Literature DB >> 27099341

Omics Profiling in Precision Oncology.

Kun-Hsing Yu1, Michael Snyder2.   

Abstract

Cancer causes significant morbidity and mortality worldwide, and is the area most targeted in precision medicine. Recent development of high-throughput methods enables detailed omics analysis of the molecular mechanisms underpinning tumor biology. These studies have identified clinically actionable mutations, gene and protein expression patterns associated with prognosis, and provided further insights into the molecular mechanisms indicative of cancer biology and new therapeutics strategies such as immunotherapy. In this review, we summarize the techniques used for tumor omics analysis, recapitulate the key findings in cancer omics studies, and point to areas requiring further research on precision oncology.
© 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

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Year:  2016        PMID: 27099341      PMCID: PMC4974334          DOI: 10.1074/mcp.O116.059253

Source DB:  PubMed          Journal:  Mol Cell Proteomics        ISSN: 1535-9476            Impact factor:   5.911


  116 in total

Review 1.  Metabolomics: available results, current research projects in breast cancer, and future applications.

Authors:  Wederson Marcos Claudino; Alessandro Quattrone; Laura Biganzoli; Marta Pestrin; Ivano Bertini; Angelo Di Leo
Journal:  J Clin Oncol       Date:  2007-05-14       Impact factor: 44.544

2.  Protein array technology to detect HER2 (erbB-2)-induced 'cytokine signature' in breast cancer.

Authors:  Alejandro Vazquez-Martin; Ramon Colomer; Javier A Menendez
Journal:  Eur J Cancer       Date:  2007-03-26       Impact factor: 9.162

3.  Genome-scale analysis of aberrant DNA methylation in colorectal cancer.

Authors:  Toshinori Hinoue; Daniel J Weisenberger; Christopher P E Lange; Hui Shen; Hyang-Min Byun; David Van Den Berg; Simeen Malik; Fei Pan; Houtan Noushmehr; Cornelis M van Dijk; Rob A E M Tollenaar; Peter W Laird
Journal:  Genome Res       Date:  2011-06-09       Impact factor: 9.043

Review 4.  Cancer as an evolutionary and ecological process.

Authors:  Lauren M F Merlo; John W Pepper; Brian J Reid; Carlo C Maley
Journal:  Nat Rev Cancer       Date:  2006-11-16       Impact factor: 60.716

Review 5.  Tumor heterogeneity: causes and consequences.

Authors:  Andriy Marusyk; Kornelia Polyak
Journal:  Biochim Biophys Acta       Date:  2009-11-18

6.  A novel grading system for clear cell renal cell carcinoma incorporating tumor necrosis.

Authors:  Brett Delahunt; Jesse K McKenney; Christine M Lohse; Bradley C Leibovich; Robert Houston Thompson; Stephen A Boorjian; John C Cheville
Journal:  Am J Surg Pathol       Date:  2013-03       Impact factor: 6.394

7.  Global levels of histone modifications predict prognosis in different cancers.

Authors:  David B Seligson; Steve Horvath; Matthew A McBrian; Vei Mah; Hong Yu; Sheila Tze; Qun Wang; David Chia; Lee Goodglick; Siavash K Kurdistani
Journal:  Am J Pathol       Date:  2009-04-06       Impact factor: 4.307

Review 8.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

9.  Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer.

Authors:  Klarisa Rikova; Ailan Guo; Qingfu Zeng; Anthony Possemato; Jian Yu; Herbert Haack; Julie Nardone; Kimberly Lee; Cynthia Reeves; Yu Li; Yerong Hu; Zhiping Tan; Matthew Stokes; Laura Sullivan; Jeffrey Mitchell; Randy Wetzel; Joan Macneill; Jian Min Ren; Jin Yuan; Corey E Bakalarski; Judit Villen; Jon M Kornhauser; Bradley Smith; Daiqiang Li; Xinmin Zhou; Steven P Gygi; Ting-Lei Gu; Roberto D Polakiewicz; John Rush; Michael J Comb
Journal:  Cell       Date:  2007-12-14       Impact factor: 41.582

10.  The future of genomics in pathology.

Authors:  Dennis P Wall; Peter J Tonellato
Journal:  F1000 Med Rep       Date:  2012-07-02
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  28 in total

1.  Classifying non-small cell lung cancer types and transcriptomic subtypes using convolutional neural networks.

Authors:  Kun-Hsing Yu; Feiran Wang; Gerald J Berry; Christopher Ré; Russ B Altman; Michael Snyder; Isaac S Kohane
Journal:  J Am Med Inform Assoc       Date:  2020-05-01       Impact factor: 4.497

Review 2.  Application of metabolomics in sarcoma: From biomarkers to therapeutic targets.

Authors:  Li Min; Edwin Choy; Chongqi Tu; Francis Hornicek; Zhenfeng Duan
Journal:  Crit Rev Oncol Hematol       Date:  2017-05-13       Impact factor: 6.312

3.  DNA-Targeted Precision Medicine; Have we Been Caught Sleeping?

Authors:  William C Reinhold; Anish Thomas; Yves Pommier
Journal:  Trends Cancer       Date:  2017-01

4.  An integrated analysis identifies STAT4 as a key regulator of ovarian cancer metastasis.

Authors:  L Zhao; G Ji; X Le; Z Luo; C Wang; M Feng; L Xu; Y Zhang; W B Lau; B Lau; Y Yang; L Lei; H Yang; Y Xuan; Y Chen; X Deng; T Yi; S Yao; X Zhao; Y Wei; S Zhou
Journal:  Oncogene       Date:  2017-01-23       Impact factor: 9.867

5.  Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma.

Authors:  Kun-Hsing Yu; Gerald J Berry; Daniel L Rubin; Christopher Ré; Russ B Altman; Michael Snyder
Journal:  Cell Syst       Date:  2017-11-15       Impact factor: 10.304

6.  Omics AnalySIs System for PRecision Oncology (OASISPRO): a web-based omics analysis tool for clinical phenotype prediction.

Authors:  Kun-Hsing Yu; Michael R Fitzpatrick; Luke Pappas; Warren Chan; Jessica Kung; Michael Snyder
Journal:  Bioinformatics       Date:  2018-01-15       Impact factor: 6.937

Review 7.  Integrative omics for health and disease.

Authors:  Konrad J Karczewski; Michael P Snyder
Journal:  Nat Rev Genet       Date:  2018-02-26       Impact factor: 53.242

Review 8.  Genetics of Food Allergy.

Authors:  Elisabet Johansson; Tesfaye B Mersha
Journal:  Immunol Allergy Clin North Am       Date:  2021-03-26       Impact factor: 3.479

9.  Predicting Ovarian Cancer Patients' Clinical Response to Platinum-Based Chemotherapy by Their Tumor Proteomic Signatures.

Authors:  Kun-Hsing Yu; Douglas A Levine; Hui Zhang; Daniel W Chan; Zhen Zhang; Michael Snyder
Journal:  J Proteome Res       Date:  2016-07-08       Impact factor: 4.466

Review 10.  Resolving Clinical Phenotypes into Endotypes in Allergy: Molecular and Omics Approaches.

Authors:  Tesfaye B Mersha; Yashira Afanador; Elisabet Johansson; Steven P Proper; Jonathan A Bernstein; Marc E Rothenberg; Gurjit K Khurana Hershey
Journal:  Clin Rev Allergy Immunol       Date:  2021-04       Impact factor: 8.667

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