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Collaborative intra-tumor heterogeneity detection

2019 Bioinformatics  
Besides that, the majority of the existing datasets consist of bulk sequencing data of single tumor sample of an individual.  ...  , a phenomenon known as intra-tumor heterogeneity (ITH).  ...  Conclusions We presented Hintra as a new method for collaborative ITH detection.  ... 
doi:10.1093/bioinformatics/btz355 pmid:31510674 pmcid:PMC6612880 fatcat:kgivksnfwna5tmtnznjncr3unq

Glioblastoma Multiforme: A Look Inside Its Heterogeneous Nature

Maria-del-Mar Inda, Rudy Bonavia, Joan Seoane
2014 Cancers  
There are two types of heterogeneity: inter-tumor and intra-tumor heterogeneity.  ...  While inter-tumor heterogeneity has been studied widely, intra-tumor heterogeneity has been neglected even though numerous studies support this aspect of tumor pathobiology.  ...  Models for the origin of intra-tumor heterogeneity.  ... 
doi:10.3390/cancers6010226 pmid:24473088 pmcid:PMC3980595 fatcat:vn4s5dxuinesdjhjpt434cxm4u

Intra-tumor heterogeneity in head and neck cancer and its clinical implications

Edmund A. Mroz, James W. Rocco
2016 World Journal of Otorhinolaryngology-Head and Neck Surgery  
The presence of heritable differences among cancer cells within a tumor, called intra-tumor genetic heterogeneity, has long been suspected of playing a role in poor responses to therapy.  ...  After a brief review of this background, we describe the development of a measure of intra-tumor genetic heterogeneity, based on whole-exome sequencing of individual tumor samples, that could be applied  ...  Sequencing methods and intra-tumor heterogeneity The most direct way to examine intra-tumor genetic heterogeneity is to compare DNA sequences among regions of a tumor.  ... 
doi:10.1016/j.wjorl.2016.05.007 pmid:28642939 pmcid:PMC5477669 fatcat:i6oupafrurgvthmwbt72lw37z4

Quantitative Characterization of CD8+ T Cell Clustering and Spatial Heterogeneity in Solid Tumors

Chang Gong, Robert A. Anders, Qingfeng Zhu, Janis M. Taube, Benjamin Green, Wenting Cheng, Imke H. Bartelink, Paolo Vicini, Bing Wang, Aleksander S. Popel
2019 Frontiers in Oncology  
The results indicate a higher intra-tumoral heterogeneity compared with the heterogeneity across patients.  ...  The intra- and inter-tumoral spatial heterogeneities are potentially key to the understanding of the dose-response relationships, but they also bring challenges to properly parameterizing and validating  ...  We also detected cell aggregates using cluster analysis, and used the calculated shape descriptors for each cluster to capture the intra-tumoral heterogeneity.  ... 
doi:10.3389/fonc.2018.00649 pmid:30666298 pmcid:PMC6330341 fatcat:2xfaumohhnfvxnbqxonchtfd44

The Promise and Challenges of Personalized Medicine in Hematologic Malignancies

2015 Journal of Hematology & Thrombosis  
Personalized medicine in oncology seeks to individualize cancer care and treatment decisions based upon features unique to each patient and each patient's tumor.  ...  The concept of personalized medicine hopes to not only enhance the patient quality of life and survival but also to lower overall healthcare costs through early-detection, prevention, accurate risk assessments  ...  The fundamental basis that underlies intra tumor heterogeneity is the molecular variability of the tissue microenvironment and neoplastic cells within a single tumor, in particular with epigenetic heterogeneity  ... 
doi:10.13188/2380-6842.1000007 fatcat:6alp55o6encq5amp55z2ie7ogi

Tumor Quantification in Clinical Positron Emission Tomography

Bing Bai, James Bading, Peter S Conti
2013 Theranostics  
Positron emission tomography (PET) is used extensively in clinical oncology for tumor detection, staging and therapy response assessment.  ...  We describe current efforts to improve the accuracy of tumor uptake measurements, characterize overall metabolic tumor burden and heterogeneity of tumor uptake, and account for the effects of image noise  ...  Intra-tumoral heterogeneity can be caused by cell proliferation, blood flow, hypoxia and necrosis. 73 Quantification of intra-tumoral heterogeneity is useful in monitoring and predicting response to  ... 
doi:10.7150/thno.5629 pmid:24312151 pmcid:PMC3840412 fatcat:pyvibhbszfcbxj72wqjfwglyya

Circulating Tumor Cells as a Tool to Untangle the Breast Cancer Heterogeneity Issue

Tania Rossi, Giulia Gallerani, Giovanni Martinelli, Roberta Maltoni, Francesco Fabbri
2021 Biomedicines  
In this review, we report the latest findings in the field of CTCs for intra-tumoral heterogeneity unmasking in BC, supporting the need to deepen their analysis to investigate their role in metastatic  ...  Breast cancer (BC) is a disease characterized by high degrees of heterogeneity at morphologic, genomic, and genetic levels, even within the same tumor mass or among patients.  ...  Contextually, in addition to the differences occurring among different patients (intertumor heterogeneity), high levels of diversity have been described even within each individual tumor (intra-tumor heterogeneity  ... 
doi:10.3390/biomedicines9091242 pmid:34572427 fatcat:kbs6m5szkvg4tf25fpmjsmif4u

Concepts of Precision Medicine in Breast Cancer

Eleni Andreopoulou
2018 Oncology & Hematology Review (US)  
How can precision medicine address the challenge of intra-tumor heterogeneity resulting from clonal evolution of the disease?  ...  Advances in genetic sequencing analysis are helping to illuminate the prevalence of intra-tumor heterogeneity, which allows us to answer compelling high priority clinical questions.  ... 
doi:10.17925/ohr.2018.14.1.16 fatcat:ecnjdeni35ewpmoaz2bx6p4evy

Personalized Medicine for Gliomas

EricC Holland, ChibawanyeI Ene
2015 Surgical neurology international  
In glioblastoma multiforme (GBM), the most common adult brain tumor, this inter-tumoral heterogeneity is further complicated by intra-tumoral heterogeneity within the tumor.  ...  Our ability to molecularly characterize tumor cells has increased dramatically and shown that there are significant differences between samples from patients with the same tumor type.  ...  For instance, till date, no mouse model demonstrates the significant intra-tumoral heterogeneity seen in human GBM.  ... 
doi:10.4103/2152-7806.151351 pmid:25722938 pmcid:PMC4338492 fatcat:ra3wykdepnecjielkk3b5yyxiy

Frequent provirus insertional mutagenesis of Notch1 in thymomas of MMTVD/myc transgenic mice suggests a collaboration of c-myc and Notch1 for oncogenesis

L Girard, Z Hanna, N Beaulieu, C D Hoemann, C Simard, C A Kozak, P Jolicoeur
1996 Genes & Development  
The MMTVD/myc transgenic mice spontaneously develop oligoclonal CD4+CD8 + T-ceU tumors. We used provirus insertional mutagenesis in these mice to identify putative collaborators of c-myc.  ...  These results suggest that Notchl can be a frequent collaborator of c-myc for oncogenesis.  ...  We thank Yves Paquette for providing transgenic mice for assessment of tumor latencies. We thank Benoit Laganihre and Ginette Mass6 for their excellent technical assistance.  ... 
doi:10.1101/gad.10.15.1930 pmid:8756350 fatcat:attpgdz3mze6bkpb3ynpaus7gm

The Role of Genomic Profiling in Advanced Breast Cancer: The Two Faces of Janus

Yesim Eralp
2016 Translational Oncogenomics  
Next, is the puzzle on spatial and temporal tumoral heterogeneity, which remains to be solved by ultra-deep sequencing and optimizing liquid biopsy techniques.  ...  heterogeneity SUPPLEMENT: status of cancer Dna sequencing in the clinic CITATIoN:  ...  within the same tumor called "intra-tumor heterogeneity". 20 The term "spatial intra-tumor heterogeneity" refers to the occurrence of genetic aberrations at different geographic locations within the  ... 
doi:10.4137/tog.s39410 pmid:27547031 pmcid:PMC4986714 fatcat:qibdbdfagjhkjkzf2q36y6w23m

Innate Genetic Evolution of Lung Cancers and Spatial Heterogeneity: Analysis of Treatment-Naïve Lesions

Kenichi Suda, Jihye Kim, Isao Murakami, Leslie Rozeboom, Masaki Shimoji, Shigeki Shimizu, Christopher J. Rivard, Tetsuya Mitsudomi, Aik-Choon Tan, Fred R. Hirsch
2018 Journal of Thoracic Oncology  
Methods-We performed RNA sequencing to analyze inter-tumor heterogeneity in thirty specimens (primary tumors, intra-thoracic, and extra-thoracic metastatic lesions) obtained from five treatment-naïve lung  ...  Introduction-Data regarding the pre-treatment inter-tumor heterogeneity of potential biomarkers in advanced-stage lung cancers is limited.  ...  regions in clinically resectable non-small cell lung cancers (NSCLCs; intra-tumor heterogeneity) 7 , or between multiple intrathoracic lesions obtained from operable NSCLCs 5 .  ... 
doi:10.1016/j.jtho.2018.05.039 pmid:29933065 pmcid:PMC6153034 fatcat:earb6iw66rejfkmxsb2rjoyrga

T cell receptor β-chain repertoire analysis of tumor infiltrating lymphocytes in pancreatic cancer

Can Cui, Xiuyun Tian, Jianhui Wu, Chaoting Zhang, Qin Tan, Xiaoya Guan, Bin Dong, Min Zhao, Zheming Lu, Chunyi Hao
2018 Cancer Science  
This study aimed to test the relationship between the TCR β repertoire of the tumor and peripheral blood, and also to investigate the intra-tumor spatial heterogeneity of the TCR β repertoire in pancreatic  ...  Whereas, intra-tumoral TCR β repertoires were spatially homogeneous between different regions of a single tumor tissue.  ...  The heterogeneity is probably driven by intra-tumoral competition and selection by the host's immune response to tumor therapeutics. 17, 18 It is necessary to assess the clonal composition of TIL across  ... 
doi:10.1111/cas.13877 pmid:30426614 pmcid:PMC6317932 fatcat:z3tewhsdazbc7fhpbexldqye5e

Limited utility of tissue micro-arrays in detecting intra-tumoral heterogeneity in stem cell characteristics and tumor progression markers in breast cancer

Pascale Kündig, Charlotte Giesen, Hartland Jackson, Bernd Bodenmiller, Bärbel Papassotirolopus, Sandra Nicole Freiberger, Catharine Aquino, Lennart Opitz, Zsuzsanna Varga
2018 Journal of Translational Medicine  
In this study, we addressed the question whether intra-tumoral heterogeneity can be reliably detected in tissue-micro-arrays in breast cancer by comparing expression levels of conventional predictive/prognostic  ...  Intra-tumoral heterogeneity has been recently addressed in different types of cancer, including breast cancer.  ...  Results Intra-tumoral heterogeneity Expression levels of all markers were compared between tissue cores of central and peripheral tumor parts to assess intra-tumoral heterogeneity.  ... 
doi:10.1186/s12967-018-1495-6 pmid:29739401 pmcid:PMC5941467 fatcat:hfogamxu5jhfdgbif3xrloplti

Avoiding Pitfalls in the Statistical Analysis of Heterogeneous Tumors

David E. Axelrod, Naomi Miller, Judith-Anne W. Chapman
2009 Biomedical Informatics Insights  
Differences between cells within individual tumors (intratumor heterogeneity) and between tumors of different patients (intertumor heterogeneity) may mean that a small sample is not representative of the  ...  tumor as a whole, particularly for solid tumors which are the focus of this paper.  ...  However, intra-tumor heterogeneity will not be detected once the data for many cells or many regions within each tumor are combined to characterize each patient's tumor.  ... 
doi:10.4137/bii.s2222 fatcat:43viqnreojaubbd26i3ssqjgay
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