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Literature DB >> 26513549

TransVar: a multilevel variant annotator for precision genomics.

Wanding Zhou¹, Tenghui Chen¹, Zechen Chong¹, Mary A Rohrdanz¹, James M Melott¹, Chris Wakefield¹, Jia Zeng², John N Weinstein^1,3, Funda Meric-Bernstam^2,4,5, Gordon B Mills^2,3, Ken Chen¹.

Abstract

Entities: Disease Gene Mutation Species

Mesh：

Substances：

Year: 2015 PMID： 26513549 PMCID： PMC4772859 DOI： 10.1038/nmeth.3622

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

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6 in total

1. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.

Authors: Pablo Cingolani; Adrian Platts; Le Lily Wang; Melissa Coon; Tung Nguyen; Luan Wang; Susan J Land; Xiangyi Lu; Douglas M Ruden
Journal: Fly (Austin) Date: 2012 Apr-Jun Impact factor: 2.160

2. Oncotator: cancer variant annotation tool.

Authors: Alex H Ramos; Lee Lichtenstein; Manaswi Gupta; Michael S Lawrence; Trevor J Pugh; Gordon Saksena; Matthew Meyerson; Gad Getz
Journal: Hum Mutat Date: 2015-03-16 Impact factor: 4.878

3. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.

Authors: Kai Wang; Mingyao Li; Hakon Hakonarson
Journal: Nucleic Acids Res Date: 2010-07-03 Impact factor: 16.971

4. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.

Authors: William McLaren; Bethan Pritchard; Daniel Rios; Yuan Chen; Paul Flicek; Fiona Cunningham
Journal: Bioinformatics Date: 2010-06-18 Impact factor: 6.937

5. PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse.

Authors: Peter V Hornbeck; Jon M Kornhauser; Sasha Tkachev; Bin Zhang; Elzbieta Skrzypek; Beth Murray; Vaughan Latham; Michael Sullivan
Journal: Nucleic Acids Res Date: 2011-12-01 Impact factor: 16.971

6. Acquired resistance L747S mutation in an epidermal growth factor receptor-tyrosine kinase inhibitor-naïve patient: A report of three cases.

Authors: Fumihiro Yamaguchi; Kunihiko Fukuchi; Yohei Yamazaki; Hiromi Takayasu; Sakiko Tazawa; Hidetsugu Tateno; Eisuke Kato; Aya Wakabayashi; Mami Fujimori; Takuya Iwasaki; Makoto Hayashi; Yutaka Tsuchiya; Jun Yamashita; Norikazu Takeda; Fumio Kokubu
Journal: Oncol Lett Date: 2013-11-25 Impact factor: 2.967

6 in total

25 in total

1. Nm-seq maps 2'-O-methylation sites in human mRNA with base precision.

Authors: Qing Dai; Sharon Moshitch-Moshkovitz; Dali Han; Nitzan Kol; Ninette Amariglio; Gideon Rechavi; Dan Dominissini; Chuan He
Journal: Nat Methods Date: 2017-05-15 Impact factor: 28.547

2. mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers.

Authors: Mulin Jun Li; Hongcheng Yao; Dandan Huang; Huanhuan Liu; Zipeng Liu; Hang Xu; Yiming Qin; Jeanette Prinz; Weiyi Xia; Panwen Wang; Bin Yan; Nhan L Tran; Jean-Pierre Kocher; Pak C Sham; Junwen Wang
Journal: Nucleic Acids Res Date: 2017-07-03 Impact factor: 16.971

Review 3. Operationalization of Next-Generation Sequencing and Decision Support for Precision Oncology.

Authors: Jia Zeng; Amber Johnson; Md Abu Shufean; Michael Kahle; Dong Yang; Scott E Woodman; Thuy Vu; Shhyam Moorthy; Vijaykumar Holla; Funda Meric-Bernstam
Journal: JCO Clin Cancer Inform Date: 2019-09

4. Novel candidates of pathogenic variants of the BRCA1 and BRCA2 genes from a dataset of 3,552 Japanese whole genomes (3.5KJPNv2).

Authors: Hideki Tokunaga; Keita Iida; Atsushi Hozawa; Soichi Ogishima; Yoh Watanabe; Shogo Shigeta; Muneaki Shimada; Yumi Yamaguchi-Kabata; Shu Tadaka; Fumiki Katsuoka; Shin Ito; Kazuki Kumada; Yohei Hamanaka; Nobuo Fuse; Kengo Kinoshita; Masayuki Yamamoto; Nobuo Yaegashi; Jun Yasuda
Journal: PLoS One Date: 2021-01-11 Impact factor: 3.240

5. Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability.

Authors: Kuan-Lin Huang; Yige Wu; Tina Primeau; Yi-Ting Wang; Yuqian Gao; Joshua F McMichael; Adam D Scott; Song Cao; Michael C Wendl; Kimberly J Johnson; Kelly Ruggles; Jason Held; Samuel H Payne; Sherri Davies; Arvin Dar; Christopher R Kinsinger; Mehdi Mesri; Henry Rodriguez; Matthew J Ellis; R Reid Townsend; Feng Chen; David Fenyö; Shunqiang Li; Tao Liu; Steven A Carr; Li Ding
Journal: Mol Cell Proteomics Date: 2019-06-13 Impact factor: 5.911

6. Circulating Tumor DNA Profiling in Small-Cell Lung Cancer Identifies Potentially Targetable Alterations.

Authors: Siddhartha Devarakonda; Sumithra Sankararaman; Brett H Herzog; Kathryn A Gold; Saiama N Waqar; Jeffrey P Ward; Victoria M Raymond; Richard B Lanman; Aadel A Chaudhuri; Taofeek K Owonikoko; Bob T Li; John T Poirier; Charles M Rudin; Ramaswamy Govindan; Daniel Morgensztern
Journal: Clin Cancer Res Date: 2019-07-12 Impact factor: 12.531

7. Systematic analysis of alterations in the ubiquitin proteolysis system reveals its contribution to driver mutations in cancer.

Authors: Francisco Martínez-Jiménez; Ferran Muiños; Erika López-Arribillaga; Nuria Lopez-Bigas; Abel Gonzalez-Perez
Journal: Nat Cancer Date: 2019-12-02