Literature DB >> 29392688

Whole Genome DNA Methylation Analysis of Human Glioblastoma Using Illumina BeadArrays.

Jonathan Serrano1, Matija Snuderl2.   

Abstract

In this chapter, we describe the use of Illumina® Infinium® HD Assay in conjunction with Illumina's EPIC Methylation 8-sample array platform to obtain glioblastoma molecular profiles. The procedure spans four days, and can be performed by a single laboratory technician. Starting with as little as 250 ng of DNA input, this method allows the flexibility to begin with DNA derived from either formalin-fixed, paraffin-embedded (FFPE) or fresh tissue and is compatible with an Illumina iScan or HiScan system.

Entities:  

Keywords:  Array; DNA; DNA methylation; FFPE; GBM; Illumina; Multiplex; Profiling; Subgroup classification; Tumor

Mesh：

Year:  2018        PMID： 29392688     DOI： 10.1007/978-1-4939-7659-1_2

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  13 in total

1.  MR imaging phenotype correlates with extent of genome-wide copy number abundance in IDH mutant gliomas.

Authors:  Chih-Chun Wu; Rajan Jain; Lucidio Neto; Seema Patel; Laila M Poisson; Jonathan Serrano; Victor Ng; Sohil H Patel; Dimitris G Placantonakis; David Zagzag; John Golfinos; Andrew S Chi; Matija Snuderl
Journal:  Neuroradiology       Date:  2019-05-27       Impact factor: 2.804

Review 2.  Precision Neuro-oncology: the Role of Genomic Testing in the Management of Adult and Pediatric Gliomas.

Authors:  Lori A Ramkissoon; Nicholas Britt; Alexander Guevara; Emily Whitt; Eric Severson; Pratheesh Sathyan; Laurie Gay; Julia Elvin; Jeffrey S Ross; Charlotte Brown; Kimberly Stogner-Underwood; Ryan Mott; David Kram; Roy Strowd; Glenn J Lesser; Shakti H Ramkissoon
Journal:  Curr Treat Options Oncol       Date:  2018-06-21

3.  Somatic Focal Copy Number Gains of Noncoding Regions of Receptor Tyrosine Kinase Genes in Treatment-Resistant Epilepsy.

Authors:  Varshini Vasudevaraja; Javier Hernaez Rodriguez; Cristiana Pelorosso; Kaicen Zhu; Anna Maria Buccoliero; Maristela Onozato; Hussein Mohamed; Jonathan Serrano; Lily Tredwin; Marianna Garonzi; Claudio Forcato; Briana Zeck; Sitharam Ramaswami; James Stafford; Arline Faustin; Daniel Friedman; Eveline Teresa Hidalgo; David Zagzag; Jane Skok; Adriana Heguy; Luis Chiriboga; Valerio Conti; Renzo Guerrini; A John Iafrate; Orrin Devinsky; Aristotelis Tsirigos; John G Golfinos; Matija Snuderl
Journal:  J Neuropathol Exp Neurol       Date:  2021-01-20       Impact factor: 3.685

4.  Spatial progression and molecular heterogeneity of IDH-mutant glioblastoma determined by DNA methylation-based mapping.

Authors:  Timothy E Richardson; Mariano S Viapiano; James F Lyon; Varshini Vasudevaraja; Kanish Mirchia; Jamie M Walker; Robert J Corona; Lawrence S Chin; Ivy Tran; Matija Snuderl
Journal:  Acta Neuropathol Commun       Date:  2021-06-30       Impact factor: 7.801

5.  TSC2-mutant uterine sarcomas with JAZF1-SUZ12 fusions demonstrate hybrid features of endometrial stromal sarcoma and PEComa and are responsive to mTOR inhibition.

Authors:  Sarah Chiang; Varshini Vasudevaraja; Jonathan Serrano; Colin J R Stewart; Esther Oliva; Amir Momeni-Boroujeni; Achim A Jungbluth; Arnaud Da Cruz Paula; Edaise M da Silva; Britta Weigelt; Kay J Park; Robert A Soslow; Rajmohan Murali; Lora H Ellenson; Ryma Benayed; Marc Ladanyi; Nadeem R Abu-Rustum; Mark A Dickson; Seth Cohen; Carol Aghajanian; Martee L Hensley; Cheng-Han Lee; Matija Snuderl; Jason A Konner
Journal:  Mod Pathol       Date:  2021-09-24       Impact factor: 8.209

6.  Expression profiling of the adhesion G protein-coupled receptor GPR133 (ADGRD1) in glioma subtypes.

Authors:  Joshua D Frenster; Michael Kader; Scott Kamen; James Sun; Luis Chiriboga; Jonathan Serrano; Devin Bready; Danielle Golub; Niklas Ravn-Boess; Gabriele Stephan; Andrew S Chi; Sylvia C Kurz; Rajan Jain; Christopher Y Park; David Fenyo; Ines Liebscher; Torsten Schöneberg; Giselle Wiggin; Robert Newman; Matt Barnes; John K Dickson; Douglas J MacNeil; Xinyan Huang; Nadim Shohdy; Matija Snuderl; David Zagzag; Dimitris G Placantonakis
Journal:  Neurooncol Adv       Date:  2020-04-28

7.  Functional and topographic effects on DNA methylation in IDH1/2 mutant cancers.

Authors:  Ramona Bledea; Varshini Vasudevaraja; Seema Patel; James Stafford; Jonathan Serrano; Gianna Esposito; Lilian M Tredwin; Nina Goodman; Andreas Kloetgen; John G Golfinos; David Zagzag; Britta Weigelt; A John Iafrate; Erik P Sulman; Andrew S Chi; Snjezana Dogan; Jorge S Reis-Filho; Sarah Chiang; Dimitris Placantonakis; Aristotelis Tsirigos; Matija Snuderl
Journal:  Sci Rep       Date:  2019-11-14       Impact factor: 4.996

8.  Dissecting the immunosuppressive tumor microenvironments in Glioblastoma-on-a-Chip for optimized PD-1 immunotherapy.

Authors:  Xin Cui; Chao Ma; Varshini Vasudevaraja; Jonathan Serrano; Jie Tong; Yansong Peng; Michael Delorenzo; Guomiao Shen; Joshua Frenster; Renee-Tyler Tan Morales; Weiyi Qian; Aristotelis Tsirigos; Andrew S Chi; Rajan Jain; Sylvia C Kurz; Erik P Sulman; Dimitris G Placantonakis; Matija Snuderl; Weiqiang Chen
Journal:  Elife       Date:  2020-09-10       Impact factor: 8.140

9.  Molecular and clinicopathologic features of gliomas harboring NTRK fusions.

Authors:  Matthew Torre; Varshini Vasudevaraja; Jonathan Serrano; Michael DeLorenzo; Seth Malinowski; Anne-Florence Blandin; Melanie Pages; Azra H Ligon; Fei Dong; David M Meredith; MacLean P Nasrallah; Craig Horbinski; Sonika Dahiya; Keith L Ligon; Mariarita Santi; Shakti H Ramkissoon; Mariella G Filbin; Matija Snuderl; Sanda Alexandrescu
Journal:  Acta Neuropathol Commun       Date:  2020-07-14       Impact factor: 7.578

10.  MiR-1253 exerts tumor-suppressive effects in medulloblastoma via inhibition of CDK6 and CD276 (B7-H3).

Authors:  Ranjana K Kanchan; Naveenkumar Perumal; Pranita Atri; Ramakanth Chirravuri Venkata; Ishwor Thapa; David L Klinkebiel; Andrew M Donson; Deborah Perry; Michael Punsoni; Geoffrey A Talmon; Donald W Coulter; Daniel R Boue'; Matija Snuderl; Mohd W Nasser; Surinder K Batra; Rajeev Vibhakar; Sidharth Mahapatra
Journal:  Brain Pathol       Date:  2020-03-30       Impact factor: 6.508
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