Peter W Laird

Peter W Laird

UNVERIFIED PROFILE

Are you Peter W Laird?   Register this Author

Register author
Peter W Laird

Peter W Laird

Publications by authors named "Peter W Laird"

Are you Peter W Laird?   Register this Author

100Publications

3771Reads

43Profile Views

Non-invasive diagnosis of early-stage lung cancer using high-throughput targeted DNA methylation sequencing of circulating tumor DNA (ctDNA).

Theranostics 2019 6;9(7):2056-2070. Epub 2019 Apr 6.

First Affiliated Hospital of Guangzhou Department of Thoracic Surgery/Oncology, the First Affiliated Hospital of Guangzhou Medical University; Guangzhou Institute of Respiratory Disease & Health; China State Key Laboratory and National Clinical Research Center for Respiratory Disease, Guangzhou, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7150/thno.28119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485294PMC
April 2019

SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.

Nucleic Acids Res 2018 11;46(20):e123

Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503 USA.

View Article

Download full-text PDF

Source
https://academic.oup.com/nar/advance-article/doi/10.1093/nar
Publisher Site
http://dx.doi.org/10.1093/nar/gky691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237738PMC
November 2018

MethyLight and Digital MethyLight.

Methods Mol Biol 2018 ;1708:497-513

Van Andel Research Institute, Center for Epigenetics, Room 5006W, 333 Bostwick Ave., N.E., Grand Rapids, MI, 49503, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-7481-8_25DOI Listing
July 2018

DNA methylation loss in late-replicating domains is linked to mitotic cell division.

Nat Genet 2018 04 2;50(4):591-602. Epub 2018 Apr 2.

Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-018-0073-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5893360PMC
April 2018

Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits.

Epigenetics Chromatin 2016 9;9:50. Epub 2016 Nov 9.

Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13072-016-0102-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103450PMC
January 2018

The REMOTE-control system: a system for reversible and tunable control of endogenous gene expression in mice.

Nucleic Acids Res 2017 Dec;45(21):12256-12269

Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkx829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716148PMC
December 2017

Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes.

Nucleic Acids Res 2017 02;45(4):e22

Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkw967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389466PMC
February 2017

Transcriptional heterogeneity in the lactase gene within cell-type is linked to the epigenome.

Sci Rep 2017 01 31;7:41843. Epub 2017 Jan 31.

Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep41843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282553PMC
January 2017

All Things in Moderation: Prevention of Intestinal Adenomas by DNA Hypomethylation.

Cancer Prev Res (Phila) 2016 07 17;9(7):509-11. Epub 2016 May 17.

Van Andel Research Institute, Center for Epigenetics, Grand Rapids, Michigan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1940-6207.CAPR-16-0097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5784773PMC
July 2016

Effects of folylpolyglutamate synthase modulation on global and gene-specific DNA methylation and gene expression in human colon and breast cancer cells.

J Nutr Biochem 2016 Mar 17;29:27-35. Epub 2015 Nov 17.

Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada M5S 1A8; Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Toronto, ON, Canada M5B 1T8; Department of Medicine, University of Toronto, Toronto, ON, Canada M5S 1A8; Division of Gastroenterology, St. Michael's Hospital, Toronto, ON, Canada M5B 1W8.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S09552863150033
Publisher Site
http://dx.doi.org/10.1016/j.jnutbio.2015.10.019DOI Listing
March 2016

Clinicopathologic Risk Factor Distributions for MLH1 Promoter Region Methylation in CIMP-Positive Tumors.

Cancer Epidemiol Biomarkers Prev 2016 Jan 28;25(1):68-75. Epub 2015 Oct 28.

Department of Biochemistry and Molecular Biology, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1055-9965.EPI-15-0935DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4713308PMC
January 2016

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

Authors:
W Marston Linehan Paul T Spellman Christopher J Ricketts Chad J Creighton Suzanne S Fei Caleb Davis David A Wheeler Bradley A Murray Laura Schmidt Cathy D Vocke Myron Peto Abu Amar M Al Mamun Eve Shinbrot Anurag Sethi Samira Brooks W Kimryn Rathmell Angela N Brooks Katherine A Hoadley A Gordon Robertson Denise Brooks Reanne Bowlby Sara Sadeghi Hui Shen Daniel J Weisenberger Moiz Bootwalla Stephen B Baylin Peter W Laird Andrew D Cherniack Gordon Saksena Scott Haake Jun Li Han Liang Yiling Lu Gordon B Mills Rehan Akbani Mark D M Leiserson Benjamin J Raphael Pavana Anur Donald Bottaro Laurence Albiges Nandita Barnabas Toni K Choueiri Bogdan Czerniak Andrew K Godwin A Ari Hakimi Thai H Ho James Hsieh Michael Ittmann William Y Kim Bhavani Krishnan Maria J Merino Kenna R Mills Shaw Victor E Reuter Ed Reznik Carl S Shelley Brian Shuch Sabina Signoretti Ramaprasad Srinivasan Pheroze Tamboli George Thomas Satish Tickoo Kenneth Burnett Daniel Crain Johanna Gardner Kevin Lau David Mallery Scott Morris Joseph D Paulauskis Robert J Penny Candace Shelton W Troy Shelton Mark Sherman Eric Thompson Peggy Yena Melissa T Avedon Jay Bowen Julie M Gastier-Foster Mark Gerken Kristen M Leraas Tara M Lichtenberg Nilsa C Ramirez Tracie Santos Lisa Wise Erik Zmuda John A Demchok Ina Felau Carolyn M Hutter Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean C Zenklusen Jiashan Zhang Brenda Ayala Julien Baboud Sudha Chudamani Jia Liu Laxmi Lolla Rashi Naresh Todd Pihl Qiang Sun Yunhu Wan Ye Wu Adrian Ally Miruna Balasundaram Saianand Balu Rameen Beroukhim Tom Bodenheimer Christian Buhay Yaron S N Butterfield Rebecca Carlsen Scott L Carter Hsu Chao Eric Chuah Amanda Clarke Kyle R Covington Mahmoud Dahdouli Ninad Dewal Noreen Dhalla Harsha V Doddapaneni Jennifer A Drummond Stacey B Gabriel Richard A Gibbs Ranabir Guin Walker Hale Alicia Hawes D Neil Hayes Robert A Holt Alan P Hoyle Stuart R Jefferys Steven J M Jones Corbin D Jones Divya Kalra Christie Kovar Lora Lewis Jie Li Yussanne Ma Marco A Marra Michael Mayo Shaowu Meng Matthew Meyerson Piotr A Mieczkowski Richard A Moore Donna Morton Lisle E Mose Andrew J Mungall Donna Muzny Joel S Parker Charles M Perou Jeffrey Roach Jacqueline E Schein Steven E Schumacher Yan Shi Janae V Simons Payal Sipahimalani Tara Skelly Matthew G Soloway Carrie Sougnez Angela Tam Donghui Tan Nina Thiessen Umadevi Veluvolu Min Wang Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Jane Zhou Jason Bedford Fengju Chen Yao Fu Mark Gerstein David Haussler Katayoon Kasaian Phillip Lai Shiyun Ling Amie Radenbaugh David Van Den Berg John N Weinstein Jingchun Zhu Monique Albert Iakovina Alexopoulou Jeremiah J Andersen J Todd Auman John Bartlett Sheldon Bastacky Julie Bergsten Michael L Blute Lori Boice Roni J Bollag Jeff Boyd Erik Castle Ying-Bei Chen John C Cheville Erin Curley Benjamin Davies April DeVolk Rajiv Dhir Laura Dike John Eckman Jay Engel Jodi Harr Ronald Hrebinko Mei Huang Lori Huelsenbeck-Dill Mary Iacocca Bruce Jacobs Michael Lobis Jodi K Maranchie Scott McMeekin Jerome Myers Joel Nelson Jeremy Parfitt Anil Parwani Nicholas Petrelli Brenda Rabeno Somak Roy Andrew L Salner Joel Slaton Melissa Stanton R Houston Thompson Leigh Thorne Kelinda Tucker Paul M Weinberger Cynthia Winemiller Leigh Anne Zach Rosemary Zuna

Promoter Methylation Analysis Reveals That KCNA5 Ion Channel Silencing Supports Ewing Sarcoma Cell Proliferation.

Mol Cancer Res 2016 Jan 16;14(1):26-34. Epub 2015 Nov 16.

Translational Oncology Program, University of Michigan, Ann Arbor, Michigan. Department of Pediatrics, University of Michigan, Ann Arbor, Michigan. Department of Pathology, University of Michigan, Ann Arbor, Michigan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1541-7786.MCR-15-0343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4716008PMC
January 2016

Tumor Budding in Colorectal Carcinoma: Confirmation of Prognostic Significance and Histologic Cutoff in a Population-based Cohort.

Am J Surg Pathol 2015 Oct;39(10):1340-6

*Division of Anatomic Pathology †Department of Health Sciences Research ‡Division of Experimental Pathology #Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN §Van Andel Research Institute, Grand Rapids, MI ∥University of Southern California, USC/Norris Comprehensive Cancer Center, Los Angeles, CA ¶Department of Epidemiology, The University of Iowa, Iowa City, IA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1097/PAS.0000000000000504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4567920PMC
October 2015

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.

Genome Biol 2015 May 21;16:105. Epub 2015 May 21.

Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT 6503, Los Angeles, CA, 90089-9601, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-015-0668-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460959PMC
May 2015

Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution.

Genome Res 2015 Mar 3;25(3):316-27. Epub 2015 Feb 3.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.180612.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352879PMC
March 2015

Association between molecular subtypes of colorectal cancer and patient survival.

Gastroenterology 2015 Jan 30;148(1):77-87.e2. Epub 2014 Sep 30.

Epidemiology Department, University of Washington, Seattle, Washington; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1053/j.gastro.2014.09.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274235PMC
January 2015

Non-specific filtering of beta-distributed data.

BMC Bioinformatics 2014 Jun 19;15:199. Epub 2014 Jun 19.

Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, 2001 N Soto Street, Suite 202W, Los Angeles 90089-9239 California, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-15-199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230495PMC
June 2014

Inferring tumour purity and stromal and immune cell admixture from expression data.

Nat Commun 2013 ;4:2612

1] Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Centre, Houston, Texas 77030, USA [2] Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms3612DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3826632PMC
May 2014

An epidemiologic and genomic investigation into the obesity paradox in renal cell carcinoma.

J Natl Cancer Inst 2013 Dec 27;105(24):1862-70. Epub 2013 Nov 27.

Affiliations of authors: Urology Service, Department of Surgery (AAH, NM, BF, PHK, PR), Human Oncology & Pathogenesis Program (AAH, JJH); Epidemiology and Biostatistics (HF, ECZ), Computational Biology (AJ, NS, GC, CS), Genitourinary Oncology (MHV, RJM, JJH), and Department of Pathology (VER), Memorial Sloan-Kettering Cancer Center, New York, NY; USC Epigenome Center, University of Southern California, Los Angeles, California (HS, PWL); Weill Medical College, Cornell University, New York, NY (RJM, JJH, PR).

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/jnci/djt310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866155PMC
December 2013

The landscape of microsatellite instability in colorectal and endometrial cancer genomes.

Cell 2013 Nov;155(4):858-68

Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 137-701, Korea.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2013.10.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3871995PMC
November 2013

Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer.

Authors:
Hui Shen Brooke L Fridley Honglin Song Kate Lawrenson Julie M Cunningham Susan J Ramus Mine S Cicek Jonathan Tyrer Douglas Stram Melissa C Larson Martin Köbel Argyrios Ziogas Wei Zheng Hannah P Yang Anna H Wu Eva L Wozniak Yin Ling Woo Boris Winterhoff Elisabeth Wik Alice S Whittemore Nicolas Wentzensen Rachel Palmieri Weber Allison F Vitonis Daniel Vincent Robert A Vierkant Ignace Vergote David Van Den Berg Anne M Van Altena Shelley S Tworoger Pamela J Thompson Daniel C Tessier Kathryn L Terry Soo-Hwang Teo Claire Templeman Daniel O Stram Melissa C Southey Weiva Sieh Nadeem Siddiqui Yurii B Shvetsov Xiao-Ou Shu Viji Shridhar Shan Wang-Gohrke Gianluca Severi Ira Schwaab Helga B Salvesen Iwona K Rzepecka Ingo B Runnebaum Mary Anne Rossing Lorna Rodriguez-Rodriguez Harvey A Risch Stefan P Renner Elizabeth M Poole Malcolm C Pike Catherine M Phelan Liisa M Pelttari Tanja Pejovic James Paul Irene Orlow Siti Zawiah Omar Sara H Olson Kunle Odunsi Stefan Nickels Heli Nevanlinna Roberta B Ness Steven A Narod Toru Nakanishi Kirsten B Moysich Alvaro N A Monteiro Joanna Moes-Sosnowska Francesmary Modugno Usha Menon John R McLaughlin Valerie McGuire Keitaro Matsuo Noor Azmi Mat Adenan Leon F A G Massuger Galina Lurie Lene Lundvall Jan Lubiński Jolanta Lissowska Douglas A Levine Arto Leminen Alice W Lee Nhu D Le Sandrina Lambrechts Diether Lambrechts Jolanta Kupryjanczyk Camilla Krakstad Gottfried E Konecny Susanne Krüger Kjaer Lambertus A Kiemeney Linda E Kelemen Gary L Keeney Beth Y Karlan Rod Karevan Kimberly R Kalli Hiroaki Kajiyama Bu-Tian Ji Allan Jensen Anna Jakubowska Edwin Iversen Satoyo Hosono Claus K Høgdall Estrid Høgdall Maureen Hoatlin Peter Hillemanns Florian Heitz Rebecca Hein Philipp Harter Mari K Halle Per Hall Jacek Gronwald Martin Gore Marc T Goodman Graham G Giles Aleksandra Gentry-Maharaj Montserrat Garcia-Closas James M Flanagan Peter A Fasching Arif B Ekici Robert Edwards Diana Eccles Douglas F Easton Matthias Dürst Andreas du Bois Thilo Dörk Jennifer A Doherty Evelyn Despierre Agnieszka Dansonka-Mieszkowska Cezary Cybulski Daniel W Cramer Linda S Cook Xiaoqing Chen Bridget Charbonneau Jenny Chang-Claude Ian Campbell Ralf Butzow Clareann H Bunker Doerthe Brueggmann Robert Brown Angela Brooks-Wilson Louise A Brinton Natalia Bogdanova Matthew S Block Elizabeth Benjamin Jonathan Beesley Matthias W Beckmann Elisa V Bandera Laura Baglietto François Bacot Sebastian M Armasu Natalia Antonenkova Hoda Anton-Culver Katja K Aben Dong Liang Xifeng Wu Karen Lu Michelle A T Hildebrandt Joellen M Schildkraut Thomas A Sellers David Huntsman Andrew Berchuck Georgia Chenevix-Trench Simon A Gayther Paul D P Pharoah Peter W Laird Ellen L Goode Celeste Leigh Pearce

Nat Commun 2013 ;4:1628

USC Epigenome Center, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms2629DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848248PMC
October 2013

Pan-cancer patterns of somatic copy number alteration.

Nat Genet 2013 Oct;45(10):1134-40

Broad Institute, Cambridge, Massachusetts, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Biophysics Program, Harvard University, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ng.2760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3966983PMC
October 2013

The somatic genomic landscape of glioblastoma.

Cell 2013 Oct;155(2):462-77

Human Oncology and Pathogenesis Program, Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, Department of Neurological Surgery, Weill Cornell Medical Center, New York, NY 10065, USA. Electronic address:

View Article

Download full-text PDF

Source
https://www.genome.gov/Multimedia/Slides/TCGA2/27_Verhaak.pd
Web Search
http://linkinghub.elsevier.com/retrieve/pii/S009286741301208
Publisher Site
http://dx.doi.org/10.1016/j.cell.2013.09.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910500PMC
October 2013

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

N Engl J Med 2013 05 1;368(22):2059-74. Epub 2013 May 1.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1056/NEJMoa1301689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767041PMC
May 2013

Low-level processing of Illumina Infinium DNA Methylation BeadArrays.

Nucleic Acids Res 2013 Apr 9;41(7):e90. Epub 2013 Mar 9.

Department of Preventive Medicine, USC Keck School of Medicine of USC, Los Angeles, CA 90089, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkt090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627582PMC
April 2013

Interplay between the cancer genome and epigenome.

Cell 2013 Mar;153(1):38-55

USC Epigenome Center, University of Southern California, Room G511B, 1450 Biggy Street, Los Angeles, CA 90089-9061, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2013.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648790PMC
March 2013

A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force.

Cancer Res 2012 Dec 27;72(24):6319-24. Epub 2012 Nov 27.

Research Department of Cancer Biology, University College London Cancer Institute, University College London, London, United Kingdom.

View Article

Download full-text PDF

Source
http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
Publisher Site
http://dx.doi.org/10.1158/0008-5472.CAN-12-3658DOI Listing
December 2012

Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships.

Hum Genet 2012 Oct 28;131(10):1565-89. Epub 2012 Jun 28.

Department of Preventive Medicine, Keck School of Medicine, University of Southern California, USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00439-012-1189-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432200PMC
October 2012

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data.

Nucleic Acids Res 2012 Oct 8;40(19):9379-91. Epub 2012 Aug 8.

Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

View Article

Download full-text PDF

Source
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
Publisher Site
http://dx.doi.org/10.1093/nar/gks725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479191PMC
October 2012

In epigenetic therapy, less is more.

Cell Stem Cell 2012 Apr;10(4):353-4

USC Epigenome Center, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90089-9601, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2012.03.012DOI Listing
April 2012

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

Genome Res 2012 Feb 9;22(2):271-82. Epub 2011 Jun 9.

Department of Surgery and Department of Biochemistry and Molecular Biology, University of Southern California, USC Epigenome Center, Los Angeles, California 90089-9601, USA.

View Article

Download full-text PDF

Source
http://genome.cshlp.org/cgi/doi/10.1101/gr.117523.110
Publisher Site
http://dx.doi.org/10.1101/gr.117523.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266034PMC
February 2012

Cancer risks for the relatives of colorectal cancer cases with a methylated MLH1 promoter region: data from the Colorectal Cancer Family Registry.

Cancer Prev Res (Phila) 2012 Feb 5;5(2):328-35. Epub 2011 Dec 5.

Department of Preventive Medicine, Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1940-6207.CAPR-11-0419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273599PMC
February 2012

Repeated assessment by high-throughput assay demonstrates that sperm DNA methylation levels are highly reproducible.

Fertil Steril 2011 Dec 26;96(6):1325-30. Epub 2011 Oct 26.

Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fertnstert.2011.09.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448450PMC
December 2011

Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage.

Authors:
Katherine Amps Peter W Andrews George Anyfantis Lyle Armstrong Stuart Avery Hossein Baharvand Julie Baker Duncan Baker Maria B Munoz Stephen Beil Nissim Benvenisty Dalit Ben-Yosef Juan-Carlos Biancotti Alexis Bosman Romulo Martin Brena Daniel Brison Gunilla Caisander María V Camarasa Jieming Chen Eric Chiao Young Min Choi Andre B H Choo Daniel Collins Alan Colman Jeremy M Crook George Q Daley Anne Dalton Paul A De Sousa Chris Denning Janet Downie Petr Dvorak Karen D Montgomery Anis Feki Angela Ford Victoria Fox Ana M Fraga Tzvia Frumkin Lin Ge Paul J Gokhale Tamar Golan-Lev Hamid Gourabi Michal Gropp Guangxiu Lu Ales Hampl Katie Harron Lyn Healy Wishva Herath Frida Holm Outi Hovatta Johan Hyllner Maneesha S Inamdar Astrid Kresentia Irwanto Tetsuya Ishii Marisa Jaconi Ying Jin Susan Kimber Sergey Kiselev Barbara B Knowles Oded Kopper Valeri Kukharenko Anver Kuliev Maria A Lagarkova Peter W Laird Majlinda Lako Andrew L Laslett Neta Lavon Dong Ryul Lee Jeoung Eun Lee Chunliang Li Linda S Lim Tenneille E Ludwig Yu Ma Edna Maltby Ileana Mateizel Yoav Mayshar Maria Mileikovsky Stephen L Minger Takamichi Miyazaki Shin Yong Moon Harry Moore Christine Mummery Andras Nagy Norio Nakatsuji Kavita Narwani Steve K W Oh Sun Kyung Oh Cia Olson Timo Otonkoski Fei Pan In-Hyun Park Steve Pells Martin F Pera Lygia V Pereira Ouyang Qi Grace Selva Raj Benjamin Reubinoff Alan Robins Paul Robson Janet Rossant Ghasem H Salekdeh Thomas C Schulz Karen Sermon Jameelah Sheik Mohamed Hui Shen Eric Sherrer Kuldip Sidhu Shirani Sivarajah Heli Skottman Claudia Spits Glyn N Stacey Raimund Strehl Nick Strelchenko Hirofumi Suemori Bowen Sun Riitta Suuronen Kazutoshi Takahashi Timo Tuuri Parvathy Venu Yuri Verlinsky Dorien Ward-van Oostwaard Daniel J Weisenberger Yue Wu Shinya Yamanaka Lorraine Young Qi Zhou

Nat Biotechnol 2011 Nov 27;29(12):1132-44. Epub 2011 Nov 27.

Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, UK.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/nbt.2051
Publisher Site
http://dx.doi.org/10.1038/nbt.2051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3454460PMC
November 2011

Modeling measurement error in tumor characterization studies.

BMC Bioinformatics 2011 Jul 13;12:284. Epub 2011 Jul 13.

Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, California 90089-9176, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-12-284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213130PMC
July 2011

Reduction of pancreatic acinar cell tumor multiplicity in Dnmt1 hypomorphic mice.

Carcinogenesis 2011 Jun 1;32(6):829-35. Epub 2011 Mar 1.

Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, CA 90089-9176, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/carcin/bgr039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106433PMC
June 2011

Vitamin C promotes widespread yet specific DNA demethylation of the epigenome in human embryonic stem cells.

Stem Cells 2010 Oct;28(10):1848-55

Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/stem.493DOI Listing
October 2010

Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue.

Cancer Res 2010 Oct 14;70(20):8169-78. Epub 2010 Sep 14.

Department of Urology, USC Epigenome Center, and Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA.

View Article

Download full-text PDF

Source
http://cancerres.aacrjournals.org/content/early/2010/10/07/0
Web Search
http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
Publisher Site
http://dx.doi.org/10.1158/0008-5472.CAN-10-1335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955801PMC
October 2010

Epigenomics-based diagnostics.

Clin Chem 2010 Aug 14;56(8):1216-9. Epub 2010 May 14.

Department of Clinical Biochemistry, Mount Sinai Hospital and University Health Network, University of Toronto, Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1373/clinchem.2010.148007DOI Listing
August 2010

Epigenetic analysis of KSHV latent and lytic genomes.

PLoS Pathog 2010 Jul 22;6(7):e1001013. Epub 2010 Jul 22.

Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America.

View Article

Download full-text PDF

Source
https://dx.plos.org/10.1371/journal.ppat.1001013
Publisher Site
http://dx.doi.org/10.1371/journal.ppat.1001013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2908616PMC
July 2010

Hormone therapy, DNA methylation and colon cancer.

Carcinogenesis 2010 Jun 11;31(6):1060-7. Epub 2010 Jan 11.

Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/carcin/bgq009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878358PMC
June 2010

Principles and challenges of genomewide DNA methylation analysis.

Authors:
Peter W Laird

Nat Rev Genet 2010 Mar;11(3):191-203

USC Epigenome Center, University of Southern California, Keck School of Medicine, Los Angeles, 90089‑9601, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/nrg2732
Publisher Site
http://dx.doi.org/10.1038/nrg2732DOI Listing
March 2010

DNA methylation as a biomarker for cardiovascular disease risk.

PLoS One 2010 Mar 15;5(3):e9692. Epub 2010 Mar 15.

Department of Surgery, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009692PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837739PMC
March 2010

DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines.

PLoS One 2010 Feb 22;5(2):e9359. Epub 2010 Feb 22.

Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, California, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009359PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825254PMC
February 2010