7851423 fatcat:bk5hv4er7remhjpkq2jr2s36ey

Hypoxanthine Phosphoribosyl Transferase 1 Is Upregulated, Predicts Clinical Outcome and Controls Gene Expression in Breast Cancer

Melina J. Sedano, Enrique I. Ramos, Ramesh Choudhari, Alana L. Harrison, Ramadevi Subramani, Rajkumar Lakshmanaswamy, Mina Zilaie, Shrikanth S. Gadad
2020 Cancers  
Further, in breast cancer, the subtype-specific analysis showed that its expression was highest in basal and triple-negative breast cancer, and HPRT1 knockdown in breast cancer cells suggested that HPRT1  ...  Hypoxanthine phosphoribosyl transferase 1 (HPRT1) is traditionally believed to be a housekeeping gene; however, recent reports suggest that it is upregulated in several cancers and is associated with clinical  ...  Acknowledgments: The authors thank members of the Gadad lab. for their suggestions and comments. The authors thank proteomics core at UT Southwestern Medical Center for TMT analysis.  ... 
doi:10.3390/cancers12061522 pmid:32532008 fatcat:tlsw2c45ejd27m6i6dmzv22rsy

Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain

Wesley L. Cai, Celeste B. Greer, Jocelyn F. Chen, Anna Arnal-Estapé, Jian Cao, Qin Yan, Don X. Nguyen
2020 BMC Medical Genomics  
We identify distinctive epigenomic properties of breast cancer cells that metastasize to the lung and brain.  ...  To identify these, we performed RNA-seq, Chromatin Immunoprecipitation and sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) of the MDA-MB-231 cell line and  ...  Acknowledgements Sequencing was conducted at Yale Stem Cell Center Genomics Core facility which was supported by the Connecticut Regenerative Medicine Research Fund and the Li Ka Shing Foundation.  ... 
doi:10.1186/s12920-020-0695-0 pmid:32143622 pmcid:PMC7060551 fatcat:ugyh7weisnemnfftecfq5o36fu

Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer

Marni B. Siegel, Xiaping He, Katherine A. Hoadley, Alan Hoyle, Julia B. Pearce, Amy L. Garrett, Sunil Kumar, Vincent J. Moylan, Claudia M. Brady, Amanda E.D. Van Swearingen, David Marron, Gaorav P. Gupta (+9 others)
2018 Journal of Clinical Investigation  
We identified tumor-specific drivers by integrating known protein-protein network information with RNA expression and somatic DNA alterations and found that genetic drivers were predominantly established  ...  Breast cancer metastasis remains a clinical challenge, even within a single patient across multiple sites of the disease.  ...  Komen (to LAC and CMP); National Cancer Institute (NCI), NIH, Breast Specialized Programs of Research Excellence (SPOREs) (P50-CA58223, to LAC and CMP; RO1-CA195754-01 and RO1-  ... 
doi:10.1172/jci96153 pmid:29480819 pmcid:PMC5873890 fatcat:7zxgh5ltqbet5dhyotghibtz5e

Integrative analysis of somatic mutations and transcriptomic data to functionally stratify breast cancer patients

Jie Zhang, Zachary Abrams, Jeffrey D. Parvin, Kun Huang
2016 BMC Genomics  
Interestingly, we identified a stable subgroup of breast cancer patients that are highly enriched with ER-negative and triple-negative subtypes, and the somatic mutation genes they harbor were capable  ...  We developed a novel approach for integrating patient somatic mutation, transcriptome and clinical data to mine underlying functional gene groups that can be used to stratify cancer patients into groups  ...  Availability of data and materials All datasets used in this study were publicly available from the website described in the Methods section.  ... 
doi:10.1186/s12864-016-2902-0 pmid:27556157 pmcid:PMC5001235 fatcat:n3uaea2hdzbqnk6r75wpjfv6q4

The Nuclear Receptor, RORγ, Regulates Pathways Necessary for Breast Cancer Metastasis

Tae Gyu Oh, Shu-Ching M. Wang, Bipul R. Acharya, Joel M. Goode, J. Dinny Graham, Christine L. Clarke, Alpha S. Yap, George E.O. Muscat
2016 EBioMedicine  
Furthermore, integration of RNA-seq and ChIP-chip data reveals that RORγ regulates the expression of many genes involved in TGF-β/EMT-signaling, DNA-repair and MaSC pathways (including the non-coding RNA  ...  We demonstrate that RORγ expression is: (i) decreased in basal-like subtype cancers, and (ii) inversely correlated with histological grade and drivers of carcinogenesis in breast cancer cohorts.  ...  The authors declare there are no conflicts of interest and/or competing interests to disclose.  ... 
doi:10.1016/j.ebiom.2016.02.028 pmid:27211549 pmcid:PMC4856749 fatcat:5yopccbdxzf4nbuqazflo4p4li

Molecular natural history of breast cancer: Leveraging transcriptomics to predict breast cancer progression and aggressiveness

Daniel J Cook, Jonatan Kallus, Rebecka Jörnsten, Jens Nielsen
2020 Cancer Medicine  
cells (specifically, single-cell topological data analysis and Wanderlust) to create a continuous metric describing breast cancer progression using bulk RNA-seq samples from individual patient tumors.  ...  We also created a linear regression-based method to predict tumor aggressiveness in vivo from bulk RNA-seq data.  ...  based on RNA-seq data from clinical patients.  ... 
doi:10.1002/cam4.2996 pmid:32207233 fatcat:nd4ipb5g2jfkzojecndfe45m7y

A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer

Diogo F. T. Veiga, Alex Nesta, Yuqi Zhao, Anne Deslattes Mays, Richie Huynh, Robert Rossi, Te-Chia Wu, Karolina Palucka, Olga Anczukow, Christine R. Beck, Jacques Banchereau
2022 Science Advances  
Together, our results demonstrate the complexity, cancer subtype specificity, and clinical relevance of previously unidentified isoforms and splicing events in breast cancer that are only annotatable by  ...  Of these, 21 are absent from GENCODE and 10 are enriched in specific breast cancer subtypes.  ...  Our analyses identified tumor-specific isoforms, including isoforms associated with poor survival and specific breast cancer subtypes, and provide a library of novel breast tumor-specific isoforms as a  ... 
doi:10.1126/sciadv.abg6711 pmid:35044822 pmcid:PMC8769553 fatcat:f3pzpq2jyfexfkmr2q2wphr7um

Long intergenic non-coding RNA expression signature in human breast cancer

Yanfeng Zhang, Erin K. Wagner, Xingyi Guo, Isaac May, Qiuyin Cai, Wei Zheng, Chunyan He, Jirong Long
2016 Scientific Reports  
To further use lincRNAs as robust biomarkers, we performed an integrative analysis on RNA-seq data from approximately 1,000 breast tumors from the TCGA and an independent RNA-seq dataset of 50 pairs of  ...  We designed a two-stage study, including 1,000 breast tumor RNA-seq data from The Cancer Genome Atlas (TCGA) as the discovery stage, and RNA-seq data of matched tumor and adjacent normal tissue from 50  ...  We also thank the Indiana University Simon Cancer Center at Indiana University School of Medicine for the use of the Tissue Procurement & Distribution Core, which provided breast tumor specimens.  ... 
doi:10.1038/srep37821 pmid:27897201 pmcid:PMC5126689 fatcat:cjg5buggxzhyvout3ia4odotmq

SURVIV for survival analysis of mRNA isoform variation

Shihao Shen, Yuanyuan Wang, Chengyang Wang, Ying Nian Wu, Yi Xing
2016 Nature Communications  
The rapid accumulation of clinical RNA-seq data sets has provided the opportunity to associate mRNA isoform variations to clinical outcomes.  ...  We applied SURVIV to TCGA RNA-seq data of invasive ductal carcinoma as well as five additional cancer types.  ...  Acknowledgements This study is supported by National Institutes of Health grants (R01GM088342 and R01GM105431 to Y.X.), and National Science Foundation grant (DMS 1310391 to Y.N.W.).  ... 
doi:10.1038/ncomms11548 pmid:27279334 pmcid:PMC4906168 fatcat:2bxqeiylmnewfnsihgyo3mpzim

Comprehensive Transcriptomic Analysis Identifies ST8SIA1 as a Survival-Related Sialyltransferase Gene in Breast Cancer

Jung-Yu Kan, Sin-Hua Moi, Wen-Chun Hung, Ming-Feng Hou, Fang-Ming Chen, Shen-Liang Shih, Jun-Ping Shiau, Chung-Liang Li, Chih-Po Chiang
2020 Genes  
In this study, we conducted a comprehensive analysis of STs in the clinical database and identified the STs related with the survival of breast cancer patients.  ...  RNA sequencing (RNA-Seq) data of 496 patients were obtained from The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA).  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/genes11121436 pmid:33260650 fatcat:ggsqeman2jc4nmspjvqdcaaf2m

Ror2 Signaling and Its Relevance in Breast Cancer Progression

Michaela Bayerlová, Kerstin Menck, Florian Klemm, Alexander Wolff, Tobias Pukrop, Claudia Binder, Tim Beißbarth, Annalen Bleckmann
2017 Frontiers in Oncology  
The results were further used in the analysis of an independent dataset of breast cancer patients with metastasis-free survival annotation.  ...  Furthermore, the genes of the Ror2/Wnt module were assessed as a gene signature in patient gene expression data and showed an association with clinical outcome.  ...  Gene Set Enrichment and Network Integration Analyses Differential targets identified in the analysis of RNA-Seq data were further subjected to enrichment and network integration analyses.  ... 
doi:10.3389/fonc.2017.00135 pmid:28695110 pmcid:PMC5483589 fatcat:ssctjfqyjbeglayt3357sv5uzq
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