Literature DB >> 30535306

Database of evidence for precision oncology portal.

Sam Q Sun1,2, R Jay Mashl1,2, Sohini Sengupta1,2, Adam D Scott1,2, Weihua Wang1,2, Prag Batra2, Liang-Bo Wang1,2, Matthew A Wyczalkowski1,2, Li Ding1,2,3,4.   

Abstract

Summary: A database of curated genomic variants with clinically supported drug therapies and other oncological annotations is described. The accompanying web portal provides a search engine with two modes: one that allows users to query gene, cancer type, variant type or position for druggable mutations, and another to search for and to visualize, on three-dimensional protein structures, putative druggable sites that cluster with known druggable mutations. Availability and implementation: http://dinglab.wustl.edu/depo.

Entities:  

Mesh：

Year:  2018        PMID： 30535306      PMCID： PMC6289129          DOI： 10.1093/bioinformatics/bty531

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  8 in total

Review 1.  Next-Generation Sequencing to Guide Clinical Trials.

Authors:  Lillian L Siu; Barbara A Conley; Scott Boerner; Patricia M LoRusso
Journal:  Clin Cancer Res       Date:  2015-10-15       Impact factor: 12.531

2.  The right drugs at the right time for the right patient: the MD Anderson precision oncology decision support platform.

Authors:  Amber Johnson; Jia Zeng; Ann M Bailey; Vijaykumar Holla; Beate Litzenburger; Humberto Lara-Guerra; Gordon B Mills; John Mendelsohn; Kenna R Shaw; Funda Meric-Bernstam
Journal:  Drug Discov Today       Date:  2015-07-03       Impact factor: 7.851

3.  Database of genomic biomarkers for cancer drugs and clinical targetability in solid tumors.

Authors:  Rodrigo Dienstmann; In Sock Jang; Brian Bot; Stephen Friend; Justin Guinney
Journal:  Cancer Discov       Date:  2015-02       Impact factor: 39.397

4.  Protein-structure-guided discovery of functional mutations across 19 cancer types.

Authors:  Beifang Niu; Adam D Scott; Sohini Sengupta; Matthew H Bailey; Prag Batra; Jie Ning; Matthew A Wyczalkowski; Wen-Wei Liang; Qunyuan Zhang; Michael D McLellan; Sam Q Sun; Piyush Tripathi; Carolyn Lou; Kai Ye; R Jay Mashl; John Wallis; Michael C Wendl; Feng Chen; Li Ding
Journal:  Nat Genet       Date:  2016-06-13       Impact factor: 38.330

5.  Somatic cancer variant curation and harmonization through consensus minimum variant level data.

Authors:  Deborah I Ritter; Sameek Roychowdhury; Angshumoy Roy; Shruti Rao; Melissa J Landrum; Dmitriy Sonkin; Mamatha Shekar; Caleb F Davis; Reece K Hart; Christine Micheel; Meredith Weaver; Eliezer M Van Allen; Donald W Parsons; Howard L McLeod; Michael S Watson; Sharon E Plon; Shashikant Kulkarni; Subha Madhavan
Journal:  Genome Med       Date:  2016-11-04       Impact factor: 11.117

6.  CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.

Authors:  Malachi Griffith; Nicholas C Spies; Kilannin Krysiak; Joshua F McMichael; Adam C Coffman; Arpad M Danos; Benjamin J Ainscough; Cody A Ramirez; Damian T Rieke; Lynzey Kujan; Erica K Barnell; Alex H Wagner; Zachary L Skidmore; Amber Wollam; Connor J Liu; Martin R Jones; Rachel L Bilski; Robert Lesurf; Yan-Yang Feng; Nakul M Shah; Melika Bonakdar; Lee Trani; Matthew Matlock; Avinash Ramu; Katie M Campbell; Gregory C Spies; Aaron P Graubert; Karthik Gangavarapu; James M Eldred; David E Larson; Jason R Walker; Benjamin M Good; Chunlei Wu; Andrew I Su; Rodrigo Dienstmann; Adam A Margolin; David Tamborero; Nuria Lopez-Bigas; Steven J M Jones; Ron Bose; David H Spencer; Lukas D Wartman; Richard K Wilson; Elaine R Mardis; Obi L Griffith
Journal:  Nat Genet       Date:  2017-01-31       Impact factor: 38.330

7.  Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations.

Authors:  David Tamborero; Carlota Rubio-Perez; Jordi Deu-Pons; Michael P Schroeder; Ana Vivancos; Ana Rovira; Ignasi Tusquets; Joan Albanell; Jordi Rodon; Josep Tabernero; Carmen de Torres; Rodrigo Dienstmann; Abel Gonzalez-Perez; Nuria Lopez-Bigas
Journal:  Genome Med       Date:  2018-03-28       Impact factor: 11.117

8.  CancerDR: cancer drug resistance database.

Authors:  Rahul Kumar; Kumardeep Chaudhary; Sudheer Gupta; Harinder Singh; Shailesh Kumar; Ankur Gautam; Pallavi Kapoor; Gajendra P S Raghava
Journal:  Sci Rep       Date:  2013       Impact factor: 4.379
  8 in total
  10 in total

1.  Proteogenomic and metabolomic characterization of human glioblastoma.

Authors:  Liang-Bo Wang; Alla Karpova; Marina A Gritsenko; Jennifer E Kyle; Song Cao; Yize Li; Dmitry Rykunov; Antonio Colaprico; Joseph H Rothstein; Runyu Hong; Vasileios Stathias; MacIntosh Cornwell; Francesca Petralia; Yige Wu; Boris Reva; Karsten Krug; Pietro Pugliese; Emily Kawaler; Lindsey K Olsen; Wen-Wei Liang; Xiaoyu Song; Yongchao Dou; Michael C Wendl; Wagma Caravan; Wenke Liu; Daniel Cui Zhou; Jiayi Ji; Chia-Feng Tsai; Vladislav A Petyuk; Jamie Moon; Weiping Ma; Rosalie K Chu; Karl K Weitz; Ronald J Moore; Matthew E Monroe; Rui Zhao; Xiaolu Yang; Seungyeul Yoo; Azra Krek; Alexis Demopoulos; Houxiang Zhu; Matthew A Wyczalkowski; Joshua F McMichael; Brittany L Henderson; Caleb M Lindgren; Hannah Boekweg; Shuangjia Lu; Jessika Baral; Lijun Yao; Kelly G Stratton; Lisa M Bramer; Erika Zink; Sneha P Couvillion; Kent J Bloodsworth; Shankha Satpathy; Weiva Sieh; Simina M Boca; Stephan Schürer; Feng Chen; Maciej Wiznerowicz; Karen A Ketchum; Emily S Boja; Christopher R Kinsinger; Ana I Robles; Tara Hiltke; Mathangi Thiagarajan; Alexey I Nesvizhskii; Bing Zhang; D R Mani; Michele Ceccarelli; Xi S Chen; Sandra L Cottingham; Qing Kay Li; Albert H Kim; David Fenyö; Kelly V Ruggles; Henry Rodriguez; Mehdi Mesri; Samuel H Payne; Adam C Resnick; Pei Wang; Richard D Smith; Antonio Iavarone; Milan G Chheda; Jill S Barnholtz-Sloan; Karin D Rodland; Tao Liu; Li Ding
Journal:  Cancer Cell       Date:  2021-02-11       Impact factor: 31.743

2.  Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment.

Authors:  Hua Sun; Song Cao; R Jay Mashl; Chia-Kuei Mo; Simone Zaccaria; Michael C Wendl; Sherri R Davies; Matthew H Bailey; Tina M Primeau; Jeremy Hoog; Jacqueline L Mudd; Dennis A Dean; Rajesh Patidar; Li Chen; Matthew A Wyczalkowski; Reyka G Jayasinghe; Fernanda Martins Rodrigues; Nadezhda V Terekhanova; Yize Li; Kian-Huat Lim; Andrea Wang-Gillam; Brian A Van Tine; Cynthia X Ma; Rebecca Aft; Katherine C Fuh; Julie K Schwarz; Jose P Zevallos; Sidharth V Puram; John F Dipersio; Brandi Davis-Dusenbery; Matthew J Ellis; Michael T Lewis; Michael A Davies; Meenhard Herlyn; Bingliang Fang; Jack A Roth; Alana L Welm; Bryan E Welm; Funda Meric-Bernstam; Feng Chen; Ryan C Fields; Shunqiang Li; Ramaswamy Govindan; James H Doroshow; Jeffrey A Moscow; Yvonne A Evrard; Jeffrey H Chuang; Benjamin J Raphael; Li Ding
Journal:  Nat Commun       Date:  2021-08-24       Impact factor: 17.694

Review 3.  Contributions from the 2018 Literature on Bioinformatics and Translational Informatics.

Authors:  Malika Smaïl-Tabbone; Bastien Rance
Journal:  Yearb Med Inform       Date:  2019-08-16

4.  Evolution and structure of clinically relevant gene fusions in multiple myeloma.

Authors:  Steven M Foltz; Qingsong Gao; Christopher J Yoon; Hua Sun; Lijun Yao; Yize Li; Reyka G Jayasinghe; Song Cao; Justin King; Daniel R Kohnen; Mark A Fiala; Li Ding; Ravi Vij
Journal:  Nat Commun       Date:  2020-05-29       Impact factor: 14.919

5.  Evidence-Based Network Approach to Recommending Targeted Cancer Therapies.

Authors:  Jayaram Kancherla; Shruti Rao; Krithika Bhuvaneshwar; Rebecca B Riggins; Robert A Beckman; Subha Madhavan; Héctor Corrada Bravo; Simina M Boca
Journal:  JCO Clin Cancer Inform       Date:  2020-01

6.  Pan-Cancer Analysis Reveals the Diverse Landscape of Novel Sense and Antisense Fusion Transcripts.

Authors:  Neetha Nanoth Vellichirammal; Abrar Albahrani; Jasjit K Banwait; Nitish K Mishra; You Li; Shrabasti Roychoudhury; Mathew J Kling; Sameer Mirza; Kishor K Bhakat; Vimla Band; Shantaram S Joshi; Chittibabu Guda
Journal:  Mol Ther Nucleic Acids       Date:  2020-01-29       Impact factor: 8.886

7.  Chemogenomic profiling of breast cancer patient-derived xenografts reveals targetable vulnerabilities for difficult-to-treat tumors.

Authors:  Paul Savage; Alain Pacis; Hellen Kuasne; Leah Liu; Daniel Lai; Adrian Wan; Matthew Dankner; Constanza Martinez; Valentina Muñoz-Ramos; Virginie Pilon; Anie Monast; Hong Zhao; Margarita Souleimanova; Matthew G Annis; Adriana Aguilar-Mahecha; Josiane Lafleur; Nicholas R Bertos; Jamil Asselah; Nathaniel Bouganim; Kevin Petrecca; Peter M Siegel; Atilla Omeroglu; Sohrab P Shah; Samuel Aparicio; Mark Basik; Sarkis Meterissian; Morag Park
Journal:  Commun Biol       Date:  2020-06-16

8.  Japanese version of The Cancer Genome Atlas, JCGA, established using fresh frozen tumors obtained from 5143 cancer patients.

Authors:  Takeshi Nagashima; Ken Yamaguchi; Kenichi Urakami; Yuji Shimoda; Sumiko Ohnami; Keiichi Ohshima; Tomoe Tanabe; Akane Naruoka; Fukumi Kamada; Masakuni Serizawa; Keiichi Hatakeyama; Kenya Matsumura; Shumpei Ohnami; Koji Maruyama; Tohru Mochizuki; Masatoshi Kusuhara; Akio Shiomi; Yasuhisa Ohde; Masanori Terashima; Katsuhiko Uesaka; Tetsuro Onitsuka; Seiichiro Nishimura; Yasuyuki Hirashima; Nakamasa Hayashi; Yoshio Kiyohara; Yasuhiro Tsubosa; Hirohisa Katagiri; Masashi Niwakawa; Kaoru Takahashi; Hiroya Kashiwagi; Masahiro Nakagawa; Yuji Ishida; Takashi Sugino; Mitsuru Takahashi; Yasuto Akiyama
Journal:  Cancer Sci       Date:  2020-01-22       Impact factor: 6.716

9.  ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps.

Authors:  Deepak Balamurali; Alessandro Gorohovski; Rajesh Detroja; Vikrant Palande; Dorith Raviv-Shay; Milana Frenkel-Morgenstern
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

Review 10.  A Review of Precision Oncology Knowledgebases for Determining the Clinical Actionability of Genetic Variants.

Authors:  Xuanyi Li; Jeremy L Warner
Journal:  Front Cell Dev Biol       Date:  2020-02-11
  10 in total

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