Literature DB >> 21947516

Integrative, multimodal analysis of glioblastoma using TCGA molecular data, pathology images, and clinical outcomes.

Jun Kong1, Lee A D Cooper, Fusheng Wang, David A Gutman, Jingjing Gao, Candace Chisolm, Ashish Sharma, Tony Pan, Erwin G Van Meir, Tahsin M Kurc, Carlos S Moreno, Joel H Saltz, Daniel J Brat.   

Abstract

Multimodal, multiscale data synthesis is becoming increasingly critical for successful translational biomedical research. In this letter, we present a large-scale investigative initiative on glioblastoma, a high-grade brain tumor, with complementary data types using in silico approaches. We integrate and analyze data from The Cancer Genome Atlas Project on glioblastoma that includes novel nuclear phenotypic data derived from microscopic slides, genotypic signatures described by transcriptional class and genetic alterations, and clinical outcomes defined by response to therapy and patient survival. Our preliminary results demonstrate numerous clinically and biologically significant correlations across multiple data types, revealing the power of in silico multimodal data integration for cancer research.

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Mesh:

Year:  2011        PMID: 21947516      PMCID: PMC3292263          DOI: 10.1109/TBME.2011.2169256

Source DB:  PubMed          Journal:  IEEE Trans Biomed Eng        ISSN: 0018-9294            Impact factor:   4.538


  16 in total

1.  An optimal transportation approach for nuclear structure-based pathology.

Authors:  Wei Wang; John A Ozolek; Dejan Slepčev; Ann B Lee; Cheng Chen; Gustavo K Rohde
Journal:  IEEE Trans Med Imaging       Date:  2010-10-25       Impact factor: 10.048

Review 2.  Exciting new advances in neuro-oncology: the avenue to a cure for malignant glioma.

Authors:  Erwin G Van Meir; Costas G Hadjipanayis; Andrew D Norden; Hui-Kuo Shu; Patrick Y Wen; Jeffrey J Olson
Journal:  CA Cancer J Clin       Date:  2010 May-Jun       Impact factor: 508.702

3.  MORPHOLOGICAL SIGNATURES AND GENOMIC CORRELATES IN GLIOBLASTOMA.

Authors:  Lee A D Cooper; Jun Kong; Fusheng Wang; Tahsin Kurc; Carlos S Moreno; Daniel J Brat; Joel H Saltz
Journal:  Proc IEEE Int Symp Biomed Imaging       Date:  2011-03-30

4.  ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology.

Authors:  David J Foran; Lin Yang; Wenjin Chen; Jun Hu; Lauri A Goodell; Michael Reiss; Fusheng Wang; Tahsin Kurc; Tony Pan; Ashish Sharma; Joel H Saltz
Journal:  J Am Med Inform Assoc       Date:  2011-05-23       Impact factor: 4.497

5.  An integrative approach for in silico glioma research.

Authors:  Lee A D Cooper; Jun Kong; David A Gutman; Fusheng Wang; Sharath R Cholleti; Tony C Pan; Patrick M Widener; Ashish Sharma; Tom Mikkelsen; Adam E Flanders; Daniel L Rubin; Erwin G Van Meir; Tahsin M Kurc; Carlos S Moreno; Daniel J Brat; Joel H Saltz
Journal:  IEEE Trans Biomed Eng       Date:  2010-07-23       Impact factor: 4.538

6.  Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.

Authors:  Roel G W Verhaak; Katherine A Hoadley; Elizabeth Purdom; Victoria Wang; Yuan Qi; Matthew D Wilkerson; C Ryan Miller; Li Ding; Todd Golub; Jill P Mesirov; Gabriele Alexe; Michael Lawrence; Michael O'Kelly; Pablo Tamayo; Barbara A Weir; Stacey Gabriel; Wendy Winckler; Supriya Gupta; Lakshmi Jakkula; Heidi S Feiler; J Graeme Hodgson; C David James; Jann N Sarkaria; Cameron Brennan; Ari Kahn; Paul T Spellman; Richard K Wilson; Terence P Speed; Joe W Gray; Matthew Meyerson; Gad Getz; Charles M Perou; D Neil Hayes
Journal:  Cancer Cell       Date:  2010-01-19       Impact factor: 31.743

Review 7.  Clinicopathologic aspects of 1p/19q loss and the diagnosis of oligodendroglioma.

Authors:  Kenneth Aldape; Peter C Burger; Arie Perry
Journal:  Arch Pathol Lab Med       Date:  2007-02       Impact factor: 5.534

8.  Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

Authors: 
Journal:  Nature       Date:  2008-09-04       Impact factor: 49.962

9.  Feedback circuit among INK4 tumor suppressors constrains human glioblastoma development.

Authors:  Ruprecht Wiedemeyer; Cameron Brennan; Timothy P Heffernan; Yonghong Xiao; John Mahoney; Alexei Protopopov; Hongwu Zheng; Graham Bignell; Frank Furnari; Webster K Cavenee; William C Hahn; Koichi Ichimura; V Peter Collins; Gerald C Chu; Michael R Stratton; Keith L Ligon; P Andrew Futreal; Lynda Chin
Journal:  Cancer Cell       Date:  2008-04       Impact factor: 31.743

10.  Functional copy-number alterations in cancer.

Authors:  Barry S Taylor; Jordi Barretina; Nicholas D Socci; Penelope Decarolis; Marc Ladanyi; Matthew Meyerson; Samuel Singer; Chris Sander
Journal:  PLoS One       Date:  2008-09-11       Impact factor: 3.240

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  30 in total

Review 1.  Molecular heterogeneity of glioblastoma and its clinical relevance.

Authors:  Katalin Eder; Bernadette Kalman
Journal:  Pathol Oncol Res       Date:  2014-08-27       Impact factor: 3.201

2.  Augmentation of Physician Assessments with Multi-Omics Enhances Predictability of Drug Response: A Case Study of Major Depressive Disorder.

Authors:  Arjun Athreya; Ravishankar Iyer; Drew Neavin; Liewei Wang; Richard Weinshilboum; Rima Kaddurah-Daouk; John Rush; Mark Frye; William Bobo
Journal:  IEEE Comput Intell Mag       Date:  2018-07-20       Impact factor: 11.356

3.  Towards Building a High Performance Spatial Query System for Large Scale Medical Imaging Data.

Authors:  Ablimit Aji; Fusheng Wang; Joel H Saltz
Journal:  Proc ACM SIGSPATIAL Int Conf Adv Inf       Date:  2012-11-06

4.  A combined diffusion tensor imaging and Ki-67 labeling index study for evaluating the extent of tumor infiltration using the F98 rat glioma model.

Authors:  Kai Wang; Tingting Ha; Xuzhu Chen; Shaowu Li; Lin Ai; Jun Ma; Jianping Dai
Journal:  J Neurooncol       Date:  2018-01-02       Impact factor: 4.130

5.  PANOPLY: Omics-Guided Drug Prioritization Method Tailored to an Individual Patient.

Authors:  Krishna R Kalari; Jason P Sinnwell; Kevin J Thompson; Xiaojia Tang; Erin E Carlson; Jia Yu; Peter T Vedell; James N Ingle; Richard M Weinshilboum; Judy C Boughey; Liewei Wang; Matthew P Goetz; Vera Suman
Journal:  JCO Clin Cancer Inform       Date:  2018-12

6.  Biological Interpretation of Morphological Patterns in Histopathological Whole-Slide Images.

Authors:  Sonal Kothari; John H Phan; Adeboye O Osunkoya; May D Wang
Journal:  ACM BCB       Date:  2012-10

7.  High-Performance Computational Analysis of Glioblastoma Pathology Images with Database Support Identifies Molecular and Survival Correlates.

Authors:  Jun Kong; Fusheng Wang; George Teodoro; Lee Cooper; Carlos S Moreno; Tahsin Kurc; Tony Pan; Joel Saltz; Daniel Brat
Journal:  Proceedings (IEEE Int Conf Bioinformatics Biomed)       Date:  2013-12

8.  Claudin-7 indirectly regulates the integrin/FAK signaling pathway in human colon cancer tissue.

Authors:  Lei Ding; Liyong Wang; Leiming Sui; Huanying Zhao; Xiaoxue Xu; Tengyan Li; Xiaonan Wang; Wenjing Li; Ping Zhou; Lu Kong
Journal:  J Hum Genet       Date:  2016-04-28       Impact factor: 3.172

9.  Radiological features combined with IDH1 status for predicting the survival outcome of glioblastoma patients.

Authors:  Kai Wang; Yinyan Wang; Xing Fan; Jiangfei Wang; Guilin Li; Jieling Ma; Jun Ma; Tao Jiang; Jianping Dai
Journal:  Neuro Oncol       Date:  2015-09-25       Impact factor: 12.300

10.  Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data.

Authors:  David A Gutman; Jake Cobb; Dhananjaya Somanna; Yuna Park; Fusheng Wang; Tahsin Kurc; Joel H Saltz; Daniel J Brat; Lee A D Cooper
Journal:  J Am Med Inform Assoc       Date:  2013-07-25       Impact factor: 4.497

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