Literature DB >> 27594925

Strategies for Genomic and Proteomic Profiling of Cancers.

Gilbert S Omenn1.   

Abstract

Omics-based technology platforms have made new kinds of cancer profiling tests feasible. There are several valuable examples in clinical practice, and many more under development. A concerted, transparent process of discovery with lock-down of candidate assays and classifiers and clear specification of intended clinical use is essential. The Institute of Medicine has now proposed a three-stage scheme of confirming and validating analytical findings, validating performance on clinical specimens, and demonstrating explicit clinical utility for an approvable test (Micheel et al., Evolution of translational omics: lessons learned and path forward, 2012).

Entities:  

Keywords:  Bioinformatics; Biomarker discovery; Cancer proteomics; Her2/neu breast cancer; Omics-based clinical assays; Splice isoforms

Year:  2014        PMID: 27594925      PMCID: PMC5006946          DOI: 10.1007/s12561-014-9111-7

Source DB:  PubMed          Journal:  Stat Biosci        ISSN: 1867-1764


  16 in total

1.  Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers.

Authors:  Rajasree Menon; Ambrish Roy; Srayanta Mukherjee; Saveliy Belkin; Yang Zhang; Gilbert S Omenn
Journal:  J Proteome Res       Date:  2011-10-28       Impact factor: 4.466

2.  Research agenda. Opportunities for research and NIH.

Authors:  Francis S Collins
Journal:  Science       Date:  2010-01-01       Impact factor: 47.728

3.  Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers.

Authors:  Rajasree Menon; Gilbert S Omenn
Journal:  Cancer Res       Date:  2010-04-13       Impact factor: 12.701

4.  The road from discovery to clinical diagnostics: lessons learned from the first FDA-cleared in vitro diagnostic multivariate index assay of proteomic biomarkers.

Authors:  Zhen Zhang; Daniel W Chan
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2010-10-20       Impact factor: 4.254

5.  Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression.

Authors:  Arun Sreekumar; Laila M Poisson; Thekkelnaycke M Rajendiran; Amjad P Khan; Qi Cao; Jindan Yu; Bharathi Laxman; Rohit Mehra; Robert J Lonigro; Yong Li; Mukesh K Nyati; Aarif Ahsan; Shanker Kalyana-Sundaram; Bo Han; Xuhong Cao; Jaeman Byun; Gilbert S Omenn; Debashis Ghosh; Subramaniam Pennathur; Danny C Alexander; Alvin Berger; Jeffrey R Shuster; John T Wei; Sooryanarayana Varambally; Christopher Beecher; Arul M Chinnaiyan
Journal:  Nature       Date:  2009-02-12       Impact factor: 49.962

6.  Unifying gene expression measures from multiple platforms using factor analysis.

Authors:  Xin Victoria Wang; Roel G W Verhaak; Elizabeth Purdom; Paul T Spellman; Terence P Speed
Journal:  PLoS One       Date:  2011-03-11       Impact factor: 3.240

7.  Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer.

Authors:  Rajasree Menon; Qing Zhang; Yan Zhang; Damian Fermin; Nabeel Bardeesy; Ronald A DePinho; Chunxia Lu; Samir M Hanash; Gilbert S Omenn; David J States
Journal:  Cancer Res       Date:  2009-01-01       Impact factor: 12.701

8.  A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas.

Authors:  Terry Farrah; Eric W Deutsch; Gilbert S Omenn; David S Campbell; Zhi Sun; Julie A Bletz; Parag Mallick; Jonathan E Katz; Johan Malmström; Reto Ossola; Julian D Watts; Biaoyang Lin; Hui Zhang; Robert L Moritz; Ruedi Aebersold
Journal:  Mol Cell Proteomics       Date:  2011-06-01       Impact factor: 5.911

Review 9.  Alternative splice variants, a new class of protein cancer biomarker candidates: findings in pancreatic cancer and breast cancer with systems biology implications.

Authors:  Gilbert S Omenn; Anastasia K Yocum; Rajasree Menon
Journal:  Dis Markers       Date:  2010       Impact factor: 3.434

10.  Michigan molecular interactions r2: from interacting proteins to pathways.

Authors:  V Glenn Tarcea; Terry Weymouth; Alex Ade; Aaron Bookvich; Jing Gao; Vasudeva Mahavisno; Zach Wright; Adriane Chapman; Magesh Jayapandian; Arzucan Ozgür; Yuanyuan Tian; Jim Cavalcoli; Barbara Mirel; Jignesh Patel; Dragomir Radev; Brian Athey; David States; H V Jagadish
Journal:  Nucleic Acids Res       Date:  2008-10-31       Impact factor: 16.971

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  2 in total

1.  To Assist Oncologists: An Efficient Machine Learning-Based Approach for Anti-Cancer Peptides Classification.

Authors:  Majed Alsanea; Abdulsalam S Dukyil; Bushra Riaz; Farhan Alebeisat; Muhammad Islam; Shabana Habib
Journal:  Sensors (Basel)       Date:  2022-05-25       Impact factor: 3.847

2.  CancerPDF: A repository of cancer-associated peptidome found in human biofluids.

Authors:  Sherry Bhalla; Ruchi Verma; Harpreet Kaur; Rajesh Kumar; Salman Sadullah Usmani; Suresh Sharma; Gajendra P S Raghava
Journal:  Sci Rep       Date:  2017-05-04       Impact factor: 4.379

  2 in total

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