Literature DB >> 24336642

ChAMP: 450k Chip Analysis Methylation Pipeline.

Tiffany J Morris1, Lee M Butcher, Andrew Feber, Andrew E Teschendorff, Ankur R Chakravarthy, Tomasz K Wojdacz, Stephan Beck.   

Abstract

UNLABELLED: The Illumina Infinium HumanMethylation450 BeadChip is a new platform for high-throughput DNA methylation analysis. Several methods for normalization and processing of these data have been published recently. Here we present an integrated analysis pipeline offering a choice of the most popular normalization methods while also introducing new methods for calling differentially methylated regions and detecting copy number aberrations.
AVAILABILITY AND IMPLEMENTATION: ChAMP is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at bioconductor.org

Entities:  

Mesh：

Year:  2013        PMID： 24336642      PMCID： PMC3904520          DOI： 10.1093/bioinformatics/btt684

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


  19 in total

1.  Evaluation of the Infinium Methylation 450K technology.

Authors:  Sarah Dedeurwaerder; Matthieu Defrance; Emilie Calonne; Hélène Denis; Christos Sotiriou; François Fuks
Journal:  Epigenomics       Date:  2011-12       Impact factor: 4.778

2.  Complete pipeline for Infinium(®) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation.

Authors:  Nizar Touleimat; Jörg Tost
Journal:  Epigenomics       Date:  2012-06       Impact factor: 4.778

Review 3.  Phenotypic plasticity and the epigenetics of human disease.

Authors:  Andrew P Feinberg
Journal:  Nature       Date:  2007-05-24       Impact factor: 49.962

4.  Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies.

Authors:  Andrew E Teschendorff; Joanna Zhuang; Martin Widschwendter
Journal:  Bioinformatics       Date:  2011-04-06       Impact factor: 6.937

Review 5.  Analysing and interpreting DNA methylation data.

Authors:  Christoph Bock
Journal:  Nat Rev Genet       Date:  2012-10       Impact factor: 53.242

Review 6.  Epigenome-wide association studies for common human diseases.

Authors:  Vardhman K Rakyan; Thomas A Down; David J Balding; Stephan Beck
Journal:  Nat Rev Genet       Date:  2011-07-12       Impact factor: 53.242

7.  Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome.

Authors:  Juan Sandoval; Holger Heyn; Sebastian Moran; Jordi Serra-Musach; Miguel A Pujana; Marina Bibikova; Manel Esteller
Journal:  Epigenetics       Date:  2011-06-01       Impact factor: 4.528

8.  SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips.

Authors:  Jovana Maksimovic; Lavinia Gordon; Alicia Oshlack
Journal:  Genome Biol       Date:  2012-06-15       Impact factor: 13.583

9.  A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform.

Authors:  Joanna Zhuang; Martin Widschwendter; Andrew E Teschendorff
Journal:  BMC Bioinformatics       Date:  2012-04-24       Impact factor: 3.169

10.  An integrated map of genetic variation from 1,092 human genomes.

Authors:  Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean
Journal:  Nature       Date:  2012-11-01       Impact factor: 49.962
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  349 in total

1.  Epigenetics of neuroinflammation: Immune response, inflammatory response and cholinergic synaptic involvement evidenced by genome-wide DNA methylation analysis of delirious inpatients.

Authors:  Taku Saito; Hiroyuki Toda; Gabrielle N Duncan; Sydney S Jellison; Tong Yu; Mason J Klisares; Sophia Daniel; Allison J Andreasen; Lydia R Leyden; Mandy M Hellman; Eri Shinozaki; Sangil Lee; Aihide Yoshino; Hyunkeun R Cho; Gen Shinozaki
Journal:  J Psychiatr Res       Date:  2020-06-06       Impact factor: 4.791

2.  DNA Methylation Profiling in Inflammatory Bowel Disease Provides New Insights into Disease Pathogenesis.

Authors:  Edel McDermott; Elizabeth J Ryan; Miriam Tosetto; David Gibson; Joe Burrage; Denise Keegan; Kathryn Byrne; Eimear Crowe; Gillian Sexton; Kevin Malone; R Alan Harris; Richard Kellermayer; Jonathan Mill; Garret Cullen; Glen A Doherty; Hugh Mulcahy; Therese M Murphy
Journal:  J Crohns Colitis       Date:  2015-09-28       Impact factor: 9.071

3.  Methylomic profiles reveal sex-specific differences in leukocyte composition associated with post-traumatic stress disorder.

Authors:  Grace S Kim; Alicia K Smith; Fei Xue; Vasiliki Michopoulos; Adriana Lori; Don L Armstrong; Allison E Aiello; Karestan C Koenen; Sandro Galea; Derek E Wildman; Monica Uddin
Journal:  Brain Behav Immun       Date:  2019-06-19       Impact factor: 7.217

4.  Prenatal exposures and DNA methylation in newborns: a pilot study in Durban, South Africa.

Authors:  Jaclyn M Goodrich; Poovendhree Reddy; Rajen N Naidoo; Kareshma Asharam; Stuart Batterman; Dana C Dolinoy
Journal:  Environ Sci Process Impacts       Date:  2016-07-13       Impact factor: 4.238

5.  Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence.

Authors:  Sevin Turcan; Vladimir Makarov; Julian Taranda; Yuxiang Wang; Armida W M Fabius; Wei Wu; Yupeng Zheng; Nour El-Amine; Sara Haddock; Gouri Nanjangud; H Carl LeKaye; Cameron Brennan; Justin Cross; Jason T Huse; Neil L Kelleher; Pavel Osten; Craig B Thompson; Timothy A Chan
Journal:  Nat Genet       Date:  2017-11-27       Impact factor: 38.330

6.  Integrated Genomics for Pinpointing Survival Loci within Arm-Level Somatic Copy Number Alterations.

Authors:  David M Roy; Logan A Walsh; Alexis Desrichard; Jason T Huse; Wei Wu; JianJiong Gao; Promita Bose; William Lee; Timothy A Chan
Journal:  Cancer Cell       Date:  2016-05-09       Impact factor: 31.743

7.  Cigarette smoking significantly alters sperm DNA methylation patterns.

Authors:  T G Jenkins; E R James; D F Alonso; J R Hoidal; P J Murphy; J M Hotaling; B R Cairns; D T Carrell; K I Aston
Journal:  Andrology       Date:  2017-09-26       Impact factor: 3.842

8.  Aberrant Function of the C-Terminal Tail of HIST1H1E Accelerates Cellular Senescence and Causes Premature Aging.

Authors:  Elisabetta Flex; Simone Martinelli; Anke Van Dijck; Andrea Ciolfi; Serena Cecchetti; Elisa Coluzzi; Luca Pannone; Cristina Andreoli; Francesca Clementina Radio; Simone Pizzi; Giovanna Carpentieri; Alessandro Bruselles; Giuseppina Catanzaro; Lucia Pedace; Evelina Miele; Elena Carcarino; Xiaoyan Ge; Chieko Chijiwa; M E Suzanne Lewis; Marije Meuwissen; Sandra Kenis; Nathalie Van der Aa; Austin Larson; Kathleen Brown; Melissa P Wasserstein; Brian G Skotko; Amber Begtrup; Richard Person; Maria Karayiorgou; J Louw Roos; Koen L Van Gassen; Marije Koopmans; Emilia K Bijlsma; Gijs W E Santen; Daniela Q C M Barge-Schaapveld; Claudia A L Ruivenkamp; Mariette J V Hoffer; Seema R Lalani; Haley Streff; William J Craigen; Brett H Graham; Annette P M van den Elzen; Daan J Kamphuis; Katrin Õunap; Karit Reinson; Sander Pajusalu; Monica H Wojcik; Clara Viberti; Cornelia Di Gaetano; Enrico Bertini; Simona Petrucci; Alessandro De Luca; Rossella Rota; Elisabetta Ferretti; Giuseppe Matullo; Bruno Dallapiccola; Antonella Sgura; Magdalena Walkiewicz; R Frank Kooy; Marco Tartaglia
Journal:  Am J Hum Genet       Date:  2019-08-22       Impact factor: 11.025

9.  Measuring DNA Copy Number Variation Using High-Density Methylation Microarrays.

Authors:  Soonweng Cho; Hyun-Seok Kim; Martha A Zeiger; Christopher B Umbricht; Leslie M Cope
Journal:  J Comput Biol       Date:  2019-02-21       Impact factor: 1.479

10.  Maternal adiposity negatively influences infant brain white matter development.

Authors:  Xiawei Ou; Keshari M Thakali; Kartik Shankar; Aline Andres; Thomas M Badger
Journal:  Obesity (Silver Spring)       Date:  2015-05       Impact factor: 5.002
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