Literature DB >> 19155300

Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome.

J Keith Killian1, Sven Bilke, Sean Davis, Robert L Walker, M Scott Killian, Erich B Jaeger, Yidong Chen, Jason Hipp, Stefania Pittaluga, Mark Raffeld, Robert Cornelison, William I Smith, Marina Bibikova, Jian-Bing Fan, Michael R Emmert-Buck, Elaine S Jaffe, Paul S Meltzer.   

Abstract

Emerging technologies allow broad profiling of the cancer genome for differential DNA methylation relative to benign cells. Herein, bisulfite-modified DNA from lymph nodes with either reactive hyperplasia or follicular lymphoma (FL) were analyzed using a commercial C/UpG genotyping assay. Two hundred fifty-nine differentially methylated targets (DMT) distributed among 183 unique genes were identified in FL. Comparison of matched formalin-fixed, paraffin-embedded and frozen surgical pathology replicates showed the complete preservation of the cancer methylome among differently archived tissue specimens. Analysis of the DMT profile is consistent with a pervasive epigenomic remodeling process in FL that affects predominantly nonlymphoid genes.

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Year:  2009        PMID： 19155300      PMCID： PMC7213763          DOI： 10.1158/0008-5472.CAN-08-2984

Source DB:  PubMed          Journal:  Cancer Res        ISSN： 0008-5472            Impact factor:   12.701


  16 in total

1.  A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations.

Authors:  Felix Naef; Nicholas D Socci; Marcelo Magnasco
Journal:  Bioinformatics       Date:  2003-01-22       Impact factor: 6.937

2.  Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays.

Authors:  Marina Bibikova; Dimitri Talantov; Eugene Chudin; Joanne M Yeakley; Jing Chen; Dennis Doucet; Eliza Wickham; David Atkins; David Barker; Mark Chee; Yixin Wang; Jian-Bing Fan
Journal:  Am J Pathol       Date:  2004-11       Impact factor: 4.307

3.  Idiopathic multicentric Castleman's disease. A clinicopathologic and immunohistochemical study of five cases.

Authors:  Masaru Kojima; Shigeo Nakamura; Masafumi Nishikawa; Hideaki Itoh; Shuichi Miyawaki; Nobuhide Masawa
Journal:  Pathol Res Pract       Date:  2005       Impact factor: 3.250

Review 4.  Epigenetics in cancer.

Authors:  Manel Esteller
Journal:  N Engl J Med       Date:  2008-03-13       Impact factor: 91.245

5.  DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status.

Authors:  B L Pike; T C Greiner; X Wang; D D Weisenburger; Y-H Hsu; G Renaud; T G Wolfsberg; M Kim; D J Weisenberger; K D Siegmund; W Ye; S Groshen; R Mehrian-Shai; J Delabie; W C Chan; P W Laird; J G Hacia
Journal:  Leukemia       Date:  2008-02-21       Impact factor: 11.528

6.  COBRA: a sensitive and quantitative DNA methylation assay.

Authors:  Z Xiong; P W Laird
Journal:  Nucleic Acids Res       Date:  1997-06-15       Impact factor: 16.971

7.  Differential DNA methylation patterns of small B-cell lymphoma subclasses with different clinical behavior.

Authors:  F B Rahmatpanah; S Carstens; J Guo; O Sjahputera; K H Taylor; D Duff; H Shi; J W Davis; S I Hooshmand; R Chitma-Matsiga; C W Caldwell
Journal:  Leukemia       Date:  2006-08-10       Impact factor: 11.528

8.  Diagnosis of multiple cancer types by shrunken centroids of gene expression.

Authors:  Robert Tibshirani; Trevor Hastie; Balasubramanian Narasimhan; Gilbert Chu
Journal:  Proc Natl Acad Sci U S A       Date:  2002-05-14       Impact factor: 11.205

9.  High-throughput DNA methylation profiling using universal bead arrays.

Authors:  Marina Bibikova; Zhenwu Lin; Lixin Zhou; Eugene Chudin; Eliza Wickham Garcia; Bonnie Wu; Dennis Doucet; Neal J Thomas; Yunhua Wang; Ekkehard Vollmer; Torsten Goldmann; Carola Seifart; Wei Jiang; David L Barker; Mark S Chee; Joanna Floros; Jian-Bing Fan
Journal:  Genome Res       Date:  2006-01-31       Impact factor: 9.043

10.  In situ localization of follicular lymphoma: description and analysis by laser capture microdissection.

Authors:  Peijie Cong; Mark Raffeld; Julie Teruya-Feldstein; Lynn Sorbara; Stefania Pittaluga; Elaine S Jaffe
Journal:  Blood       Date:  2002-05-01       Impact factor: 22.113
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  31 in total

1.  Hypermethylation of CpG islands is more prevalent than hypomethylation across the entire genome in breast carcinogenesis.

Authors:  Jianxin Tan; Yumei Gu; Xiaomei Zhang; Sihong You; Xiaowei Lu; Senqing Chen; Xiao Han; Yujie Sun
Journal:  Clin Exp Med       Date:  2012-01-04       Impact factor: 3.984

2.  Immunoguided laser assisted microdissection techniques for DNA methylation analysis of archival tissue specimens.

Authors:  Franziska C Eberle; Jeffrey C Hanson; J Keith Killian; Lai Wei; Kris Ylaya; Stephen M Hewitt; Elaine S Jaffe; Michael R Emmert-Buck; Jaime Rodriguez-Canales
Journal:  J Mol Diagn       Date:  2010-04-22       Impact factor: 5.568

3.  Simultaneous recovery of DNA and RNA from formalin-fixed paraffin-embedded tissue and application in epidemiologic studies.

Authors:  Wen-Yi Huang; Timothy M Sheehy; Lee E Moore; Ann W Hsing; Mark P Purdue
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2010-03-23       Impact factor: 4.254

4.  The Promise and the Problems of Epigenetics Biomarkers in Cancer.

Authors:  Attila T Lorincz
Journal:  Expert Opin Med Diagn       Date:  2011-09-01

Review 5.  Principles and challenges of genomewide DNA methylation analysis.

Authors:  Peter W Laird
Journal:  Nat Rev Genet       Date:  2010-03       Impact factor: 53.242

6.  Array-based DNA methylation profiling of primary lymphomas of the central nervous system.

Authors:  Julia Richter; Ole Ammerpohl; José I Martín-Subero; Manuel Montesinos-Rongen; Marina Bibikova; Eliza Wickham-Garcia; Otmar D Wiestler; Martina Deckert; Reiner Siebert
Journal:  BMC Cancer       Date:  2009-12-21       Impact factor: 4.430

7.  Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing.

Authors:  Jeong-Hyeon Choi; Yajun Li; Juyuan Guo; Lirong Pei; Tibor A Rauch; Robin S Kramer; Simone L Macmil; Graham B Wiley; Lynda B Bennett; Jennifer L Schnabel; Kristen H Taylor; Sun Kim; Dong Xu; Arun Sreekumar; Gerd P Pfeifer; Bruce A Roe; Charles W Caldwell; Kapil N Bhalla; Huidong Shi
Journal:  PLoS One       Date:  2010-09-29       Impact factor: 3.240

8.  Identification of methylated genes associated with aggressive bladder cancer.

Authors:  Carmen J Marsit; E Andres Houseman; Brock C Christensen; Luc Gagne; Margaret R Wrensch; Heather H Nelson; Joseph Wiemels; Shichun Zheng; John K Wiencke; Angeline S Andrew; Alan R Schned; Margaret R Karagas; Karl T Kelsey
Journal:  PLoS One       Date:  2010-08-23       Impact factor: 3.240

9.  Functional analysis of 5-lipoxygenase promoter repeat variants.

Authors:  Susanna Vikman; Romulo M Brena; Patrice Armstrong; Jaana Hartiala; Charles B Stephensen; Hooman Allayee
Journal:  Hum Mol Genet       Date:  2009-08-28       Impact factor: 6.150

10.  A comprehensive microarray-based DNA methylation study of 367 hematological neoplasms.

Authors:  Jose I Martin-Subero; Ole Ammerpohl; Marina Bibikova; Eliza Wickham-Garcia; Xabier Agirre; Sara Alvarez; Monika Brüggemann; Stefanie Bug; Maria J Calasanz; Martina Deckert; Martin Dreyling; Ming Q Du; Jan Dürig; Martin J S Dyer; Jian-Bing Fan; Stefan Gesk; Martin-Leo Hansmann; Lana Harder; Sylvia Hartmann; Wolfram Klapper; Ralf Küppers; Manuel Montesinos-Rongen; Inga Nagel; Christiane Pott; Julia Richter; José Román-Gómez; Marc Seifert; Harald Stein; Javier Suela; Lorenz Trümper; Inga Vater; Felipe Prosper; Claudia Haferlach; Juan Cruz Cigudosa; Reiner Siebert
Journal:  PLoS One       Date:  2009-09-11       Impact factor: 3.240
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